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Bisht MS, Mahajan S, Chakraborty A, Sharma VK. A high-quality genome assembly of Annona squamosa (custard apple) provides functional insights into an emerging fruit crop. DNA Res 2025; 32:dsaf007. [PMID: 40371876 PMCID: PMC12116420 DOI: 10.1093/dnares/dsaf007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 03/03/2025] [Accepted: 05/10/2025] [Indexed: 05/16/2025] Open
Abstract
Annona squamosa, also known as custard apple, is an emerging fruit crop with medicinal significance. We constructed a high-quality genome of A. squamosa along with transcriptome data to gain insights into its phylogeny, evolution, and demographic history. The genome has a size of 730.4 Mb with an N50 value of 93.2 Mb assembled into seven pseudochromosomes. The demographic history showed a continuous decline in the effective population size of A. squamosa. Phylogenetic analysis revealed that magnoliids were sister to eudicots. Genome syntenic and Ks distribution analyses confirmed the absence of a recent whole-genome duplication event in the A. squamosa. Gene families related to photosynthesis, oxidative phosphorylation, and plant thermogenesis were found to be highly expanded in the genome. Comparative analysis with other magnoliids revealed the adaptive evolution in the genes of flavonoid biosynthesis pathway, amino sugar, nucleotide sugar and sucrose metabolism, conferring medicinal value, and enhanced hexose sugar accumulation. In addition, we performed genome-wide identification of SWEET genes. Our high-quality genome and evolutionary insights of this emerging fruit crop, thus, serve as a valuable resource for advancing studies in functional genomics, evolutionary biology, and crop improvement.
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Affiliation(s)
- Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal – 462066, Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal – 462066, Madhya Pradesh, India
| | - Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal – 462066, Madhya Pradesh, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal – 462066, Madhya Pradesh, India
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2
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Schell T, Greve C, Podsiadlowski L. Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide. Front Zool 2025; 22:7. [PMID: 40247279 PMCID: PMC12004614 DOI: 10.1186/s12983-025-00561-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 03/23/2025] [Indexed: 04/19/2025] Open
Abstract
Reference genome assemblies are the basis for comprehensive genomic analyses and comparisons. Due to declining sequencing costs and growing computational power, genome projects are now feasible in smaller labs. De novo genome sequencing for non-model or emerging model organisms requires knowledge about genome size and techniques for extracting high molecular weight DNA. Next to quality, the amount of DNA obtained from single individuals is crucial, especially, when dealing with small organisms. While long-read sequencing technologies are the methods of choice for creating high quality genome assemblies, pure short-read assemblies might bear most of the coding parts of a genome but are usually much more fragmented and do not well resolve repeat elements or structural variants. Several genome initiatives produce more and more non-model organism genomes and provide rules for standards in genome sequencing and assembly. However, sometimes the organism of choice is not part of such an initiative or does not meet its standards. Therefore, if the scientific question can be answered with a genome of low contiguity in intergenic parts, missing the high standards of chromosome scale assembly should not prevent publication. This review describes how to set up an animal genome sequencing project in the lab, how to estimate costs and resources, and how to deal with suboptimal conditions. Thus, we aim to suggest optimal strategies for genome sequencing that fulfil the needs according to specific research questions, e.g. "How are species related to each other based on whole genomes?" (phylogenomics), "How do genomes of populations within a species differ?" (population genomics), "Are differences between populations relevant for conservation?" (conservation genomics), "Which selection pressure is acting on certain genes?" (identification of genes under selection), "Did repeats expand or contract recently?" (repeat dynamics).
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Affiliation(s)
- Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics, Senckenberganlage 25, 60325, Frankfurt, Germany
- Senckenberg Research Institute, Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Lars Podsiadlowski
- LIB, Museum Koenig Bonn, Centre for Molecular Biodiversity Research (zmb), Adenauerallee 127, 53113, Bonn, Germany.
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3
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Huang YH, Escalona HE, Sun YF, Zhang PF, Du XY, Gong SR, Tang XF, Liang YS, Yang D, Chen PT, Yang HY, Chen ML, Hüttel B, Hlinka O, Wang X, Meusemann K, Ślipiński A, Zwick A, Waterhouse RM, Misof B, Niehuis O, Li HS, Pang H. Molecular evolution of dietary shifts in ladybird beetles (Coleoptera: Coccinellidae): from fungivory to carnivory and herbivory. BMC Biol 2025; 23:67. [PMID: 40022128 PMCID: PMC11871716 DOI: 10.1186/s12915-025-02174-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 02/19/2025] [Indexed: 03/03/2025] Open
Abstract
BACKGROUND Dietary shifts are major evolutionary steps that shape ecological niches and biodiversity. The beetle family Coccinellidae, commonly known as ladybirds, first transitioned from a fungivorous to an insectivorous and subsequently a plant diet. However, the molecular basis of this dietary diversification remained unexplored. RESULTS We investigated the molecular evolution of dietary shifts in ladybirds, focusing on the transitions from fungivory to carnivory (Coccinellidae) and from carnivory to herbivory (Epilachnini), by comparing 25 genomes and 62 transcriptomes of beetles. Our analysis shows that chemosensory gene families have undergone significant expansions at both nodes of diet change and were differentially expressed in feeding experiments, suggesting that they may be related to foraging. We found expansions of digestive and detoxifying gene families and losses of chitin-related digestive genes in the herbivorous ladybirds, and absence of most plant cell wall-degrading enzymes in the ladybirds dating from the transition to carnivory, likely indicating the effect of different digestion requirements on the gene repertoire. Immunity effector genes tend to emerge or have specific amino acid sequence compositions in carnivorous ladybirds and are downregulated under suboptimal dietary treatments, suggesting a potential function of these genes related to microbial symbionts in the sternorrhynchan prey. CONCLUSIONS Our study provides a comprehensive comparative genomic analysis to address evolution of chemosensory, digestive, detoxifying, and immune genes associated with dietary shifts in ladybirds. Ladybirds can be considered a ubiquitous example of dietary shifts in insects, and thus a promising model system for evolutionary and applied biology.
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Affiliation(s)
- Yu-Hao Huang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Hermes E Escalona
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Yi-Fei Sun
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Pei-Fang Zhang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xue-Yong Du
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Sen-Rui Gong
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xue-Fei Tang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
- College of Forestry, Henan Agricultural University, Zhengzhou, 450002, China
| | - Yuan-Sen Liang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Dan Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Pei-Tao Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Huan-Ying Yang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China
| | - Mei-Lan Chen
- School of Environmental and Life Sciences, Nanning Normal University, Nanning, 530001, China
| | - Bruno Hüttel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Ondrej Hlinka
- CSIRO Information, Management and Technology, Pullenvale, QLD, Australia
| | - Xingmin Wang
- College of Plant Protection, South China Agricultural University, Guangzhou, 510642, China
| | - Karen Meusemann
- Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, Bonn, 53113, Germany
| | - Adam Ślipiński
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Andreas Zwick
- Australian National Insect Collection, CSIRO, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Bernhard Misof
- Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, Bonn, 53113, Germany
| | - Oliver Niehuis
- Department of Evolutionary Biology and Ecology, Institute for Biology I (Zoology), University of Freiburg, Freiburg, 79104, Germany
| | - Hao-Sen Li
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China.
| | - Hong Pang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Shenzhen, 518107, China.
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Al-Ajli FO, Formenti G, Fedrigo O, Tracey A, Sims Y, Howe K, Al-Karkhi IM, Althani AA, Jarvis ED, Rahman S, Ayub Q. Chromosome-level reference genome assembly of the gyrfalcon (Falco rusticolus) and population genomics offer insights into the falcon population in Mongolia. Sci Rep 2025; 15:4154. [PMID: 39900672 PMCID: PMC11790892 DOI: 10.1038/s41598-025-88216-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 01/24/2025] [Indexed: 02/05/2025] Open
Abstract
The taxonomic classification of a falcon population found in the Mongolian Altai region in Asia has been heavily debated for two centuries and previous studies have been inconclusive, hindering a more informed conservation approach. Here, we generated a chromosome-level gyrfalcon reference genome using the Vertebrate Genomes Project (VGP) assembly pipeline. Using whole genome sequences of 49 falcons from different species and populations, including "Altai" falcons, we analyzed their population structure, admixture patterns, and demographic history. We find that the Altai falcons are genomic mosaics of saker and gyrfalcon ancestries, and carry distinct W and mitochondrial haplotypes that cluster with the lanner falcon. The Altai maternally-inherited haplotypes diverged 422,000 years before present (290,000-550,000 YBP) from the ancestor of sakers and gyrfalcons, both of which, in turn, split 109,000 YBP (70,000-150,000 YBP). The Altai W chromosome has 31 coding variants in 29 genes that may possibly influence important structural, behavioral, and reproductive traits. These findings provide insights into the question of Altai falcons as a candidate distinct species.
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Affiliation(s)
- Farooq Omar Al-Ajli
- Qatar Falcon Genome Project, Doha, Qatar.
- School of Science, Monash University, Subang Jaya, Malaysia.
- Vertebrate Genome Laboratory, The Rockefeller University, NY, USA.
| | - Giulio Formenti
- Vertebrate Genome Laboratory, The Rockefeller University, NY, USA
| | - Olivier Fedrigo
- Vertebrate Genome Laboratory, The Rockefeller University, NY, USA
| | | | - Ying Sims
- Wellcome Sanger Institute, Cambridge, UK
| | | | | | - Asmaa Ali Althani
- Biomedical Research Center, Qatar University, Doha, Qatar
- Health Cluster, Qatar University, Doha, Qatar
| | - Erich D Jarvis
- Vertebrate Genome Laboratory, The Rockefeller University, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Sadequr Rahman
- School of Science, Monash University, Subang Jaya, Malaysia
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University, Subang Jaya, Malaysia
| | - Qasim Ayub
- School of Science, Monash University, Subang Jaya, Malaysia.
- Tropical Medicine and Biology Multidisciplinary Platform, School of Science, Monash University, Subang Jaya, Malaysia.
- Genomics Platform, School of Science, Monash University, Subang Jaya, Malaysia.
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5
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Hsiang TF, Yamane H, Lin YJ, Sugimori M, Nishiyama S, Nagasaka K, Nakano R, Tao R. The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume. DNA Res 2024; 32:dsae034. [PMID: 39656749 PMCID: PMC11747360 DOI: 10.1093/dnares/dsae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 11/22/2024] [Accepted: 12/03/2024] [Indexed: 12/17/2024] Open
Abstract
Bud dormancy is a vital physiological process in woody perennials, facilitating their adaptation to seasonal environmental changes. Satisfying genotype-specific chilling requirements (CR) and heat requirements (HR) through exposure to specific chilling and warm temperatures is essential for dormancy release and the subsequent resumption of growth. The genetic mechanisms regulating bud dormancy traits in Prunus mume remain unclear. In this study, we first assembled the genome of 'Nanko', the leading P. mume cultivar in Japan, in a haplotype-resolved manner. Using an F1 segregating population from a cross between 'Nanko' (high-chill) and 'SC' (low-chill), a cultivar adapted to subtropical conditions, we identified quantitative trait loci (QTLs) for vegetative bud dormancy traits on chromosome 4 (LG4 QTLs) in the 'Nanko' genome and for CR and HR on chromosome 7 (LG7 QTL) in the 'SC' genome. A notable 5.6 Mb chromosome inversion was overlapped with LG4 QTL interval in one of the 'Nanko' haplotypes. We also identified candidate genes based on haplotyping, differential expression between the parents or the presence of trait-correlated variants in coding regions. Notably, genes such as PmuMAIN, PmuNAC2, PmuDOG1, PmuSUI1, PmuATG8CL, PmubZIP44, and PmuSAUR50 were identified. This study provides valuable insights into the genetic regulation of vegetative bud dormancy in Prunus species.
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Affiliation(s)
- Tzu-Fan Hsiang
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Hisayo Yamane
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Yuan-Jui Lin
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Miku Sugimori
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | | | - Kyoka Nagasaka
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kyoto 619-0218, Japan
| | - Ryohei Nakano
- Experimental Farm, Graduate School of Agriculture, Kyoto University, Kyoto 619-0218, Japan
| | - Ryutaro Tao
- Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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6
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Liu P, Vigneau J, Craig RJ, Barrera-Redondo J, Avdievich E, Martinho C, Borg M, Haas FB, Liu C, Coelho SM. 3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization. Nat Commun 2024; 15:9590. [PMID: 39505852 PMCID: PMC11541908 DOI: 10.1038/s41467-024-53453-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Accepted: 10/08/2024] [Indexed: 11/08/2024] Open
Abstract
Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene expression regulation and correct developmental programs, but little is known about the 3D architecture of sex chromosomes within the nucleus, and how that impacts their role in sex determination. Here, we determine the sex-specific 3D organization of the model brown alga Ectocarpus chromosomes at 2 kb resolution, by mapping long-range chromosomal interactions using Hi-C coupled with Oxford Nanopore long reads. We report that Ectocarpus interphase chromatin exhibits a non-Rabl conformation, with strong contacts among telomeres and among centromeres, which feature centromere-specific LTR retrotransposons. The Ectocarpus chromosomes do not contain large local interactive domains that resemble TADs described in animals, but their 3D genome organization is largely shaped by post-translational modifications of histone proteins. We show that the sex determining region (SDR) within the U and V chromosomes are insulated and span the centromeres and we link sex-specific chromatin dynamics and gene expression levels to the 3D chromatin structure of the U and V chromosomes. Finally, we uncover the unique conformation of a large genomic region on chromosome 6 harboring an endogenous viral element, providing insights regarding the impact of a latent giant dsDNA virus on the host genome's 3D chromosomal folding.
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Affiliation(s)
- Pengfei Liu
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Jeromine Vigneau
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Rory J Craig
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Josué Barrera-Redondo
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Elena Avdievich
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Claudia Martinho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
- School of Life Sciences, Division of Plant Sciences, University of Dundee, At James Hutton Institute, Errol Road, Invergowrie, Dundee, UK
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Fabian B Haas
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany
| | - Chang Liu
- Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Susana M Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen, Tübingen, Germany.
