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Sonets IV, Solovyev MA, Ivanova VA, Vasiluev PA, Kachalkin AV, Ochkalova SD, Korobeynikov AI, Razin SV, Ulianov SV, Tyakht AV. Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider. Food Microbiol 2024; 121:104520. [PMID: 38637082 DOI: 10.1016/j.fm.2024.104520] [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: 12/24/2023] [Revised: 03/06/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.
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Affiliation(s)
- Ignat V Sonets
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia.
| | - Mikhail A Solovyev
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | | | - Petr A Vasiluev
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Research Center for Medical Genetics, Moscow, Russia
| | - Aleksey V Kachalkin
- Department of Soil Biology, Faculty of Soil Science, Lomonosov Moscow State University, Moscow, Russia; G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms of RAS, Pushchino, Russia
| | - Sofia D Ochkalova
- Applied Genomics Laboratory, SCAMT Institute, ITMO University, Saint Petersburg, 197101, Russia; Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia
| | - Anton I Korobeynikov
- Center for Algorithmic Biotechnology, Saint Petersburg State University, Saint Petersburg, 199004, Russia; Department of Statistical Modelling, Saint Petersburg State University, Saint Petersburg, 199004, Russia
| | - Sergey V Razin
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Sergey V Ulianov
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia; Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
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2
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Li K, Barrett K, Agger JW, Zeuner B, Meyer AS. Bioinformatics-based identification of GH12 endoxyloglucanases in citrus-pathogenic Penicillium spp. Enzyme Microb Technol 2024; 178:110441. [PMID: 38574421 DOI: 10.1016/j.enzmictec.2024.110441] [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: 12/21/2023] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
Millions of tons of citrus peel waste are produced every year as a byproduct of the juice industry. Citrus peel is rich in pectin and xyloglucan, but while the pectin is extracted for use in the food industry, the xyloglucan is currently not valorized. To target hydrolytic degradation of citrus peel xyloglucan into oligosaccharides, we have used bioinformatics to identify three glycoside hydrolase 12 (GH12) endoxyloglucanases (EC 3.2.1.151) from the citrus fruit pathogens Penicillium italicum GL-Gan1 and Penicillium digitatum Pd1 and characterized them on xyloglucan obtained by alkaline extraction from citrus peel. The enzymes displayed pH-temperature optima of pH 4.6-5.3 and 35-37°C. PdGH12 from P. digitatum and PiGH12A from P. italicum share 84% sequence identity and displayed similar kinetics, although kcat was highest for PdGH12. In contrast, PiGH12B from P. italicum, which has the otherwise conserved Trp in subsite -4 replaced with a Tyr, displayed a 3 times higher KM and a 4 times lower kcat/KM than PiGH12A, but was the most thermostable enzyme of the three Penicillium-derived endoxyloglucanases. The benchmark enzyme AnGH12 from Aspergillus nidulans was more thermally stable and had a higher pH-temperature optimum than the enzymes from Penicillum spp. The difference in structure of the xyloglucan oligosaccharides extracted from citrus peel xyloglucan and tamarind xyloglucan by the new endoxyloglucanases was determined by LC-MS. The inclusion of citrus peel xyloglucan demonstrated that the endoxyloglucanases liberated fucosylated xyloglucan oligomers, implying that these enzymes have the potential to upgrade citrus peel residues to produce oligomers useful as intermediates or bioactive compounds.
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Affiliation(s)
- Kai Li
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Kristian Barrett
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Jane W Agger
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
| | - Birgitte Zeuner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark.