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7
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Cheung K, Rollins LA, Hammond JM, Barton K, Ferguson JM, Eyck HJF, Shine R, Edwards RJ. Repeat-Rich Regions Cause False-Positive Detection of NUMTs: A Case Study in Amphibians Using an Improved Cane Toad Reference Genome. Genome Biol Evol 2024; 16:evae246. [PMID: 39548850 PMCID: PMC11606642 DOI: 10.1093/gbe/evae246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 10/08/2024] [Accepted: 11/04/2024] [Indexed: 11/18/2024] Open
Abstract
Mitochondrial DNA (mtDNA) has been widely used in genetics research for decades. Contamination from nuclear DNA of mitochondrial origin (NUMTs) can confound studies of phylogenetic relationships and mtDNA heteroplasmy. Homology searches with mtDNA are widely used to detect NUMTs in the nuclear genome. Nevertheless, false-positive detection of NUMTs is common when handling repeat-rich sequences, while fragmented genomes might result in missing true NUMTs. In this study, we investigated different NUMT detection methods and how the quality of the genome assembly affects them. We presented an improved nuclear genome assembly (aRhiMar1.3) of the invasive cane toad (Rhinella marina) with additional long-read Nanopore and 10× linked-read sequencing. The final assembly was 3.47 Gb in length with 91.3% of tetrapod universal single-copy orthologs (n = 5,310), indicating the gene-containing regions were well assembled. We used 3 complementary methods (NUMTFinder, dinumt, and PALMER) to study the NUMT landscape of the cane toad genome. All 3 methods yielded consistent results, showing very few NUMTs in the cane toad genome. Furthermore, we expanded NUMT detection analyses to other amphibians and confirmed a weak relationship between genome size and the number of NUMTs present in the nuclear genome. Amphibians are repeat-rich, and we show that the number of NUMTs found in highly repetitive genomes is prone to inflation when using homology-based detection without filters. Together, this study provides an exemplar of how to robustly identify NUMTs in complex genomes when confounding effects on mtDNA analyses are a concern.
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Affiliation(s)
- Kelton Cheung
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, Australia
- Evolution & Ecology Research Centre, School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Lee Ann Rollins
- Evolution & Ecology Research Centre, School of Biological, Earth & Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Jillian M Hammond
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Kirston Barton
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - James M Ferguson
- Centre for Population Genomics, Garvan Institute of Medical Research and Murdoch Children's Research Institute, Darlinghurst, New South Wales, Australia
| | - Harrison J F Eyck
- National Collections and Marine Infrastructure, CSIRO, Canberra, Australian Capital Territory, Australia
| | - Richard Shine
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Richard J Edwards
- Evolution & Ecology Research Centre, School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, Australia
- Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Western Australia, Australia
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8
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Jiang Z, Peng Z, Wei Z, Sun J, Luo Y, Bie L, Zhang G, Wang Y. A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes. Nucleic Acids Res 2024; 52:e92. [PMID: 39287126 PMCID: PMC11514472 DOI: 10.1093/nar/gkae789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/25/2024] [Accepted: 08/30/2024] [Indexed: 09/19/2024] Open
Abstract
The application of high-throughput chromosome conformation capture (Hi-C) technology enables the construction of chromosome-level assemblies. However, the correction of errors and the anchoring of sequences to chromosomes in the assembly remain significant challenges. In this study, we developed a deep learning-based method, AutoHiC, to address the challenges in chromosome-level genome assembly by enhancing contiguity and accuracy. Conventional Hi-C-aided scaffolding often requires manual refinement, but AutoHiC instead utilizes Hi-C data for automated workflows and iterative error correction. When trained on data from 300+ species, AutoHiC demonstrated a robust average error detection accuracy exceeding 90%. The benchmarking results confirmed its significant impact on genome contiguity and error correction. The innovative approach and comprehensive results of AutoHiC constitute a breakthrough in automated error detection, promising more accurate genome assemblies for advancing genomics research.
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Affiliation(s)
- Zijie Jiang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Zhixiang Peng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Zhaoyuan Wei
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Jiahe Sun
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Yongjiang Luo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Lingzi Bie
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Guoqing Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Yi Wang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
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9
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Jo E, Cho M, Choi S, Lee SJ, Choi E, Kim J, Kim JY, Kwon S, Lee JH, Park H. High-quality chromosome-level genome assembly of female Artemia franciscana reveals sex chromosome and Hox gene organization. Heliyon 2024; 10:e38687. [PMID: 39435060 PMCID: PMC11492255 DOI: 10.1016/j.heliyon.2024.e38687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 09/22/2024] [Accepted: 09/27/2024] [Indexed: 10/23/2024] Open
Abstract
Artemia is a crustacean genus belonging to the order Anostraca in the class Branchiopoda and lives in inland hypersaline lakes. Among the genus, A. franciscana is a valuable species as a fish food in the aquaculture industry or as an aquatic model organism for toxicity tests. However, genomic data for A. franciscana remains incomplete. In this study, high-quality genome assembly at the chromosome level of female A. franciscana was conducted by combining various sequencing and assembly technologies. The final A. franciscana assembled genome was 1.27 Gb in length, containing 21 chromosomal scaffolds (>10 Mb). The scaffold N50 was 45.3 Mb, with a complete BUSCO value of 91.0 %, thereby confirming that a high-quality genome was assembled. Gene annotation shows that the A. franciscana genome contained 67.26 % of repetitive sequences, and a total of 26,923 protein-coding genes were predicted. Among the 21 chromosome-scale scaffolds, chromosome 1 was identified as a sex chromosome Z. Additionally, five contigs of putative W chromosome fragments and the candidate sex-determining genes were suggested. Ten homeobox (Hox) genes were identified in A. franciscana on the chromosome 14, which were in two subclusters with a large gap. Hox gene organizations within 13 arthropods showed that four anostracans had conserved synteny. This study provides a new female Artemia genome with sex chromosome and the first complete genomic arrangement of the Hox cluster in Anostraca. This study will be a useful genomic and genetic reference for understanding the evolution and development of A. franciscana.
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Affiliation(s)
- Euna Jo
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Minjoo Cho
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Soyun Choi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Seung Jae Lee
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Eunkyung Choi
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Jinmu Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Jang Yeon Kim
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Sooyeon Kwon
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
| | - Jun Hyuck Lee
- Division of Life Sciences, Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Hyun Park
- Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul, 02841, South Korea
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10
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Jiang L, Quail MA, Fraser-Govil J, Wang H, Shi X, Oliver K, Mellado Gomez E, Yang F, Ning Z. The Bioinformatic Applications of Hi-C and Linked Reads. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae048. [PMID: 38905513 PMCID: PMC11580686 DOI: 10.1093/gpbjnl/qzae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 05/07/2024] [Accepted: 06/19/2024] [Indexed: 06/23/2024]
Abstract
Long-range sequencing grants insight into additional genetic information beyond what can be accessed by both short reads and modern long-read technology. Several new sequencing technologies, such as "Hi-C" and "Linked Reads", produce long-range datasets for high-throughput and high-resolution genome analyses, which are rapidly advancing the field of genome assembly, genome scaffolding, and more comprehensive variant identification. In this review, we focused on five major long-range sequencing technologies: high-throughput chromosome conformation capture (Hi-C), 10X Genomics Linked Reads, haplotagging, transposase enzyme linked long-read sequencing (TELL-seq), and single- tube long fragment read (stLFR). We detailed the mechanisms and data products of the five platforms and their important applications, evaluated the quality of sequencing data from different platforms, and discussed the currently available bioinformatics tools. This work will benefit the selection of appropriate long-range technology for specific biological studies.
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Affiliation(s)
- Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Michael A Quail
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Jack Fraser-Govil
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Haipeng Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Xuequn Shi
- College of Food Science and Technology, Hainan University, Haikou 570228, China
| | - Karen Oliver
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Esther Mellado Gomez
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Fengtang Yang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Zemin Ning
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
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11
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Cicconardi F, Morris BJ, Martelossi J, Ray DA, Montgomery SH. Novel Sex-Specific Genes and Diverse Interspecific Expression in the Antennal Transcriptomes of Ithomiine Butterflies. Genome Biol Evol 2024; 16:evae218. [PMID: 39373182 PMCID: PMC11500719 DOI: 10.1093/gbe/evae218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 09/23/2024] [Accepted: 09/24/2024] [Indexed: 10/08/2024] Open
Abstract
The olfactory sense is crucial for organisms, facilitating environmental recognition and interindividual communication. Ithomiini butterflies exemplify this importance not only because they rely strongly on olfactory cues for both inter- and intra-sexual behaviors, but also because they show convergent evolution of specialized structures within the antennal lobe, called macroglomerular complexes (MGCs). These structures, widely absent in butterflies, are present in moths where they enable heightened sensitivity to, and integration of, information from various types of pheromones. In this study, we investigate chemosensory evolution across six Ithomiini species and identify possible links between expression profiles and neuroanatomical. To enable this, we sequenced four new high-quality genome assemblies and six sex-specific antennal transcriptomes for three of these species with different MGC morphologies. With extensive genomic analyses, we found that the expression of antennal transcriptomes across species exhibit profound divergence, and identified highly expressed ORs, which we hypothesize may be associated to MGCs, as highly expressed ORs are absent in Methona, an Ithomiini lineage which also lacks MGCs. More broadly, we show how antennal sexual dimorphism is prevalent in both chemosensory genes and non-chemosensory genes, with possible relevance for behavior. As an example, we show how lipid-related genes exhibit consistent sexual dimorphism, potentially linked to lipid transport or host selection. In this study, we investigate the antennal chemosensory adaptations, suggesting a link between genetic diversity, ecological specialization, and sensory perception with the convergent evolution of MCGs. Insights into chemosensory gene evolution, expression patterns, and potential functional implications enhance our knowledge of sensory adaptations and sexual dimorphisms in butterflies, laying the foundation for future investigations into the genetic drivers of insect behavior, adaptation, and speciation.
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Affiliation(s)
- Francesco Cicconardi
- School of Biological Sciences, Bristol University, 24 Tyndall Ave, Bristol BS8 1TQ, UK
| | - Billy J Morris
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Jacopo Martelossi
- Department of Biological Geological and Environmental Science, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - David A Ray
- Department of Biological Sciences, Texas Tech University, Lubbock, TX 79409, USA
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, 24 Tyndall Ave, Bristol BS8 1TQ, UK
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12
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Johnson HA, Rondeau EB, Sutherland BJG, Minkley DR, Leong JS, Whitehead J, Despins CA, Gowen BE, Collyard BJ, Whipps CM, Farrell JM, Koop BF. Loss of genetic variation and ancestral sex determination system in North American northern pike characterized by whole-genome resequencing. G3 (BETHESDA, MD.) 2024; 14:jkae183. [PMID: 39115373 PMCID: PMC11457062 DOI: 10.1093/g3journal/jkae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/28/2024] [Indexed: 10/08/2024]
Abstract
The northern pike Esox lucius is a freshwater fish with low genetic diversity but ecological success throughout the Northern Hemisphere. Here, we generate an annotated chromosome-level genome assembly of 941 Mbp in length with 25 chromosome-length scaffolds. We then genotype 47 northern pike from Alaska through New Jersey at a genome-wide scale and characterize a striking decrease in genetic diversity along the sampling range. Individuals west of the North American Continental Divide have substantially higher diversity than those to the east (e.g. Interior Alaska and St. Lawrence River have on average 181 and 64K heterozygous SNPs per individual, or a heterozygous SNP every 5.2 and 14.6 kbp, respectively). Individuals clustered within each population with strong support, with numerous private alleles observed within each population. Evidence for recent population expansion was observed for a Manitoba hatchery and the St. Lawrence population (Tajima's D = -1.07 and -1.30, respectively). Several chromosomes have large regions with elevated diversity, including LG24, which holds amhby, the ancestral sex determining gene. As expected amhby was largely male-specific in Alaska and the Yukon and absent southeast to these populations, but we document some amhby(-) males in Alaska and amhby(+) males in the Columbia River, providing evidence for a patchwork of presence of this system in the western region. These results support the theory that northern pike recolonized North America from refugia in Alaska and expanded following deglaciation from west to east, with probable founder effects resulting in loss of both neutral and functional diversity (e.g. amhby).
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Affiliation(s)
- Hollie A Johnson
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Eric B Rondeau
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Ben J G Sutherland
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
- Sutherland Bioinformatics, Lantzville V0R 2H0, British Columbia, Canada
| | - David R Minkley
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Jong S Leong
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Joanne Whitehead
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Cody A Despins
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Brent E Gowen
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
| | - Brian J Collyard
- Alaska Department of Fish and Game, Division of Sport Fish, 1300 College Rd, Fairbanks, AK 99701-1599, USA
| | - Christopher M Whipps
- Center for Applied Microbiology, Department of Environmental Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - John M Farrell
- Thousand Island Biological Station, Department of Environmental and Forest Biology, SUNY College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Ben F Koop
- Department of Biology, Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5, Canada
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13
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Bourret A, Leung C, Puncher GN, Le Corre N, Deslauriers D, Skanes K, Bourdages H, Cassista-Da Ros M, Walkusz W, Jeffery NW, Stanley RRE, Parent GJ. Diving into broad-scale and high-resolution population genomics to decipher drivers of structure and climatic vulnerability in a marine invertebrate. Mol Ecol 2024; 33:e17448. [PMID: 38946210 DOI: 10.1111/mec.17448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/11/2024] [Accepted: 06/19/2024] [Indexed: 07/02/2024]
Abstract
Species with widespread distributions play a crucial role in our understanding of climate change impacts on population structure. In marine species, population structure is often governed by both high connectivity potential and selection across strong environmental gradients. Despite the complexity of factors influencing marine populations, studying species with broad distribution can provide valuable insights into the relative importance of these factors and the consequences of climate-induced alterations across environmental gradients. We used the northern shrimp Pandalus borealis and its wide latitudinal distribution to identify current drivers of population structure and predict the species' vulnerability to climate change. A total of 1514 individuals sampled across 24° latitude were genotyped at high geographic (54 stations) and genetic (14,331 SNPs) resolutions to assess genetic variation and environmental correlations. Four populations were identified in addition to finer substructure associated with local adaptation. Geographic patterns of neutral population structure reflected predominant oceanographic currents, while a significant proportion of the genetic variation was associated with gradients in salinity and temperature. Adaptive landscapes generated using climate projections suggest a larger genomic offset in the southern extent of the P. borealis range, where shrimp had the largest adaptive standing genetic variation. Our genomic results combined with recent observations point to further deterioration in southern regions and an impending vulnerable status in the regions at higher latitudes for P. borealis. They also provide rare insights into the drivers of population structure and climatic vulnerability of a widespread meroplanktonic species, which is crucial to understanding future challenges associated with invertebrates essential to ecosystem functioning.
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Affiliation(s)
- Audrey Bourret
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
| | - Christelle Leung
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
| | - Gregory N Puncher
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Nicolas Le Corre
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - David Deslauriers
- Institut des Sciences de la Mer de Rimouski, Université du Québec à Rimouski, Rimouski, Quebec, Canada
| | - Katherine Skanes
- Northwest Atlantic Fisheries Centre, Fisheries and Oceans Canada, St. John's, Newfoundland and Labrador, Canada
| | - Hugo Bourdages
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
| | - Manon Cassista-Da Ros
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Wojciech Walkusz
- Freshwater Institute, Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - Nicholas W Jeffery
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Ryan R E Stanley
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, Dartmouth, Nova Scotia, Canada
| | - Geneviève J Parent
- Maurice Lamontagne Institute, Fisheries and Oceans Canada, Mont-Joli, Quebec, Canada
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14
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Hogg CJ, Edwards RJ, Farquharson KA, Silver LW, Brandies P, Peel E, Escalona M, Jaya FR, Thavornkanlapachai R, Batley K, Bradford TM, Chang JK, Chen Z, Deshpande N, Dziminski M, Ewart KM, Griffith OW, Marin Gual L, Moon KL, Travouillon KJ, Waters P, Whittington CM, Wilkins MR, Helgen KM, Lo N, Ho SYW, Ruiz Herrera A, Paltridge R, Marshall Graves JA, Renfree M, Shapiro B, Ottewell K, Belov K. Extant and extinct bilby genomes combined with Indigenous knowledge improve conservation of a unique Australian marsupial. Nat Ecol Evol 2024; 8:1311-1326. [PMID: 38945974 PMCID: PMC11239497 DOI: 10.1038/s41559-024-02436-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/03/2024] [Indexed: 07/02/2024]
Abstract
Ninu (greater bilby, Macrotis lagotis) are desert-dwelling, culturally and ecologically important marsupials. In collaboration with Indigenous rangers and conservation managers, we generated the Ninu chromosome-level genome assembly (3.66 Gbp) and genome sequences for the extinct Yallara (lesser bilby, Macrotis leucura). We developed and tested a scat single-nucleotide polymorphism panel to inform current and future conservation actions, undertake ecological assessments and improve our understanding of Ninu genetic diversity in managed and wild populations. We also assessed the beneficial impact of translocations in the metapopulation (N = 363 Ninu). Resequenced genomes (temperate Ninu, 6; semi-arid Ninu, 6; and Yallara, 4) revealed two major population crashes during global cooling events for both species and differences in Ninu genes involved in anatomical and metabolic pathways. Despite their 45-year captive history, Ninu have fewer long runs of homozygosity than other larger mammals, which may be attributable to their boom-bust life history. Here we investigated the unique Ninu biology using 12 tissue transcriptomes revealing expression of all 115 conserved eutherian chorioallantoic placentation genes in the uterus, an XY1Y2 sex chromosome system and olfactory receptor gene expansions. Together, we demonstrate the holistic value of genomics in improving key conservation actions, understanding unique biological traits and developing tools for Indigenous rangers to monitor remote wild populations.
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Affiliation(s)
- Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
| | - Richard J Edwards
- Minderoo OceanOmics Centre at UWA, Oceans Institute, The University of Western Australia, Perth, Western Australia, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Katherine A Farquharson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Luke W Silver
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Parice Brandies
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Emma Peel
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Merly Escalona
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Frederick R Jaya
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Rujiporn Thavornkanlapachai
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kimberley Batley
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Tessa M Bradford
- Evolutionary Biology Unit, South Australian Museum, Adelaide, South Australia, Australia
- School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - J King Chang
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | | | - Nandan Deshpande
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Martin Dziminski
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Kyle M Ewart
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Oliver W Griffith
- School of Natural Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Laia Marin Gual
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Katherine L Moon
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kenny J Travouillon
- Collections and Research, Western Australian Museum, Welshpool, Western Australia, Australia
| | - Paul Waters
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Camilla M Whittington
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Ramaciotti Centre for Genomics and School of Biotechnology and Biomolecular Science, UNSW, Sydney, New South Wales, Australia
| | - Kristofer M Helgen
- Australian Museum Research Institute, Australian Museum, Sydney, New South Wales, Australia
| | - Nathan Lo
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Simon Y W Ho
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
| | - Aurora Ruiz Herrera
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Rachel Paltridge
- Indigenous Desert Alliance, Alice Springs, Northern Territory, Australia
| | | | - Marilyn Renfree
- School of BioSciences, University of Melbourne, Melbourne, Victoria, Australia
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, USA
- Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Kym Ottewell
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, Western Australia, Australia
| | - Katherine Belov
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
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15
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. eLife 2024; 12:RP92863. [PMID: 38767950 PMCID: PMC11105155 DOI: 10.7554/elife.92863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024] Open
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. In this manuscript, we present a genome for a laboratory-tractable Entomophthora muscae isolate that infects fruit flies. Our E. muscae assembly is 1.03 Gb, consists of 7810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with recent datasets from entomophthoralean fungi, we show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity. In addition, we find that E. muscae and its closest allies possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Finally, we offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex that support the need for taxonomic revision within this group. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-RiversideRiversideUnited States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARSIthacaUnited States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Angie M Macias
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Ann E Hajek
- Department of Entomology, Cornell UniversityIthacaUnited States
| | - Benjamin L de Bivort
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
| | - Matt T Kasson
- Division of Plant and Soil Sciences, West Virginia UniversityMorgantownUnited States
| | - Henrik H De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of CopenhagenCopenhagenDenmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard UniversityCambridgeUnited States
- Department of Molecular and Cellular Biology, Harvard UniversityCambridgeUnited States
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16
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Stajich JE, Lovett B, Lee E, Macias AM, Hajek AE, de Bivort BL, Kasson MT, De Fine Licht HH, Elya C. Signatures of transposon-mediated genome inflation, host specialization, and photoentrainment in Entomophthora muscae and allied entomophthoralean fungi. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.13.557621. [PMID: 37745330 PMCID: PMC10515909 DOI: 10.1101/2023.09.13.557621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Despite over a century of observations, the obligate insect parasites within the order Entomophthorales remain poorly characterized at the genetic level. This is in part due to their large genome sizes and difficulty in obtaining sequenceable material. In this manuscript, we leveraged a recently-isolated, laboratory-tractable Entomophthora muscae isolate and improved long-read sequencing to obtain a largely-complete entomophthoralean genome. Our E. muscae assembly is 1.03 Gb, consists of 7,810 contigs and contains 81.3% complete fungal BUSCOs. Using a comparative approach with other available (transcriptomic and genomic) datasets from entomophthoralean fungi, we provide new insight into the biology of these understudied pathogens. We offer a head-to-head comparison of morphological and molecular data for species within the E. muscae species complex. Our findings suggest that substantial taxonomic revision is needed to define species within this group and we provide recommendations for differentiating strains and species in the context of the existing body of E. muscae scientific literature. We show that giant genomes are the norm within Entomophthoraceae owing to extensive, but not recent, Ty3 retrotransposon activity, despite the presence of machinery to defend against transposable elements(RNAi). In addition, we find that E. muscae and its closest allies are enriched for M16A peptidases and possess genes that are likely homologs to the blue-light sensor white-collar 1, a Neurospora crassa gene that has a well-established role in maintaining circadian rhythms. We find that E. muscae has an expanded group of acid-trehalases, consistent with trehalose being the primary sugar component of fly (and insect) hemolymph. We uncover evidence that E. muscae diverged from other entomophthoralean fungi by expansion of existing families, rather than loss of particular domains, and possesses a potentially unique suite of secreted catabolic enzymes, consistent with E. muscae's species-specific, biotrophic lifestyle. Altogether, we provide a genetic and molecular foundation that we hope will provide a platform for the continued study of the unique biology of entomophthoralean fungi.
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Affiliation(s)
- Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA United States
| | - Brian Lovett
- Emerging Pests and Pathogens Research Unit, USDA-ARS, Ithaca, NY, United States
| | - Emily Lee
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Angie M. Macias
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Ann E. Hajek
- Department of Entomology, Cornell University, Ithaca, NY, United States
| | - Benjamin L. de Bivort
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
| | - Matt T. Kasson
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, United States
| | - Henrik H. De Fine Licht
- Section for Organismal Biology, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Carolyn Elya
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, United States
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17
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Molitor C, Kurowski TJ, Fidalgo de Almeida PM, Kevei Z, Spindlow DJ, Chacko Kaitholil SR, Iheanyichi JU, Prasanna HC, Thompson AJ, Mohareb FR. A chromosome-level genome assembly of Solanum chilense, a tomato wild relative associated with resistance to salinity and drought. FRONTIERS IN PLANT SCIENCE 2024; 15:1342739. [PMID: 38525148 PMCID: PMC10957597 DOI: 10.3389/fpls.2024.1342739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 02/12/2024] [Indexed: 03/26/2024]
Abstract
Introduction Solanum chilense is a wild relative of tomato reported to exhibit resistance to biotic and abiotic stresses. There is potential to improve tomato cultivars via breeding with wild relatives, a process greatly accelerated by suitable genomic and genetic resources. Methods In this study we generated a high-quality, chromosome-level, de novo assembly for the S. chilense accession LA1972 using a hybrid assembly strategy with ~180 Gbp of Illumina short reads and ~50 Gbp long PacBio reads. Further scaffolding was performed using Bionano optical maps and 10x Chromium reads. Results The resulting sequences were arranged into 12 pseudomolecules using Hi-C sequencing. This resulted in a 901 Mbp assembly, with a completeness of 95%, as determined by Benchmarking with Universal Single-Copy Orthologs (BUSCO). Sequencing of RNA from multiple tissues resulting in ~219 Gbp of reads was used to annotate the genome assembly with an RNA-Seq guided gene prediction, and for a de novo transcriptome assembly. This chromosome-level, high-quality reference genome for S. chilense accession LA1972 will support future breeding efforts for more sustainable tomato production. Discussion Gene sequences related to drought and salt resistance were compared between S. chilense and S. lycopersicum to identify amino acid variations with high potential for functional impact. These variants were subsequently analysed in 84 resequenced tomato lines across 12 different related species to explore the variant distributions. We identified a set of 7 putative impactful amino acid variants some of which may also impact on fruit development for example the ethylene-responsive transcription factor WIN1 and ethylene-insensitive protein 2. These variants could be tested for their ability to confer functional phenotypes to cultivars that have lost these variants.
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Affiliation(s)
- Corentin Molitor
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Tomasz J. Kurowski
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | | | - Zoltan Kevei
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Daniel J. Spindlow
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Steffimol R. Chacko Kaitholil
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - Justice U. Iheanyichi
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
| | - H. C. Prasanna
- Division of Vegetable Crops, ICAR-Indian Institute of Horticultural Research, Bangalore, India
| | - Andrew J. Thompson
- Soil, Agrifood and Biosciences, Cranfield University, Wharley End, United Kingdom
| | - Fady R. Mohareb
- The Bioinformatics Group, School of Water, Energy and Environment, Cranfield University, Wharley End, United Kingdom
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18
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Winters NP, Wafula EK, Knollenberg BJ, Hämälä T, Timilsena PR, Perryman M, Zhang D, Sheaffer LL, Praul CA, Ralph PE, Prewitt S, Leandro-Muñoz ME, Delgadillo-Duran DA, Altman NS, Tiffin P, Maximova SN, dePamphilis CW, Marden JH, Guiltinan MJ. A combination of conserved and diverged responses underlies Theobroma cacao's defense response to Phytophthora palmivora. BMC Biol 2024; 22:38. [PMID: 38360697 PMCID: PMC10870529 DOI: 10.1186/s12915-024-01831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Plants have complex and dynamic immune systems that have evolved to resist pathogens. Humans have worked to enhance these defenses in crops through breeding. However, many crops harbor only a fraction of the genetic diversity present in wild relatives. Increased utilization of diverse germplasm to search for desirable traits, such as disease resistance, is therefore a valuable step towards breeding crops that are adapted to both current and emerging threats. Here, we examine diversity of defense responses across four populations of the long-generation tree crop Theobroma cacao L., as well as four non-cacao Theobroma species, with the goal of identifying genetic elements essential for protection against the oomycete pathogen Phytophthora palmivora. RESULTS We began by creating a new, highly contiguous genome assembly for the P. palmivora-resistant genotype SCA 6 (Additional file 1: Tables S1-S5), deposited in GenBank under accessions CP139290-CP139299. We then used this high-quality assembly to combine RNA and whole-genome sequencing data to discover several genes and pathways associated with resistance. Many of these are unique, i.e., differentially regulated in only one of the four populations (diverged 40 k-900 k generations). Among the pathways shared across all populations is phenylpropanoid biosynthesis, a metabolic pathway with well-documented roles in plant defense. One gene in this pathway, caffeoyl shikimate esterase (CSE), was upregulated across all four populations following pathogen treatment, indicating its broad importance for cacao's defense response. Further experimental evidence suggests this gene hydrolyzes caffeoyl shikimate to create caffeic acid, an antimicrobial compound and known inhibitor of Phytophthora spp. CONCLUSIONS Our results indicate most expression variation associated with resistance is unique to populations. Moreover, our findings demonstrate the value of using a broad sample of evolutionarily diverged populations for revealing the genetic bases of cacao resistance to P. palmivora. This approach has promise for further revealing and harnessing valuable genetic resources in this and other long-generation plants.