| | - Anne S Meyer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 221, Kgs. Lyngby 2800, Denmark
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Bianco L, Fontana P, Marchesini A, Torre S, Moser M, Piazza S, Alessandri S, Pavese V, Pollegioni P, Vernesi C, Malnoy M, Torello Marinoni D, Murolo S, Dondini L, Mattioni C, Botta R, Sebastiani F, Micheletti D, Palmieri L. The de novo, chromosome-level genome assembly of the sweet chestnut (Castanea sativa Mill.) Cv. Marrone Di Chiusa Pesio. BMC Genom Data 2024; 25:64. [PMID: 38909221 DOI: 10.1186/s12863-024-01245-7] [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: 04/12/2024] [Accepted: 06/17/2024] [Indexed: 06/24/2024] Open
Abstract
OBJECTIVES The sweet chestnut Castanea sativa Mill. is the only native Castanea species in Europe, and it is a tree of high economic value that provides appreciated fruits and valuable wood. In this study, we assembled a high-quality nuclear genome of the ancient Italian chestnut variety 'Marrone di Chiusa Pesio' using a combination of Oxford Nanopore Technologies long reads, whole-genome and Omni-C Illumina short reads. DATA DESCRIPTION The genome was assembled into 238 scaffolds with an N50 size of 21.8 Mb and an N80 size of 7.1 Mb for a total assembled sequence of 750 Mb. The BUSCO assessment revealed that 98.6% of the genome matched the embryophyte dataset, highlighting good completeness of the genetic space. After chromosome-level scaffolding, 12 chromosomes with a total length of 715.8 and 713.0 Mb were constructed for haplotype 1 and haplotype 2, respectively. The repetitive elements represented 37.3% and 37.4% of the total assembled genome in haplotype 1 and haplotype 2, respectively. A total of 57,653 and 58,146 genes were predicted in the two haplotypes, and approximately 73% of the genes were functionally annotated using the EggNOG-mapper. The assembled genome will be a valuable resource and reference for future chestnut breeding and genetic improvement.
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Affiliation(s)
- Luca Bianco
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Paolo Fontana
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Alexis Marchesini
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Sara Torre
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
| | - Mirko Moser
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Stefano Piazza
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Sara Alessandri
- Dept. of Agricultural and Food Sciences, University of Bologna, Via Zamboni 33, Bologna, BO, 40126, Italy
| | - Vera Pavese
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Paola Pollegioni
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Cristiano Vernesi
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Mickael Malnoy
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Daniela Torello Marinoni
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Sergio Murolo
- Dep. of Agricultural, Food and Env.Sci, Marche Polytechnic University, via Brecce Bianche, Ancona, AN, 60131, Italy
| | - Luca Dondini
- Dept. of Agricultural and Food Sciences, University of Bologna, Via Zamboni 33, Bologna, BO, 40126, Italy
| | - Claudia Mattioni
- Research Institute on Terrestrial Ecosystem, National Research Council, Via Marconi 2, Porano, TR, 05010, Italy
- NBFC, National Biodiversity Future Center, Palermo, Italy
| | - Roberto Botta
- Dept. of Agricultural, Forest and Food Sci, University of Turin, L.go P. Braccini 2, Grugliasco, TO, 10095, Italy
| | - Federico Sebastiani
- Institute for Sustainable Plant Protection, National Research Council, Via Madonna del Piano 10, 50019, Sesto Fiorentino FI, Italy
| | - Diego Micheletti
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy
| | - Luisa Palmieri
- Research and Innovation Center, Edmund Mach Foundation, via Mach 1, San Michele all'Adige, TN, 38098, Italy.
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Yan Q, Li S, Yan Q, Huo X, Wang C, Wang X, Sun Y, Zhao W, Yu Z, Zhang Y, Guo R, Lv Q, He X, Yao C, Li Z, Chen F, Ji Q, Zhang A, Jin H, Wang G, Feng X, Feng L, Wu F, Ning J, Deng S, An Y, Guo DA, Martin FM, Ma X. A genomic compendium of cultivated human gut fungi characterizes the gut mycobiome and its relevance to common diseases. Cell 2024; 187:2969-2989.e24. [PMID: 38776919 DOI: 10.1016/j.cell.2024.04.043] [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: 03/24/2023] [Revised: 02/17/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
The gut fungal community represents an essential element of human health, yet its functional and metabolic potential remains insufficiently elucidated, largely due to the limited availability of reference genomes. To address this gap, we presented the cultivated gut fungi (CGF) catalog, encompassing 760 fungal genomes derived from the feces of healthy individuals. This catalog comprises 206 species spanning 48 families, including 69 species previously unidentified. We explored the functional and metabolic attributes of the CGF species and utilized this catalog to construct a phylogenetic representation of the gut mycobiome by analyzing over 11,000 fecal metagenomes from Chinese and non-Chinese populations. Moreover, we identified significant common disease-related variations in gut mycobiome composition and corroborated the associations between fungal signatures and inflammatory bowel disease (IBD) through animal experimentation. These resources and findings substantially enrich our understanding of the biological diversity and disease relevance of the human gut mycobiome.