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Affiliation(s)
- Noah P Winters
- IGDP Ecology, The Pennsylvania State University, 422 Huck Life Sciences Building, University Park, PA, 16803, USA
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Eric K Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | | | - Tuomas Hämälä
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Department of Ecology and Genetics, University of Oulu, Oulu, Finland
| | - Prakash R Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Melanie Perryman
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, USA
| | - Lena L Sheaffer
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Craig A Praul
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Paula E Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Sarah Prewitt
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | | | | | - Naomi S Altman
- Department of Statistics, The Pennsylvania State University, University Park, PA, USA
| | - Peter Tiffin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
| | - Siela N Maximova
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA
| | - Claude W dePamphilis
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA
| | - James H Marden
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
- Department of Biology, The Pennsylvania State University, University Park, PA, USA
| | - Mark J Guiltinan
- Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA.
- Department of Biology, The Pennsylvania State University, University Park, PA, USA.
- IGDP Plant Biology, The Pennsylvania State University, University Park, PA, USA.
- Department of Plant Science, The Pennsylvania State University, University Park, PA, USA.
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19
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Mahajan S, Chakraborty A, Bisht MS, Sil T, Sharma VK. Genome sequencing and functional analysis of a multipurpose medicinal herb Tinospora cordifolia (Giloy). Sci Rep 2024; 14:2799. [PMID: 38307917 PMCID: PMC10837142 DOI: 10.1038/s41598-024-53176-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Tinospora cordifolia (Willd.) Hook.f. & Thomson, also known as Giloy, is among the most important medicinal plants that have numerous therapeutic applications in human health due to the production of a diverse array of secondary metabolites. To gain genomic insights into the medicinal properties of T. cordifolia, the genome sequencing was carried out using 10× Genomics linked read and Nanopore long-read technologies. The draft genome assembly of T. cordifolia was comprised of 1.01 Gbp, which is the genome sequenced from the plant family Menispermaceae. We also performed the genome size estimation for T. cordifolia, which was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed. The genome and transcriptome assemblies were used to construct the gene set, resulting in 17,245 coding gene sequences. Further, the phylogenetic position of T. cordifolia was also positioned as basal eudicot by constructing a genome-wide phylogenetic tree using multiple species. Further, a comprehensive comparative evolutionary analysis of gene families contraction/expansion and multiple signatures of adaptive evolution was performed. The genes involved in benzyl iso-quinoline alkaloid, terpenoid, lignin and flavonoid biosynthesis pathways were found with signatures of adaptive evolution. These evolutionary adaptations in genes provide genomic insights into the presence of diverse medicinal properties of this plant. The genes involved in the common symbiosis signalling pathway associated with endosymbiosis (Arbuscular Mycorrhiza) were found to be adaptively evolved. The genes involved in adventitious root formation, peroxisome biogenesis, biosynthesis of phytohormones, and tolerance against abiotic and biotic stresses were also found to be adaptively evolved in T. cordifolia.
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Affiliation(s)
- Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Manohar S Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Titas Sil
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India
| | - Vineet K Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, 462066, India.
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20
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Ma X, Vanneste S, Chang J, Ambrosino L, Barry K, Bayer T, Bobrov AA, Boston L, Campbell JE, Chen H, Chiusano ML, Dattolo E, Grimwood J, He G, Jenkins J, Khachaturyan M, Marín-Guirao L, Mesterházy A, Muhd DD, Pazzaglia J, Plott C, Rajasekar S, Rombauts S, Ruocco M, Scott A, Tan MP, Van de Velde J, Vanholme B, Webber J, Wong LL, Yan M, Sung YY, Novikova P, Schmutz J, Reusch TBH, Procaccini G, Olsen JL, Van de Peer Y. Seagrass genomes reveal ancient polyploidy and adaptations to the marine environment. NATURE PLANTS 2024; 10:240-255. [PMID: 38278954 PMCID: PMC7615686 DOI: 10.1038/s41477-023-01608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 12/05/2023] [Indexed: 01/28/2024]
Abstract
We present chromosome-level genome assemblies from representative species of three independently evolved seagrass lineages: Posidonia oceanica, Cymodocea nodosa, Thalassia testudinum and Zostera marina. We also include a draft genome of Potamogeton acutifolius, belonging to a freshwater sister lineage to Zosteraceae. All seagrass species share an ancient whole-genome triplication, while additional whole-genome duplications were uncovered for C. nodosa, Z. marina and P. acutifolius. Comparative analysis of selected gene families suggests that the transition from submerged-freshwater to submerged-marine environments mainly involved fine-tuning of multiple processes (such as osmoregulation, salinity, light capture, carbon acquisition and temperature) that all had to happen in parallel, probably explaining why adaptation to a marine lifestyle has been exceedingly rare. Major gene losses related to stomata, volatiles, defence and lignification are probably a consequence of the return to the sea rather than the cause of it. These new genomes will accelerate functional studies and solutions, as continuing losses of the 'savannahs of the sea' are of major concern in times of climate change and loss of biodiversity.
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Affiliation(s)
- Xiao Ma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Jiyang Chang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Luca Ambrosino
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
| | - Kerrie Barry
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Till Bayer
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
| | | | - LoriBeth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Justin E Campbell
- Coastlines and Oceans Division, Institute of Environment, Florida International University-Biscayne Bay Campus, Miami, FL, USA
| | - Hengchi Chen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Maria Luisa Chiusano
- Department of Research Infrastructure for Marine Biological Resources, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Agricultural Sciences, University Federico II of Naples, Naples, Italy
| | - Emanuela Dattolo
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Guifen He
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Marina Khachaturyan
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany
- Institute of General Microbiology, University of Kiel, Kiel, Germany
| | - Lázaro Marín-Guirao
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography (IEO-CSIC), Murcia, Spain
| | - Attila Mesterházy
- Centre for Ecological Research, Wetland Ecology Research Group, Debrecen, Hungary
| | - Danish-Daniel Muhd
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jessica Pazzaglia
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- National Biodiversity Future Centre, Palermo, Italy
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Miriam Ruocco
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
- Fano Marine Center, Fano, Italy
| | - Alison Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Min Pau Tan
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Jozefien Van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jenell Webber
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Li Lian Wong
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Mi Yan
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Yeong Yik Sung
- Institute of Climate Adaptation and Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Polina Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Köln, Germany
| | - Jeremy Schmutz
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Thorsten B H Reusch
- Marine Evolutionary Ecology, GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel, Kiel, Germany.
| | - Gabriele Procaccini
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
- National Biodiversity Future Centre, Palermo, Italy.
| | - Jeanine L Olsen
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, the Netherlands.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
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21
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Lo T, Coombe L, Gagalova KK, Marr A, Warren RL, Kirk H, Pandoh P, Zhao Y, Moore RA, Mungall AJ, Ritland C, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I, Thomson A. Assembly and annotation of the black spruce genome provide insights on spruce phylogeny and evolution of stress response. G3 (BETHESDA, MD.) 2023; 14:jkad247. [PMID: 37875130 PMCID: PMC10755193 DOI: 10.1093/g3journal/jkad247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 05/17/2023] [Accepted: 10/09/2023] [Indexed: 10/26/2023]
Abstract
Black spruce (Picea mariana [Mill.] B.S.P.) is a dominant conifer species in the North American boreal forest that plays important ecological and economic roles. Here, we present the first genome assembly of P. mariana with a reconstructed genome size of 18.3 Gbp and NG50 scaffold length of 36.0 kbp. A total of 66,332 protein-coding sequences were predicted in silico and annotated based on sequence homology. We analyzed the evolutionary relationships between P. mariana and 5 other spruces for which complete nuclear and organelle genome sequences were available. The phylogenetic tree estimated from mitochondrial genome sequences agrees with biogeography; specifically, P. mariana was strongly supported as a sister lineage to P. glauca and 3 other taxa found in western North America, followed by the European Picea abies. We obtained mixed topologies with weaker statistical support in phylogenetic trees estimated from nuclear and chloroplast genome sequences, indicative of ancient reticulate evolution affecting these 2 genomes. Clustering of protein-coding sequences from the 6 Picea taxa and 2 Pinus species resulted in 34,776 orthogroups, 560 of which appeared to be specific to P. mariana. Analysis of these specific orthogroups and dN/dS analysis of positive selection signatures for 497 single-copy orthogroups identified gene functions mostly related to plant development and stress response. The P. mariana genome assembly and annotation provides a valuable resource for forest genetics research and applications in this broadly distributed species, especially in relation to climate adaptation.
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Affiliation(s)
- Theodora Lo
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Lauren Coombe
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Kristina K Gagalova
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Alex Marr
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - René L Warren
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Richard A Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Nathalie Pavy
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Steven J M Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jean Bousquet
- Canada Research Chair in Forest Genomics, Laval University, Quebec City, QC G1V 0A6, Canada
| | - Inanç Birol
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Ashley Thomson
- Faculty of Natural Resources Management, Lakehead University, Thunder Bay, ON P7B 5E1, Canada
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22
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Chakraborty A, Mahajan S, Bisht MS, Sharma VK. Genome sequencing of Syzygium cumini (jamun) reveals adaptive evolution in secondary metabolism pathways associated with its medicinal properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1260414. [PMID: 38046611 PMCID: PMC10693344 DOI: 10.3389/fpls.2023.1260414] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/22/2023] [Indexed: 12/05/2023]
Abstract
Syzygium cumini, also known as jambolan or jamun, is an evergreen tree widely known for its medicinal properties, fruits, and ornamental value. To understand the genomic and evolutionary basis of its medicinal properties, we sequenced S. cumini genome for the first time from the world's largest tree genus Syzygium using Oxford Nanopore and 10x Genomics sequencing technologies. We also sequenced and assembled the transcriptome of S. cumini in this study. The tetraploid and highly heterozygous draft genome of S. cumini had a total size of 709.9 Mbp with 61,195 coding genes. The phylogenetic position of S. cumini was established using a comprehensive genome-wide analysis including species from 18 Eudicot plant orders. The existence of neopolyploidy in S. cumini was evident from the higher number of coding genes and expanded gene families resulting from gene duplication events compared to the other two sequenced species from this genus. Comparative evolutionary analyses showed the adaptive evolution of genes involved in the phenylpropanoid-flavonoid (PF) biosynthesis pathway and other secondary metabolites biosynthesis such as terpenoid and alkaloid in S. cumini, along with genes involved in stress tolerance mechanisms, which was also supported by leaf transcriptome data generated in this study. The adaptive evolution of secondary metabolism pathways is associated with the wide range of pharmacological properties, specifically the anti-diabetic property, of this species conferred by the bioactive compounds that act as nutraceutical agents in modern medicine.
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Affiliation(s)
| | | | | | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, India
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23
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Guerreiro R, Bonthala VS, Schlüter U, Hoang NV, Triesch S, Schranz ME, Weber APM, Stich B. A genomic panel for studying C3-C4 intermediate photosynthesis in the Brassiceae tribe. PLANT, CELL & ENVIRONMENT 2023; 46:3611-3627. [PMID: 37431820 DOI: 10.1111/pce.14662] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/18/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Research on C4 and C3-C4 photosynthesis has attracted significant attention because the understanding of the genetic underpinnings of these traits will support the introduction of its characteristics into commercially relevant crop species. We used a panel of 19 taxa of 18 Brassiceae species with different photosynthesis characteristics (C3 and C3-C4) with the following objectives: (i) create draft genome assemblies and annotations, (ii) quantify orthology levels using synteny maps between all pairs of taxa, (iii) describe the phylogenetic relatedness across all the species, and (iv) track the evolution of C3-C4 intermediate photosynthesis in the Brassiceae tribe. Our results indicate that the draft de novo genome assemblies are of high quality and cover at least 90% of the gene space. Therewith we more than doubled the sampling depth of genomes of the Brassiceae tribe that comprises commercially important as well as biologically interesting species. The gene annotation generated high-quality gene models, and for most genes extensive upstream sequences are available for all taxa, yielding potential to explore variants in regulatory sequences. The genome-based phylogenetic tree of the Brassiceae contained two main clades and indicated that the C3-C4 intermediate photosynthesis has evolved five times independently. Furthermore, our study provides the first genomic support of the hypothesis that Diplotaxis muralis is a natural hybrid of D. tenuifolia and D. viminea. Altogether, the de novo genome assemblies and the annotations reported in this study are a valuable resource for research on the evolution of C3-C4 intermediate photosynthesis.
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Affiliation(s)
- Ricardo Guerreiro
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Venkata Suresh Bonthala
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
| | - Urte Schlüter
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Nam V Hoang
- Biosystematics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Sebastian Triesch
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - M Eric Schranz
- Biosystematics Group, Department of Plant Sciences, Wageningen University, Wageningen, The Netherlands
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
| | - Benjamin Stich
- Institute of Quantitative Genetics and Genomics of Plants, Faculty of Mathematics and Natural Sciences, Heinrich Heine University, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Düsseldorf, Germany
- Max Planck Institute for Plant Breeding Research, Köln, Germany
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24
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Lin D, Zou Y, Li X, Wang J, Xiao Q, Gao X, Lin F, Zhang N, Jiao M, Guo Y, Teng Z, Li S, Wei Y, Zhou F, Yin R, Zhang S, Xing L, Xu W, Wu X, Yang B, Xiao K, Wu C, Tao Y, Yang X, Zhang J, Hu S, Dong S, Li X, Ye S, Hong Z, Pan Y, Yang Y, Sun H, Cao G. MGA-seq: robust identification of extrachromosomal DNA and genetic variants using multiple genetic abnormality sequencing. Genome Biol 2023; 24:247. [PMID: 37904244 PMCID: PMC10614391 DOI: 10.1186/s13059-023-03081-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 10/04/2023] [Indexed: 11/01/2023] Open
Abstract
Genomic abnormalities are strongly associated with cancer and infertility. In this study, we develop a simple and efficient method - multiple genetic abnormality sequencing (MGA-Seq) - to simultaneously detect structural variation, copy number variation, single-nucleotide polymorphism, homogeneously staining regions, and extrachromosomal DNA (ecDNA) from a single tube. MGA-Seq directly sequences proximity-ligated genomic fragments, yielding a dataset with concurrent genome three-dimensional and whole-genome sequencing information, enabling approximate localization of genomic structural variations and facilitating breakpoint identification. Additionally, by utilizing MGA-Seq, we map focal amplification and oncogene coamplification, thus facilitating the exploration of ecDNA's transcriptional regulatory function.
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Affiliation(s)
- Da Lin
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yanyan Zou
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Informatics, Huazhong Agricultural University, Wuhan, China
| | - Xinyu Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinyue Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qin Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xiaochen Gao
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fei Lin
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ningyuan Zhang
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Ming Jiao
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yu Guo
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhaowei Teng
- The First People's Hospital of Yunnan Province, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Shiyi Li
- Baylor College of Medicine, Houston, TX, USA
- Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongchang Wei
- Department of Radiation & Medical Oncology, Zhongnan Hospital of Wuhan University, Wuhan, China
- Hubei Key Laboratory of Tumor Biological Behaviors, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Fuling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Rong Yin
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Siheng Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Lingyu Xing
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Weize Xu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaofeng Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Bing Yang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ke Xiao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengchao Wu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yingfeng Tao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Xiaoqing Yang
- Hospital of Huazhong Agricultural University, Wuhan, China
| | - Jing Zhang
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sheng Hu
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shuang Dong
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyu Li
- Department of Medical Oncology, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shengwei Ye
- Department of Gastrointestinal Surgery, Hubei Cancer Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhidan Hong
- Dapartment of Reproductive Medicine Center, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yihang Pan
- Precision Medicine Center, Scientific Research Center, School of Medicine, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, China
| | - Yuqin Yang
- Department of Laboratory Animal Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haixiang Sun
- Reproductive Medical Center, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.
- College of Bio-Medicine and Health, Huazhong Agricultural University, Wuhan, China.
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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25
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Cicconardi F, Milanetti E, Pinheiro de Castro EC, Mazo-Vargas A, Van Belleghem SM, Ruggieri AA, Rastas P, Hanly J, Evans E, Jiggins CD, Owen McMillan W, Papa R, Di Marino D, Martin A, Montgomery SH. Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies. Nat Commun 2023; 14:5620. [PMID: 37699868 PMCID: PMC10497600 DOI: 10.1038/s41467-023-41412-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 08/30/2023] [Indexed: 09/14/2023] Open
Abstract
Heliconius butterflies, a speciose genus of Müllerian mimics, represent a classic example of an adaptive radiation that includes a range of derived dietary, life history, physiological and neural traits. However, key lineages within the genus, and across the broader Heliconiini tribe, lack genomic resources, limiting our understanding of how adaptive and neutral processes shaped genome evolution during their radiation. Here, we generate highly contiguous genome assemblies for nine Heliconiini, 29 additional reference-assembled genomes, and improve 10 existing assemblies. Altogether, we provide a dataset of annotated genomes for a total of 63 species, including 58 species within the Heliconiini tribe. We use this extensive dataset to generate a robust and dated heliconiine phylogeny, describe major patterns of introgression, explore the evolution of genome architecture, and the genomic basis of key innovations in this enigmatic group, including an assessment of the evolution of putative regulatory regions at the Heliconius stem. Our work illustrates how the increased resolution provided by such dense genomic sampling improves our power to generate and test gene-phenotype hypotheses, and precisely characterize how genomes evolve.
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Affiliation(s)
- Francesco Cicconardi
- School of Biological Sciences, Bristol University, Bristol, United Kingdom.
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nano- & Neuro-Science, Italian Institute of Technology, Viale Regina Elena 291, 00161, Rome, Italy
| | | | - Anyi Mazo-Vargas
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Steven M Van Belleghem
- Department of Biology, University of Puerto Rico, Rio Piedras, PR, Puerto Rico
- Ecology, Evolution and Conservation Biology, Biology Department, KU Leuven, Leuven, Belgium
| | | | - Pasi Rastas
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Joseph Hanly
- Department of Biological Sciences, The George Washington University, Washington DC, WA, 20052, USA
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Elizabeth Evans
- Department of Biology, University of Puerto Rico, Rio Piedras, PR, Puerto Rico
| | - Chris D Jiggins
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panama City, Panama
| | - Riccardo Papa
- Department of Biology, University of Puerto Rico, Rio Piedras, PR, Puerto Rico
- Molecular Sciences and Research Center, University of Puerto Rico, San Juan, PR, Puerto Rico
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, Puerto Rico
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Neuronal Death and Neuroprotection Unit, Department of Neuroscience, Mario Negri Institute for Pharmacological Research-IRCCS, Via Mario Negri 2, 20156, Milano, Italy
- National Biodiversity Future Center (NBFC), Palermo, Italy
| | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington DC, WA, 20052, USA
| | - Stephen H Montgomery
- School of Biological Sciences, Bristol University, Bristol, United Kingdom.
- Smithsonian Tropical Research Institute, Panama City, Panama.
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26
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Mahajan S, Bisht MS, Chakraborty A, Sharma VK. Genome of Phyllanthus emblica: the medicinal plant Amla with super antioxidant properties. FRONTIERS IN PLANT SCIENCE 2023; 14:1210078. [PMID: 37727852 PMCID: PMC10505619 DOI: 10.3389/fpls.2023.1210078] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 08/15/2023] [Indexed: 09/21/2023]
Abstract
Phyllanthus emblica or Indian gooseberry, commonly known as amla, is an important medicinal horticultural plant used in traditional and modern medicines. It bears stone fruits with immense antioxidant properties due to being one of the richest natural sources of vitamin C and numerous flavonoids. This study presents the first genome sequencing of this species performed using 10x Genomics and Oxford Nanopore Technology. The draft genome assembly was 519 Mbp in size and consisted of 4,384 contigs, N50 of 597 Kbp, 98.4% BUSCO score, and 37,858 coding sequences. This study also reports the genome-wide phylogeny of this species with 26 other plant species that resolved the phylogenetic position of P. emblica. The presence of three ascorbate biosynthesis pathways including L-galactose, galacturonate, and myo-inositol pathways was confirmed in this genome. A comprehensive comparative evolutionary genomic analysis including gene family expansion/contraction and identification of multiple signatures of adaptive evolution provided evolutionary insights into ascorbate and flavonoid biosynthesis pathways and stone fruit formation through lignin biosynthesis. The availability of this genome will be beneficial for its horticultural, medicinal, dietary, and cosmetic applications and will also help in comparative genomics analysis studies.
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Affiliation(s)
| | | | | | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh, India
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27
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Kawaguchi YW, Tsuchikane Y, Tanaka K, Taji T, Suzuki Y, Toyoda A, Ito M, Watano Y, Nishiyama T, Sekimoto H, Tsuchimatsu T. Extensive Copy Number Variation Explains Genome Size Variation in the Unicellular Zygnematophycean Alga, Closterium peracerosum-strigosum-littorale Complex. Genome Biol Evol 2023; 15:evad115. [PMID: 37348049 PMCID: PMC10407611 DOI: 10.1093/gbe/evad115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/17/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023] Open
Abstract
Genome sizes are known to vary within and among closely related species, but the knowledge about genomic factors contributing to the variation and their impacts on gene functions is limited to only a small number of species. This study identified a more than 2-fold heritable genome size variation among the unicellular Zygnematophycean alga, Closterium peracerosum-strigosum-littorale (C. psl.) complex, based on short-read sequencing analysis of 22 natural strains and F1 segregation analysis. Six de novo assembled genomes revealed that genome size variation is largely attributable to genome-wide copy number variation (CNV) among strains rather than mating type-linked genomic regions or specific repeat sequences such as rDNA. Notably, about 30% of genes showed CNV even between strains that can mate with each other. Transcriptome and gene ontology analysis demonstrated that CNV is distributed nonrandomly in terms of gene functions, such that CNV was more often observed in the gene set with stage-specific expression. Furthermore, in about 30% of these genes with CNV, the expression level does not increase proportionally with the gene copy number, suggesting presence of dosage compensation, which was overrepresented in genes involved in basic biological functions, such as translation. Nonrandom patterns in gene duplications and corresponding expression changes in terms of gene functions may contribute to maintaining the high level of CNV associated with extensive genome size variation in the C. psl. complex, despite its possible detrimental effects.
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Affiliation(s)
- Yawako W Kawaguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Graduate School of Science and Engineering, Chiba University, Chiba, Chiba, Japan
| | - Yuki Tsuchikane
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Teruaki Taji
- Department of Bioscience, Tokyo University of Agriculture, Setagaya-ku, Tokyo, Japan
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Atsushi Toyoda
- Advanced Genomics Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo, Japan
| | - Yasuyuki Watano
- Graduate School of Science, Chiba University, Chiba, Chiba, Japan
| | - Tomoaki Nishiyama
- Research Center for Experimental Modeling of Human Disease, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Hiroyuki Sekimoto
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo-ku, Tokyo, Japan
| | - Takashi Tsuchimatsu
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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28
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Chakraborty A, Mondal S, Mahajan S, Sharma VK. High-quality genome assemblies provide clues on the evolutionary advantage of blue peafowl over green peafowl. Heliyon 2023; 9:e18571. [PMID: 37576271 PMCID: PMC10412995 DOI: 10.1016/j.heliyon.2023.e18571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/15/2023] Open
Abstract
An intriguing example of differential adaptability is the case of two Asian peafowl species, Pavo cristatus (blue peafowl) and Pavo muticus (green peafowl), where the former has a "Least Concern" conservation status and the latter is an "Endangered" species. To understand the genetic basis of this differential adaptability of the two peafowl species, a comparative analysis of these species is much needed to gain the genomic and evolutionary insights. Thus, we constructed a high-quality genome assembly of blue peafowl with an N50 value of 84.81 Mb (pseudochromosome-level assembly), and a high-confidence coding gene set to perform the genomic and evolutionary analyses of blue and green peafowls with 49 other avian species. The analyses revealed adaptive evolution of genes related to neuronal development, immunity, and skeletal muscle development in these peafowl species. Major genes related to axon guidance such as NEO1 and UNC5, semaphorin (SEMA), and ephrin receptor showed adaptive evolution in peafowl species. However, blue peafowl showed the presence of 42% more coding genes compared to the green peafowl along with a higher number of species-specific gene clusters, segmental duplicated genes and expanded gene families, and comparatively higher evolution in neuronal and developmental pathways. Blue peafowl also showed longer branch length compared to green peafowl in the species phylogenetic tree. These genomic insights obtained from the high-quality genome assembly of P. cristatus constructed in this study provide new clues on the superior adaptability of the blue peafowl over green peafowl despite having a recent species divergence time.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Samuel Mondal
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
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29
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Schlebusch SA, Rídl J, Poignet M, Ruiz-Ruano FJ, Reif J, Pajer P, Pačes J, Albrecht T, Suh A, Reifová R. Rapid gene content turnover on the germline-restricted chromosome in songbirds. Nat Commun 2023; 14:4579. [PMID: 37516764 PMCID: PMC10387091 DOI: 10.1038/s41467-023-40308-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/20/2023] [Indexed: 07/31/2023] Open
Abstract
The germline-restricted chromosome (GRC) of songbirds represents a taxonomically widespread example of programmed DNA elimination. Despite its apparent indispensability, we still know very little about the GRC's genetic composition, function, and evolutionary significance. Here we assemble the GRC in two closely related species, the common and thrush nightingale. In total we identify 192 genes across the two GRCs, with many of them present in multiple copies. Interestingly, the GRC appears to be under little selective pressure, with the genetic content differing dramatically between the two species and many GRC genes appearing to be pseudogenized fragments. Only one gene, cpeb1, has a complete coding region in all examined individuals of the two species and shows no copy number variation. The acquisition of this gene by the GRC corresponds with the earliest estimates of the GRC origin, making it a good candidate for the functional indispensability of the GRC in songbirds.
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Affiliation(s)
- Stephen A Schlebusch
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
| | - Jakub Rídl
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Manon Poignet
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Francisco J Ruiz-Ruano
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
- Institute of Evolutionary Biology and Ecology, University of Bonn, An der Immenburg 1, 53121, Bonn, Germany
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Jiří Reif
- Institute for Environmental Studies, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Zoology, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01, Prague 6, San Antonio, Czech Republic
| | - Jan Pačes
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague, Czech Republic
| | - Tomáš Albrecht
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Vertebrate Biology, Czech Academy of Sciences, Brno, Czech Republic
| | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich, UK
- Department of Organismal Biology - Systematic Biology, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden
- Centre for Molecular Biodiversity Research, Leibniz Institute for the Analysis of Biodiversity Change, Adenauerallee 127, 53113, Bonn, Germany
| | - Radka Reifová
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic.
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30
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Guichard A, Legeai F, Tagu D, Lemaitre C. MTG-Link: leveraging barcode information from linked-reads to assemble specific loci. BMC Bioinformatics 2023; 24:284. [PMID: 37452278 PMCID: PMC10347852 DOI: 10.1186/s12859-023-05395-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
BACKGROUND Local assembly with short and long reads has proven to be very useful in many applications: reconstruction of the sequence of a locus of interest, gap-filling in draft assemblies, as well as alternative allele reconstruction of large Structural Variants. Whereas linked-read technologies have a great potential to assemble specific loci as they provide long-range information while maintaining the power and accuracy of short-read sequencing, there is a lack of local assembly tools for linked-read data. RESULTS We present MTG-Link, a novel local assembly tool dedicated to linked-reads. The originality of the method lies in its read subsampling step which takes advantage of the barcode information contained in linked-reads mapped in flanking regions. We validated our approach on several datasets from different linked-read technologies. We show that MTG-Link is able to assemble successfully large sequences, up to dozens of Kb. We also demonstrate that the read subsampling step of MTG-Link considerably improves the local assembly of specific loci compared to other existing short-read local assembly tools. Furthermore, MTG-Link was able to fully characterize large insertion variants and deletion breakpoints in a human genome and to reconstruct dark regions in clinically-relevant human genes. It also improved the contiguity of a 1.3 Mb locus of biological interest in several individual genomes of the mimetic butterfly Heliconius numata. CONCLUSIONS MTG-Link is an efficient local assembly tool designed for different linked-read sequencing technologies. MTG-Link source code is available at https://github.com/anne-gcd/MTG-Link and as a Bioconda package.