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Affiliation(s)
- Qiulong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Shenghui Li
- Puensum Genetech Institute, Wuhan 430076, China; Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China
| | - Qingsong Yan
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaokui Huo
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Chao Wang
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Xifan Wang
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100091, China; Department of Obstetrics and Gynecology, Columbia University, New York, NY 10027, USA
| | - Yan Sun
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Wenyu Zhao
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Zhenlong Yu
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Ruochun Guo
- Puensum Genetech Institute, Wuhan 430076, China
| | - Qingbo Lv
- Puensum Genetech Institute, Wuhan 430076, China
| | - Xin He
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China; Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | - Changliang Yao
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China
| | | | - Fang Chen
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Qianru Ji
- Puensum Genetech Institute, Wuhan 430076, China
| | - Aiqin Zhang
- Puensum Genetech Institute, Wuhan 430076, China
| | - Hao Jin
- Puensum Genetech Institute, Wuhan 430076, China
| | - Guangyang Wang
- College of Basic Medical Sciences, Dalian Medical University, Dalian 116044, China
| | - Xiaoying Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Lei Feng
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Fan Wu
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Jing Ning
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Sa Deng
- Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China
| | - Yue An
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - De-An Guo
- Shanghai Research Center for Modernization of Traditional Chinese Medicine, National Engineering Laboratory for TCM Standardization Technology, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201210, China.
| | - Francis M Martin
- Université de Lorraine, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, UMR Interactions Arbres/Microorganismes, Centre INRAE Grand Est-Nancy, Champenoux 54280, France; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100091, China.
| | - Xiaochi Ma
- Second Affiliated Hospital, Dalian Medical University, Dalian 116044, China; Dalian Key Laboratory of Metabolic Target Characterization and Traditional Chinese Medicine Intervention, School of Pharmacy, Dalian Medical University, Dalian 116044, China.
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5
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Rey Redondo E, Xu Y, Yung CCM. Genomic characterisation and ecological distribution of Mantoniella tinhauana: a novel Mamiellophycean green alga from the Western Pacific. Front Microbiol 2024; 15:1358574. [PMID: 38774501 PMCID: PMC11106453 DOI: 10.3389/fmicb.2024.1358574] [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: 12/20/2023] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Mamiellophyceae are dominant marine algae in much of the ocean, the most prevalent genera belonging to the order Mamiellales: Micromonas, Ostreococcus and Bathycoccus, whose genetics and global distributions have been extensively studied. Conversely, the genus Mantoniella, despite its potential ecological importance, remains relatively under-characterised. In this study, we isolated and characterised a novel species of Mamiellophyceae, Mantoniella tinhauana, from subtropical coastal waters in the South China Sea. Morphologically, it resembles other Mantoniella species; however, a comparative analysis of the 18S and ITS2 marker genes revealed its genetic distinctiveness. Furthermore, we sequenced and assembled the first genome of Mantoniella tinhauana, uncovering significant differences from previously studied Mamiellophyceae species. Notably, the genome lacked any detectable outlier chromosomes and exhibited numerous unique orthogroups. We explored gene groups associated with meiosis, scale and flagella formation, shedding light on species divergence, yet further investigation is warranted. To elucidate the biogeography of Mantoniella tinhauana, we conducted a comprehensive analysis using global metagenomic read mapping to the newly sequenced genome. Our findings indicate this species exhibits a cosmopolitan distribution with a low-level prevalence worldwide. Understanding the intricate dynamics between Mamiellophyceae and the environment is crucial for comprehending their impact on the ocean ecosystem and accurately predicting their response to forthcoming environmental changes.