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Affiliation(s)
- Anne Guichard
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France.
| | - Fabrice Legeai
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
- Univ Rennes, Inria, CNRS, IRISA, 35000, Rennes, France
| | - Denis Tagu
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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31
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Xiong W, Berke L, Michelmore R, van Workum DJM, Becker FFM, Schijlen E, Bakker LV, Peters S, van Treuren R, Jeuken M, Bouwmeester K, Schranz ME. The genome of Lactuca saligna, a wild relative of lettuce, provides insight into non-host resistance to the downy mildew Bremia lactucae. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 115:108-126. [PMID: 36987839 DOI: 10.1111/tpj.16212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/20/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Lactuca saligna L. is a wild relative of cultivated lettuce (Lactuca sativa L.), with which it is partially interfertile. Hybrid progeny suffer from hybrid incompatibility (HI), resulting in reduced fertility and distorted transmission ratios. Lactuca saligna displays broad-spectrum resistance against lettuce downy mildew caused by Bremia lactucae Regel and is considered a non-host species. This phenomenon of resistance in L. saligna is called non-host resistance (NHR). One possible mechanism behind this NHR is through the plant-pathogen interaction triggered by pathogen recognition receptors, including nucleotide-binding leucine-rich repeat (NLR) proteins and receptor-like kinases (RLKs). We report a chromosome-level genome assembly of L. saligna (accession CGN05327), leading to the identification of two large paracentric inversions (>50 Mb) between L. saligna and L. sativa. Genome-wide searches delineated the major resistance clusters as regions enriched in NLRs and RLKs. Three of the enriched regions co-locate with previously identified NHR intervals. RNA-seq analysis of Bremia-infected lettuce identified several differentially expressed RLKs in NHR regions. Three tandem wall-associated kinase-encoding genes (WAKs) in the NHR8 interval display particularly high expression changes at an early stage of infection. We propose RLKs as strong candidates for determinants of the NHR phenotype of L. saligna.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Richard Michelmore
- Genome Center and Department of Plant Sciences, University of California, Davis, CA, USA
| | | | - Frank F M Becker
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - Elio Schijlen
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Linda V Bakker
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Sander Peters
- Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rob van Treuren
- Centre for Genetic Resources, The Netherlands (CGN), Wageningen University and Research, Wageningen, The Netherlands
| | - Marieke Jeuken
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands
| | - Klaas Bouwmeester
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
| | - M Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, The Netherlands
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32
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Xiong W, Risse J, Berke L, Zhao T, van de Geest H, Oplaat C, Busscher M, Ferreira de Carvalho J, van der Meer IM, Verhoeven KJF, Schranz ME, Vijverberg K. Phylogenomic analysis provides insights into MADS-box and TCP gene diversification and floral development of the Asteraceae, supported by de novo genome and transcriptome sequences from dandelion ( Taraxacum officinale). FRONTIERS IN PLANT SCIENCE 2023; 14:1198909. [PMCID: PMC10338227 DOI: 10.3389/fpls.2023.1198909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
The Asteraceae is the largest angiosperm family with more than 25,000 species. Individual studies have shown that MADS-box and TCP transcription factors are regulators of the development and symmetry of flowers, contributing to their iconic flower-head (capitulum) and floret. However, a systematic study of MADS-box and TCP genes across the Asteraceae is lacking. We performed a comparative analysis of genome sequences of 33 angiosperm species including our de novo assembly of diploid sexual dandelion (Taraxacum officinale) and 11 other Asteraceae to investigate the lineage-specific evolution of MADS-box and TCP genes in the Asteraceae. We compared the phylogenomic results of MADS-box and TCP genes with their expression in T. officinale floral tissues at different developmental stages to demonstrate the regulation of genes with Asteraceae-specific attributes. Here, we show that MADS-box MIKCc and TCP-CYCLOIDEA (CYC) genes have expanded in the Asteraceae. The phylogenomic analysis identified AGAMOUS-like (AG-like: SEEDSTICK [STK]-like), SEPALATA-like (SEP3-like), and TCP-PROLIFERATING CELL FACTOR (PCF)-like copies with lineage-specific genomic contexts in the Asteraceae, Cichorioideae, or dandelion. Different expression patterns of some of these gene copies suggest functional divergence. We also confirm the presence and revisit the evolutionary history of previously named “Asteraceae-Specific MADS-box genes (AS-MADS).” Specifically, we identify non-Asteraceae homologs, indicating a more ancient origin of this gene clade. Syntenic relationships support that AS-MADS is paralogous to FLOWERING LOCUS C (FLC) as demonstrated by the shared ancient duplication of FLC and SEP3.
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Affiliation(s)
- Wei Xiong
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Judith Risse
- Bioinformatics Group, Wageningen University and Research, Wageningen, Netherlands
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Lidija Berke
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Tao Zhao
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | | | - Carla Oplaat
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Marco Busscher
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
- Bioscience, Wageningen University and Research, Wageningen, Netherlands
| | - Julie Ferreira de Carvalho
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - M. Eric Schranz
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Kitty Vijverberg
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
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Luo J, Guan T, Chen G, Yu Z, Zhai H, Yan C, Luo H. SLHSD: hybrid scaffolding method based on short and long reads. Brief Bioinform 2023; 24:7152317. [PMID: 37141142 DOI: 10.1093/bib/bbad169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 01/08/2023] [Accepted: 04/12/2023] [Indexed: 05/05/2023] Open
Abstract
In genome assembly, scaffolding can obtain more complete and continuous scaffolds. Current scaffolding methods usually adopt one type of read to construct a scaffold graph and then orient and order contigs. However, scaffolding with the strengths of two or more types of reads seems to be a better solution to some tricky problems. Combining the advantages of different types of data is significant for scaffolding. Here, a hybrid scaffolding method (SLHSD) is present that simultaneously leverages the precision of short reads and the length advantage of long reads. Building an optimal scaffold graph is an important foundation for getting scaffolds. SLHSD uses a new algorithm that combines long and short read alignment information to determine whether to add an edge and how to calculate the edge weight in a scaffold graph. In addition, SLHSD develops a strategy to ensure that edges with high confidence can be added to the graph with priority. Then, a linear programming model is used to detect and remove remaining false edges in the graph. We compared SLHSD with other scaffolding methods on five datasets. Experimental results show that SLHSD outperforms other methods. The open-source code of SLHSD is available at https://github.com/luojunwei/SLHSD.
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Affiliation(s)
- Junwei Luo
- School of Software, Henan Polytechnic University, Jiaozuo 454003, China
| | - Ting Guan
- School of Software, Henan Polytechnic University, Jiaozuo 454003, China
| | - Guolin Chen
- School of Software, Henan Polytechnic University, Jiaozuo 454003, China
| | - Zhonghua Yu
- School of Software, Henan Polytechnic University, Jiaozuo 454003, China
| | - Haixia Zhai
- School of Software, Henan Polytechnic University, Jiaozuo 454003, China
| | - Chaokun Yan
- School of Computer and Information Engineering, Henan University, Kaifeng 475001, China
| | - Huimin Luo
- School of Computer and Information Engineering, Henan University, Kaifeng 475001, China
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Hoang NV, Sogbohossou EOD, Xiong W, Simpson CJC, Singh P, Walden N, van den Bergh E, Becker FFM, Li Z, Zhu XG, Brautigam A, Weber APM, van Haarst JC, Schijlen EGWM, Hendre PS, Van Deynze A, Achigan-Dako EG, Hibberd JM, Schranz ME. The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae. THE PLANT CELL 2023; 35:1334-1359. [PMID: 36691724 PMCID: PMC10118270 DOI: 10.1093/plcell/koad018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 01/18/2023] [Indexed: 06/17/2023]
Abstract
Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.
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Affiliation(s)
| | | | - Wei Xiong
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Conor J C Simpson
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Pallavi Singh
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
| | - Nora Walden
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Erik van den Bergh
- Biosystematics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Frank F M Becker
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Zheng Li
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xin-Guang Zhu
- State Key Laboratory for Plant Molecular Genetics, Center of Excellence for Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Andrea Brautigam
- Faculty of Biology, Bielefeld University, 33501 Bielefeld, Germany
| | - Andreas P M Weber
- Cluster of Excellence on Plant Science (CEPLAS), Institute of Plant Biochemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jan C van Haarst
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Elio G W M Schijlen
- Business Unit Bioscience, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - Prasad S Hendre
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
| | - Allen Van Deynze
- African Orphan Crops Consortium (AOCC), World Agroforestry (ICRAF), Nairobi 00100, Kenya
- Seed Biotechnology Center, University of California, Davis, California 95616, USA
| | - Enoch G Achigan-Dako
- Laboratory of Genetics, Biotechnology and Seed Science (GbioS), Faculty of Agronomic Sciences, University of Abomey-Calavi, BP 2549 Abomey-Calavi, Republic of Benin
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK
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Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: de novo chromosome-length genome assembly, DNA methylome, and cranial morphology. Gigascience 2023; 12:giad018. [PMID: 36994871 PMCID: PMC10353722 DOI: 10.1093/gigascience/giad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/13/2023] [Accepted: 02/28/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long-read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. FINDINGS We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on chromosomes 11, 16, 25, and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and 9 previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mitochondrial DNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified 2 differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphologic data, comprising geometric morphometric assessment of cranial morphology, place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue shows she had a larger cranial capacity than a similar-sized domestic dog. CONCLUSIONS These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphologic characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, NSW 2006, Australia
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705, USA
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Quedlinburg 06484, Germany
| | - Ksenia Skvortsova
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ozren Bogdanovic
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, Newcastle, NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital,Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Developmental Epigenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW 2006, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Lundberg M, Mackintosh A, Petri A, Bensch S. Inversions maintain differences between migratory phenotypes of a songbird. Nat Commun 2023; 14:452. [PMID: 36707538 PMCID: PMC9883250 DOI: 10.1038/s41467-023-36167-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Structural rearrangements have been shown to be important in local adaptation and speciation, but have been difficult to reliably identify and characterize in non-model species. Here we combine long reads, linked reads and optical mapping to characterize three divergent chromosome regions in the willow warbler Phylloscopus trochilus, of which two are associated with differences in migration and one with an environmental gradient. We show that there are inversions (0.4-13 Mb) in each of the regions and that the divergence times between inverted and non-inverted haplotypes are similar across the regions (~1.2 Myrs), which is compatible with a scenario where inversions arose in either of two allopatric populations that subsequently hybridized. The improved genomes allow us to detect additional functional differences in the divergent regions, providing candidate genes for migration and adaptations to environmental gradients.
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Affiliation(s)
- Max Lundberg
- Department of Biology, Lund University, Lund, Sweden.
| | | | - Anna Petri
- Science for Life Laboratory, Uppsala Genome Center, Uppsala University, Uppsala, Sweden
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37
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Ballard JWO, Field MA, Edwards RJ, Wilson LAB, Koungoulos LG, Rosen BD, Chernoff B, Dudchenko O, Omer A, Keilwagen J, Skvortsova K, Bogdanovic O, Chan E, Zammit R, Hayes V, Aiden EL. The Australasian dingo archetype: De novo chromosome-length genome assembly, DNA methylome, and cranial morphology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.26.525801. [PMID: 36747621 PMCID: PMC9900879 DOI: 10.1101/2023.01.26.525801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Background One difficulty in testing the hypothesis that the Australasian dingo is a functional intermediate between wild wolves and domesticated breed dogs is that there is no reference specimen. Here we link a high-quality de novo long read chromosomal assembly with epigenetic footprints and morphology to describe the Alpine dingo female named Cooinda. It was critical to establish an Alpine dingo reference because this ecotype occurs throughout coastal eastern Australia where the first drawings and descriptions were completed. Findings We generated a high-quality chromosome-level reference genome assembly (Canfam_ADS) using a combination of Pacific Bioscience, Oxford Nanopore, 10X Genomics, Bionano, and Hi-C technologies. Compared to the previously published Desert dingo assembly, there are large structural rearrangements on Chromosomes 11, 16, 25 and 26. Phylogenetic analyses of chromosomal data from Cooinda the Alpine dingo and nine previously published de novo canine assemblies show dingoes are monophyletic and basal to domestic dogs. Network analyses show that the mtDNA genome clusters within the southeastern lineage, as expected for an Alpine dingo. Comparison of regulatory regions identified two differentially methylated regions within glucagon receptor GCGR and histone deacetylase HDAC4 genes that are unmethylated in the Alpine dingo genome but hypermethylated in the Desert dingo. Morphological data, comprising geometric morphometric assessment of cranial morphology place dingo Cooinda within population-level variation for Alpine dingoes. Magnetic resonance imaging of brain tissue show she had a larger cranial capacity than a similar-sized domestic dog. Conclusions These combined data support the hypothesis that the dingo Cooinda fits the spectrum of genetic and morphological characteristics typical of the Alpine ecotype. We propose that she be considered the archetype specimen for future research investigating the evolutionary history, morphology, physiology, and ecology of dingoes. The female has been taxidermically prepared and is now at the Australian Museum, Sydney.
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Affiliation(s)
- J William O Ballard
- School of Biosciences, University of Melbourne, Royal Parade, Parkville, Victoria 3052, Australia
- Department of Environment and Genetics, SABE, La Trobe University, Melbourne Victoria 3086, Australia
| | - Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, Queensland 4870, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Richard J Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney NSW 2052, Australia
| | - Laura A B Wilson
- School of Archaeology and Anthropology, The Australian National University, Acton, ACT 2600, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Loukas G Koungoulos
- Department of Archaeology, School of Philosophical and Historical Inquiry, the University of Sydney, Sydney, Australia 2006
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705
| | - Barry Chernoff
- College of the Environment, Departments of Biology, and Earth & Environmental Sciences, Wesleyan University, Middletown, CT 06459, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Arina Omer
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str. 27 06484 Quedlinburg, Germany
| | | | - Ozren Bogdanovic
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Eva Chan
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Statewide Genomics, New South Wales Health Pathology, 45 Watt St, Newcastle NSW 2300, Australia
| | - Robert Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765, Australia
| | - Vanessa Hayes
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Charles Perkins Centre, Faculty of Medical Sciences, University of Sydney, Camperdown, NSW, Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030 USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX 77005, USA
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong 201210, China
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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Linscott TM, González-González A, Hirano T, Parent CE. De novo genome assembly and genome skims reveal LTRs dominate the genome of a limestone endemic Mountainsnail (Oreohelix idahoensis). BMC Genomics 2022; 23:796. [PMID: 36460988 PMCID: PMC9719178 DOI: 10.1186/s12864-022-09000-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Calcareous outcrops, rocky areas composed of calcium carbonate (CaCO3), often host a diverse, specialized, and threatened biomineralizing fauna. Despite the repeated evolution of physiological and morphological adaptations to colonize these mineral rich substrates, there is a lack of genomic resources for calcareous rock endemic species. This has hampered our ability to understand the genomic mechanisms underlying calcareous rock specialization and manage these threatened species. RESULTS Here, we present a new draft genome assembly of the threatened limestone endemic land snail Oreohelix idahoensis and genome skim data for two other Oreohelix species. The O. idahoensis genome assembly (scaffold N50: 404.19 kb; 86.6% BUSCO genes) is the largest (~ 5.4 Gb) and most repetitive mollusc genome assembled to date (85.74% assembly size). The repetitive landscape was unusually dominated by an expansion of long terminal repeat (LTR) transposable elements (57.73% assembly size) which have shaped the evolution genome size, gene composition through retrotransposition of host genes, and ectopic recombination. Genome skims revealed repeat content is more than 2-3 fold higher in limestone endemic O. idahoensis compared to non-calcareous Oreohelix species. Gene family size analysis revealed stress and biomineralization genes have expanded significantly in the O. idahoensis genome. CONCLUSIONS Hundreds of threatened land snail species are endemic to calcareous rock regions but there are very few genomic resources available to guide their conservation or determine the genomic architecture underlying CaCO3 resource specialization. Our study provides one of the first high quality draft genomes of a calcareous rock endemic land snail which will serve as a foundation for the conservation genomics of this threatened species and for other groups. The high proportion and activity of LTRs in the O. idahoensis genome is unprecedented in molluscan genomics and sheds new light how transposable element content can vary across molluscs. The genomic resources reported here will enable further studies of the genomic mechanisms underlying calcareous rock specialization and the evolution of transposable element content across molluscs.
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Affiliation(s)
- T. Mason Linscott
- grid.266456.50000 0001 2284 9900Department of Biological Sciences, University of Idaho, Moscow, ID USA ,grid.266456.50000 0001 2284 9900Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID USA
| | - Andrea González-González
- grid.15276.370000 0004 1936 8091Department of Biology, University of Florida, Gainesville, Florida USA
| | - Takahiro Hirano
- grid.69566.3a0000 0001 2248 6943Center for Northeast Asian Studies, Tohoku University, Sendai, Miyagi Japan
| | - Christine E. Parent
- grid.266456.50000 0001 2284 9900Department of Biological Sciences, University of Idaho, Moscow, ID USA ,grid.266456.50000 0001 2284 9900Institute for Interdisciplinary Data Sciences, University of Idaho, Moscow, ID USA
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Qi Y, Gu S, Zhang Y, Guo L, Xu M, Cheng X, Wang O, Sun Y, Chen J, Fang X, Liu X, Deng L, Fan G. MetaTrass: A high-quality metagenome assembler of the human gut microbiome by cobarcoding sequencing reads. IMETA 2022; 1:e46. [PMID: 38867906 PMCID: PMC10989976 DOI: 10.1002/imt2.46] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/28/2022] [Accepted: 07/20/2022] [Indexed: 06/14/2024]
Abstract
Metagenomic evidence of great genetic diversity within the nonconserved regions of the human gut microbial genomes appeals for new methods to elucidate the species-level variability at high resolution. However, current approaches cannot satisfy this methodologically challenge. In this study, we proposed an efficient binning-first-and-assembly-later strategy, named MetaTrass, to recover high-quality species-resolved genomes based on public reference genomes and the single-tube long fragment read (stLFR) technology, which enables cobarcoding. MetaTrass can generate genomes with longer contiguity, higher completeness, and lower contamination than those produced by conventional assembly-first-and-binning-later strategies. From a simulation study on a mock microbial community, MetaTrass showed the potential to improve the contiguity of assembly from kb to Mb without accuracy loss, as compared to other methods based on the next-generation sequencing technology. From four human fecal samples, MetaTrass successfully retrieved 178 high-quality genomes, whereas only 58 ones were provided by the optimal performance of other conventional strategies. Most importantly, these high-quality genomes confirmed the high level of genetic diversity among different samples and unveiled much more. MetaTrass was designed to work with metagenomic reads sequenced by stLFR technology, but is also applicable to other types of cobarcoding libraries. With the high capability of assembling high-quality genomes of metagenomic data sets, MetaTrass seeks to facilitate the study of spatial characters and dynamics of complex microbial communities at enhanced resolution. The open-source code of MetaTrass is available at https://github.com/BGI-Qingdao/MetaTrass.
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Affiliation(s)
- Yanwei Qi
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Shengqiang Gu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | | | - Lidong Guo
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- College of Life SciencesUniversity of Chinese Academy of SciencesBeijingChina
| | - Mengyang Xu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
| | - Xiaofang Cheng
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
- MGIBGI‐ShenzhenShenzhenChina
| | - Ou Wang
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
- MGIBGI‐ShenzhenShenzhenChina
| | - Ying Sun
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
| | | | - Xiaodong Fang
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
- BGI GenomicsBGI‐ShenzhenShenzhenChina
| | - Xin Liu
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Li Deng
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
| | - Guangyi Fan
- BGI‐QingdaoBGI‐ShenzhenQingdaoChina
- State Key Laboratory of Agricultural GenomicsBGI‐ShenzhenShenzhenChina
- China National GeneBankBGI‐ShenzhenShenzhenChina
- BGI‐ShenzhenBGI‐ShenzhenShenzhenChina
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Zhang H, Wafula EK, Eilers J, Harkess A, Ralph PE, Timilsena PR, dePamphilis CW, Waite JM, Honaas LA. Building a foundation for gene family analysis in Rosaceae genomes with a novel workflow: A case study in Pyrus architecture genes. FRONTIERS IN PLANT SCIENCE 2022; 13:975942. [PMID: 36452099 PMCID: PMC9702816 DOI: 10.3389/fpls.2022.975942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 09/21/2022] [Indexed: 05/26/2023]
Abstract
The rapid development of sequencing technologies has led to a deeper understanding of plant genomes. However, direct experimental evidence connecting genes to important agronomic traits is still lacking in most non-model plants. For instance, the genetic mechanisms underlying plant architecture are poorly understood in pome fruit trees, creating a major hurdle in developing new cultivars with desirable architecture, such as dwarfing rootstocks in European pear (Pyrus communis). An efficient way to identify genetic factors for important traits in non-model organisms can be to transfer knowledge across genomes. However, major obstacles exist, including complex evolutionary histories and variable quality and content of publicly available plant genomes. As researchers aim to link genes to traits of interest, these challenges can impede the transfer of experimental evidence across plant species, namely in the curation of high-quality, high-confidence gene models in an evolutionary context. Here we present a workflow using a collection of bioinformatic tools for the curation of deeply conserved gene families of interest across plant genomes. To study gene families involved in tree architecture in European pear and other rosaceous species, we used our workflow, plus a draft genome assembly and high-quality annotation of a second P. communis cultivar, 'd'Anjou.' Our comparative gene family approach revealed significant issues with the most recent 'Bartlett' genome - primarily thousands of missing genes due to methodological bias. After correcting assembly errors on a global scale in the 'Bartlett' genome, we used our workflow for targeted improvement of our genes of interest in both P. communis genomes, thus laying the groundwork for future functional studies in pear tree architecture. Further, our global gene family classification of 15 genomes across 6 genera provides a valuable and previously unavailable resource for the Rosaceae research community. With it, orthologs and other gene family members can be easily identified across any of the classified genomes. Importantly, our workflow can be easily adopted for any other plant genomes and gene families of interest.
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Affiliation(s)
- Huiting Zhang
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
- Department of Horticulture, Washington State University, Pullman, WA, United States
| | - Eric K. Wafula
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jon Eilers
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Alex E. Harkess
- College of Agriculture, Auburn University, Auburn, AL, United States
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Paula E. Ralph
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Prakash Raj Timilsena
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Claude W. dePamphilis
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
| | - Jessica M. Waite
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
| | - Loren A. Honaas
- Tree Fruit Research Laboratory, Agricultural Research Service (ARS), United States Department of Agriculture (USDA), Wenatchee, WA, United States
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Xiao C, Chen Z, Chen W, Padilla C, Colgan M, Wu W, Fang LT, Liu T, Yang Y, Schneider V, Wang C, Xiao W. Personalized genome assembly for accurate cancer somatic mutation discovery using tumor-normal paired reference samples. Genome Biol 2022; 23:237. [PMID: 36352452 PMCID: PMC9648002 DOI: 10.1186/s13059-022-02803-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/25/2022] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The use of a personalized haplotype-specific genome assembly, rather than an unrelated, mosaic genome like GRCh38, as a reference for detecting the full spectrum of somatic events from cancers has long been advocated but has never been explored in tumor-normal paired samples. Here, we provide the first demonstrated use of de novo assembled personalized genome as a reference for cancer mutation detection and quantifying the effects of the reference genomes on the accuracy of somatic mutation detection. RESULTS We generate de novo assemblies of the first tumor-normal paired genomes, both nuclear and mitochondrial, derived from the same individual with triple negative breast cancer. The personalized genome was chromosomal scale, haplotype phased, and annotated. We demonstrate that it provides individual specific haplotypes for complex regions and medically relevant genes. We illustrate that the personalized genome reference not only improves read alignments for both short-read and long-read sequencing data but also ameliorates the detection accuracy of somatic SNVs and SVs. We identify the equivalent somatic mutation calls between two genome references and uncover novel somatic mutations only when personalized genome assembly is used as a reference. CONCLUSIONS Our findings demonstrate that use of a personalized genome with individual-specific haplotypes is essential for accurate detection of the full spectrum of somatic mutations in the paired tumor-normal samples. The unique resource and methodology established in this study will be beneficial to the development of precision oncology medicine not only for breast cancer, but also for other cancers.
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Affiliation(s)
- Chunlin Xiao
- grid.94365.3d0000 0001 2297 5165National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20894 USA
| | - Zhong Chen
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, 11021 Campus St., Loma Linda, CA 92350 USA
| | - Wanqiu Chen
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, 11021 Campus St., Loma Linda, CA 92350 USA
| | - Cory Padilla
- grid.504403.6Dovetail Genomics, 100 Enterprise Way, Scotts Valley, CA 95066 USA
| | - Michael Colgan
- grid.417587.80000 0001 2243 3366The Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD USA
| | - Wenjun Wu
- grid.249335.a0000 0001 2218 7820Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111 USA
| | - Li-Tai Fang
- grid.418158.10000 0004 0534 4718Bioinformatics Research & Early Development, Roche Sequencing Solutions Inc., 1301 Shoreway Road, Belmont, CA 94002 USA
| | - Tiantian Liu
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, 11021 Campus St., Loma Linda, CA 92350 USA
| | - Yibin Yang
- grid.249335.a0000 0001 2218 7820Blood Cell Development and Function Program, Fox Chase Cancer Center, Philadelphia, PA 19111 USA
| | - Valerie Schneider
- grid.94365.3d0000 0001 2297 5165National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20894 USA
| | - Charles Wang
- grid.43582.380000 0000 9852 649XCenter for Genomics, Loma Linda University School of Medicine, 11021 Campus St., Loma Linda, CA 92350 USA
| | - Wenming Xiao
- grid.417587.80000 0001 2243 3366The Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD USA
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Chakraborty A, Mahajan S, Bisht MS, Sharma VK. Genome sequencing and comparative analysis of Ficus benghalensis and Ficus religiosa species reveal evolutionary mechanisms of longevity. iScience 2022; 25:105100. [PMID: 36164650 PMCID: PMC9508489 DOI: 10.1016/j.isci.2022.105100] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 09/04/2022] [Indexed: 11/23/2022] Open
Abstract
Ficus benghalensis and Ficus religiosa are large woody trees well known for their long lifespan, ecological and traditional significance, and medicinal properties. To understand the genomic and evolutionary aspects of these characteristics, the whole genomes of these Ficus species were sequenced using 10x Genomics linked reads and Oxford Nanopore long reads. The draft genomes of F. benghalensis and F. religiosa comprised of 392.89 Mbp and 332.97 Mbp, respectively. We established the genome-wide phylogenetic positions of the two Ficus species with respect to 50 other Angiosperm species. Comparative evolutionary analyses with other phylogenetically closer Eudicot species revealed adaptive evolution in genes involved in key cellular mechanisms associated with prolonged survival including phytohormones signaling, senescence, disease resistance, and abiotic stress tolerance, which provide genomic insights into the mechanisms conferring longevity and suggest that longevity is a multifaceted phenomenon. This study also provides clues on the existence of CAM pathway in these Ficus species.
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Affiliation(s)
- Abhisek Chakraborty
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| | - Shruti Mahajan
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| | - Manohar S. Bisht
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
| | - Vineet K. Sharma
- MetaBioSys Group, Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066 Madhya Pradesh, India
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McLay TGB, Murphy DJ, Holmes GD, Mathews S, Brown GK, Cantrill DJ, Udovicic F, Allnutt TR, Jackson CJ. A genome resource for Acacia, Australia's largest plant genus. PLoS One 2022; 17:e0274267. [PMID: 36240205 PMCID: PMC9565413 DOI: 10.1371/journal.pone.0274267] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022] Open
Abstract
Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes.
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Affiliation(s)
- Todd G. B. McLay
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Gareth D. Holmes
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Sarah Mathews
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Gillian K. Brown
- Queensland Herbarium, Department of Environment and Science, Toowong, Queensland, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | | | - Chris J. Jackson
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
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Yang T, Liu R, Luo Y, Hu S, Wang D, Wang C, Pandey MK, Ge S, Xu Q, Li N, Li G, Huang Y, Saxena RK, Ji Y, Li M, Yan X, He Y, Liu Y, Wang X, Xiang C, Varshney RK, Ding H, Gao S, Zong X. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet 2022; 54:1553-1563. [PMID: 36138232 PMCID: PMC9534762 DOI: 10.1038/s41588-022-01172-2] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/26/2022] [Indexed: 12/21/2022]
Abstract
Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.
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Affiliation(s)
- Tao Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Chenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quanle Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuning Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rachit K Saxena
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yishan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengwei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua He
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural and Forestry Sciences, Xining, China
| | - Xuejun Wang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Chao Xiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Murdoch's Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Hanfeng Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.
- College of Life Science, Shandong Normal University, Jinan, China.
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xuxiao Zong
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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Faure R, Lavenier D. QuickDeconvolution: fast and scalable deconvolution of linked-read sequencing data. BIOINFORMATICS ADVANCES 2022; 2:vbac068. [PMID: 36699389 PMCID: PMC9710601 DOI: 10.1093/bioadv/vbac068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/22/2022] [Accepted: 09/21/2022] [Indexed: 01/28/2023]
Abstract
Motivation Recently introduced, linked-read technologies, such as the 10× chromium system, use microfluidics to tag multiple short reads from the same long fragment (50-200 kb) with a small sequence, called a barcode. They are inexpensive and easy to prepare, combining the accuracy of short-read sequencing with the long-range information of barcodes. The same barcode can be used for several different fragments, which complicates the analyses. Results We present QuickDeconvolution (QD), a new software for deconvolving a set of reads sharing a barcode, i.e. separating the reads from the different fragments. QD only takes sequencing data as input, without the need for a reference genome. We show that QD outperforms existing software in terms of accuracy, speed and scalability, making it capable of deconvolving previously inaccessible data sets. In particular, we demonstrate here the first example in the literature of a successfully deconvoluted animal sequencing dataset, a 33-Gb Drosophila melanogaster dataset. We show that the taxonomic assignment of linked reads can be improved by deconvoluting reads with QD before taxonomic classification. Availability and implementation Code and instructions are available on https://github.com/RolandFaure/QuickDeconvolution. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Salazar OR, N. Arun P, Cui G, Bay LK, van Oppen MJH, Webster NS, Aranda M. The coral Acropora loripes genome reveals an alternative pathway for cysteine biosynthesis in animals. SCIENCE ADVANCES 2022; 8:eabq0304. [PMID: 36149959 PMCID: PMC9506716 DOI: 10.1126/sciadv.abq0304] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 08/10/2022] [Indexed: 05/28/2023]
Abstract
The metabolic capabilities of animals have been derived from well-studied model organisms and are generally considered to be well understood. In animals, cysteine is an important amino acid thought to be exclusively synthesized through the transsulfuration pathway. Corals of the genus Acropora have lost cystathionine β-synthase, a key enzyme of the transsulfuration pathway, and it was proposed that Acropora relies on the symbiosis with dinoflagellates of the family Symbiodiniaceae for the acquisition of cysteine. Here, we identify the existence of an alternative pathway for cysteine biosynthesis in animals through the analysis of the genome of the coral Acropora loripes. We demonstrate that these coral proteins are functional and synthesize cysteine in vivo, exhibiting previously unrecognized metabolic capabilities of animals. This pathway is also present in most animals but absent in mammals, arthropods, and nematodes, precisely the groups where most of the animal model organisms belong to, highlighting the risks of generalizing findings from model organisms.
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Affiliation(s)
- Octavio R. Salazar
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Prasanna N. Arun
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Guoxin Cui
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Line K. Bay
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- AIMS@JCU, Division of Research and Innovation, James Cook University, Townsville, Australia
| | - Madeleine J. H. van Oppen
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- School of BioSciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nicole S. Webster
- Australian Institute of Marine Science, Townsville, Queensland, Australia
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, Australia
- Australian Antarctic Division, Department of Agriculture, Water and the Environment, Kingston, Australia
| | - Manuel Aranda
- Marine Science Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
- Red Sea Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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Gagalova KK, Warren RL, Coombe L, Wong J, Nip KM, Yuen MMS, Whitehill JGA, Celedon JM, Ritland C, Taylor GA, Cheng D, Plettner P, Hammond SA, Mohamadi H, Zhao Y, Moore RA, Mungall AJ, Boyle B, Laroche J, Cottrell J, Mackay JJ, Lamothe M, Gérardi S, Isabel N, Pavy N, Jones SJM, Bohlmann J, Bousquet J, Birol I. Spruce giga-genomes: structurally similar yet distinctive with differentially expanding gene families and rapidly evolving genes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1469-1485. [PMID: 35789009 DOI: 10.1111/tpj.15889] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Spruces (Picea spp.) are coniferous trees widespread in boreal and mountainous forests of the northern hemisphere, with large economic significance and enormous contributions to global carbon sequestration. Spruces harbor very large genomes with high repetitiveness, hampering their comparative analysis. Here, we present and compare the genomes of four different North American spruces: the genome assemblies for Engelmann spruce (Picea engelmannii) and Sitka spruce (Picea sitchensis) together with improved and more contiguous genome assemblies for white spruce (Picea glauca) and for a naturally occurring introgress of these three species known as interior spruce (P. engelmannii × glauca × sitchensis). The genomes were structurally similar, and a large part of scaffolds could be anchored to a genetic map. The composition of the interior spruce genome indicated asymmetric contributions from the three ancestral genomes. Phylogenetic analysis of the nuclear and organelle genomes revealed a topology indicative of ancient reticulation. Different patterns of expansion of gene families among genomes were observed and related with presumed diversifying ecological adaptations. We identified rapidly evolving genes that harbored high rates of non-synonymous polymorphisms relative to synonymous ones, indicative of positive selection and its hitchhiking effects. These gene sets were mostly distinct between the genomes of ecologically contrasted species, and signatures of convergent balancing selection were detected. Stress and stimulus response was identified as the most frequent function assigned to expanding gene families and rapidly evolving genes. These two aspects of genomic evolution were complementary in their contribution to divergent evolution of presumed adaptive nature. These more contiguous spruce giga-genome sequences should strengthen our understanding of conifer genome structure and evolution, as their comparison offers clues into the genetic basis of adaptation and ecology of conifers at the genomic level. They will also provide tools to better monitor natural genetic diversity and improve the management of conifer forests. The genomes of four closely related North American spruces indicate that their high similarity at the morphological level is paralleled by the high conservation of their physical genome structure. Yet, the evidence of divergent evolution is apparent in their rapidly evolving genomes, supported by differential expansion of key gene families and large sets of genes under positive selection, largely in relation to stimulus and environmental stress response.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - René L Warren
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Lauren Coombe
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Johnathan Wong
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Ka Ming Nip
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Justin G A Whitehill
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Carol Ritland
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Greg A Taylor
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Dean Cheng
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Patrick Plettner
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - S Austin Hammond
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
- Next-Generation Sequencing Facility, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Hamid Mohamadi
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Yongjun Zhao
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Jérôme Laroche
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
| | - Joan Cottrell
- Forest Research, U.K. Forestry Commission, Northern Research Station, Roslin, EH25 9SY, Midlothian, UK
| | - John J Mackay
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Manuel Lamothe
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Sébastien Gérardi
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Nathalie Pavy
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jean Bousquet
- Institute for Systems and Integrative Biology, Université Laval, Québec, QC, GIV 0A6, Canada
- Canada Research Chair in Forest Genomics, Forest Research Centre, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Inanc Birol
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, V5Z 4S6, Canada
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48
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Achakkagari SR, Kyriakidou M, Gardner KM, De Koeyer D, De Jong H, Strömvik MV, Tai HH. Genome sequencing of adapted diploid potato clones. FRONTIERS IN PLANT SCIENCE 2022; 13:954933. [PMID: 36003817 PMCID: PMC9394749 DOI: 10.3389/fpls.2022.954933] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Cultivated potato is a vegetatively propagated crop, and most varieties are autotetraploid with high levels of heterozygosity. Reducing the ploidy and breeding potato at the diploid level can increase efficiency for genetic improvement including greater ease of introgression of diploid wild relatives and more efficient use of genomics and markers in selection. More recently, selfing of diploids for generation of inbred lines for F1 hybrid breeding has had a lot of attention in potato. The current study provides genomics resources for nine legacy non-inbred adapted diploid potato clones developed at Agriculture and Agri-Food Canada. De novo genome sequence assembly using 10× Genomics and Illumina sequencing technologies show the genome sizes ranged from 712 to 948 Mbp. Structural variation was identified by comparison to two references, the potato DMv6.1 genome and the phased RHv3 genome, and a k-mer based analysis of sequence reads showed the genome heterozygosity range of 1 to 9.04% between clones. A genome-wide approach was taken to scan 5 Mb bins to visualize patterns of heterozygous deleterious alleles. These were found dispersed throughout the genome including regions overlapping segregation distortions. Novel variants of the StCDF1 gene conferring earliness of tuberization were found among these clones, which all produce tubers under long days. The genomes will be useful tools for genome design for potato breeding.
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Affiliation(s)
| | - Maria Kyriakidou
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Kyle M. Gardner
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - David De Koeyer
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Hielke De Jong
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
| | - Martina V. Strömvik
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Helen H. Tai
- Fredericton Research and Development Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada
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49
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Wolf M, de Jong M, Daníel Halldórsson S, Árnason Ú, Janke A. Genomic impact of whaling in North Atlantic fin whales. Mol Biol Evol 2022; 39:6580755. [PMID: 35512360 PMCID: PMC9113106 DOI: 10.1093/molbev/msac094] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
It is generally recognized that large-scale whaling in the 19th and 20th century led to a substantial reduction of the size of many cetacean populations, particularly those of the baleen whales (Mysticeti). The impact of these operations on genomic diversity of one of the most hunted whales, the fin whale (Balaenoptera physalus), has remained largely unaddressed because of the paucity of adequate samples and the limitation of applicable techniques. Here, we have examined the effect of whaling on the North Atlantic fin whale based on genomes of 51 individuals from Icelandic waters, representing three temporally separated intervals, 1989, 2009 and 2018 and provide a reference genome for the species. Demographic models suggest a noticeable drop of the effective population size of the North Atlantic fin whale around a century ago. The present results suggest that the genome-wide heterozygosity is not markedly reduced and has remained comparable with other baleen whale species. Similarly, there are no signs of apparent inbreeding, as measured by the proportion of long runs of homozygosity, or of a distinctively increased mutational load, as measured by the amount of putative deleterious mutations. Compared with other baleen whales, the North Atlantic fin whale appears to be less affected by anthropogenic influences than other whales such as the North Atlantic right whale, consistent with the presence of long runs of homozygosity and higher levels of mutational load in an otherwise more heterozygous genome. Thus, genome-wide assessments of other species and populations are essential for future, more specific, conservation efforts.
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Affiliation(s)
- Magnus Wolf
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany
| | - Menno de Jong
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany
| | | | - Úlfur Árnason
- Department of Clinical Sciences Lund, Lund University, Sweden, Department of Neurosurgery, Skane University Hospital in Lund, Sweden
| | - Axel Janke
- Senckenberg Biodiversity and Climate Research Centre (BiK-F), Georg-Voigt-Strasse 14-16, Frankfurt am Main, Germany.,Institute for Ecology, Evolution and Diversity, Goethe University, Max-von-Laue-Strasse. 9, Frankfurt am Main, Germany.,LOEWE-Centre for Translational Biodiversity Genomics (TBG), Senckenberg Nature Research Society, Georg-Voigt-Straße 14-16, Frankfurt am Main, Germany
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50
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Pinto BJ, Keating SE, Nielsen SV, Scantlebury DP, Daza JD, Gamble T. Chromosome-Level Genome Assembly Reveals Dynamic Sex Chromosomes in Neotropical Leaf-Litter Geckos (Sphaerodactylidae: Sphaerodactylus). J Hered 2022; 113:272-287. [PMID: 35363859 PMCID: PMC9270867 DOI: 10.1093/jhered/esac016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 03/24/2022] [Indexed: 02/07/2023] Open
Abstract
Sex determination is a critical element of successful vertebrate development, suggesting that sex chromosome systems might be evolutionarily stable across lineages. For example, mammals and birds have maintained conserved sex chromosome systems over long evolutionary time periods. Other vertebrates, in contrast, have undergone frequent sex chromosome transitions, which is even more amazing considering we still know comparatively little across large swaths of their respective phylogenies. One reptile group in particular, the gecko lizards (infraorder Gekkota), shows an exceptional lability with regard to sex chromosome transitions and may possess the majority of transitions within squamates (lizards and snakes). However, detailed genomic and cytogenetic information about sex chromosomes is lacking for most gecko species, leaving large gaps in our understanding of the evolutionary processes at play. To address this, we assembled a chromosome-level genome for a gecko (Sphaerodactylidae: Sphaerodactylus) and used this assembly to search for sex chromosomes among six closely related species using a variety of genomic data, including whole-genome re-sequencing, RADseq, and RNAseq. Previous work has identified XY systems in two species of Sphaerodactylus geckos. We expand upon that work to identify between two and four sex chromosome cis-transitions (XY to a new XY) within the genus. Interestingly, we confirmed two different linkage groups as XY sex chromosome systems that were previously unknown to act as sex chromosomes in tetrapods (syntenic with Gallus chromosome 3 and Gallus chromosomes 18/30/33), further highlighting a unique and fascinating trend that most linkage groups have the potential to act as sex chromosomes in squamates.
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Affiliation(s)
- Brendan J Pinto
- Address correspondence to B. J. Pinto at the address above, or e-mail:
| | - Shannon E Keating
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Stuart V Nielsen
- Department of Biological Sciences, Louisiana State University in Shreveport, Shreveport, LA 71115, USA,Division of Herpetology, Florida Museum of Natural History, Gainesville, FL 32611, USA
| | | | - Juan D Daza
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX 77340, USA
| | - Tony Gamble
- Milwaukee Public Museum, Milwaukee, WI 53233, USA,Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, St Paul, MN 55455, USA
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