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Affiliation(s)
| | | | - Charmaine Cheuk Man Yung
- Department of Ocean Science, The Hong Kong University of Science and Technology, Kowloon, Hong Kong SAR, China
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Bruna T, Lomsadze A, Borodovsky M. A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.13.524024. [PMID: 36711453 PMCID: PMC9882169 DOI: 10.1101/2023.01.13.524024] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Large-scale genomic initiatives, such as the Earth BioGenome Project, require efficient methods for eukaryotic genome annotation. Here we present an automatic gene finder, GeneMark-ETP, integrating genomic-, transcriptomic- and protein-derived evidence that has been developed with a focus on large plant and animal genomes. GeneMark-ETP first identifies genomic loci where extrinsic data is sufficient for making gene predictions with 'high confidence'. The genes situated in the genomic space between the high confidence genes are predicted in the next stage. The set of high confidence genes serves as an initial training set for the statistical model. Further on, the model parameters are iteratively updated in the rounds of gene prediction and parameter re-estimation. Upon reaching convergence, GeneMark-ETP makes the final predictions and delivers the whole complement of predicted genes. GeneMark-ETP outperformed gene finders using a single type of extrinsic evidence. Comparisons with gene finders utilizing both transcript- and protein-derived extrinsic evidence, MAKER2, and TSEBRA, demonstrated that GeneMark-ETP delivered state-of-the-art gene prediction accuracy with the margin of outperforming existing approaches increasing in its applications to larger and more complex eukaryotic genomes.
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Affiliation(s)
- Tomas Bruna
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexandre Lomsadze
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Mark Borodovsky
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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7
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Li Z, Yang J, Ji X, Liu J, Yin C, Bhadauria V, Zhao W, Peng YL. First telomere-to-telomere gapless assembly of the rice blast fungus Pyricularia oryzae. Sci Data 2024; 11:380. [PMID: 38615081 PMCID: PMC11016069 DOI: 10.1038/s41597-024-03209-z] [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: 08/23/2023] [Accepted: 04/02/2024] [Indexed: 04/15/2024] Open
Abstract
Rice blast caused by Pyricularia oryzae (syn., Magnaporthe oryzae) was one of the most destructive diseases of rice throughout the world. Genome assembly was fundamental to genetic variation identification and critically impacted the understanding of its ability to overcome host resistance. Here, we report a gapless genome assembly of rice blast fungus P. oryzae strain P131 using PacBio, Illumina and high throughput chromatin conformation capture (Hi-C) sequencing data. This assembly contained seven complete chromosomes (43,237,743 bp) and a circular mitochondrial genome (34,866 bp). Approximately 14.31% of this assembly carried repeat sequences, significantly greater than its previous assembled version. This assembly had a 99.9% complement in BUSCO evaluation. A total of 14,982 genes protein-coding genes were predicted. In summary, we assembled the first telomere-to-telomere gapless genome of P. oryzae, which would be a valuable genome resource for future research on the genome evolution and host adaptation.
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Affiliation(s)
- Zhigang Li
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
- Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Jun Yang
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Xiaobei Ji
- Sanya Institute of Breeding and Multiplication/School of Tropical Agriculture and Forestry, Hainan University, Haikou, 570228, China
| | - Jintao Liu
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Changfa Yin
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Vijai Bhadauria
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Wensheng Zhao
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - You-Liang Peng
- MARA Key Laboratory of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China.
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8
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Dewa AA, Khalil ZG, Hussein WM, Jin S, Wang Y, Cruz-Morales P, Capon RJ. Pullenvalenes A-D: Nitric Oxide-Mediated Transcriptional Activation (NOMETA) Enables Discovery of Triterpene Aminoglycosides from Australian Termite Nest-Derived Fungi. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38575516 DOI: 10.1021/acs.jnatprod.3c01233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
We report on the use of nitric oxide-mediated transcriptional activation (NOMETA) as an innovative means to detect and access new classes of microbial natural products encoded within silent biosynthetic gene clusters. A small library of termite nest- and mangrove-derived fungi and actinomyces was subjected to cultivation profiling using a miniaturized 24-well format approach (MATRIX) in the presence and absence of nitric oxide, with the resulting metabolomes subjected to comparative chemical analysis using UPLC-DAD and GNPS molecular networking. This strategy prompted study of Talaromyces sp. CMB-TN6F and Coccidiodes sp. CMB-TN39F, leading to discovery of the triterpene glycoside pullenvalenes A-D (1-4), featuring an unprecedented triterpene carbon skeleton and rare 6-O-methyl-N-acetyl-d-glucosaminyl glycoside residues. Structure elucidation of 1-4 was achieved by a combination of detailed spectroscopic analysis, chemical degradation, derivatization and synthesis, and biosynthetic considerations.
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Affiliation(s)
- Amila Agampodi Dewa
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Zeinab G Khalil
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Waleed M Hussein
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Shengbin Jin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Yanan Wang
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lynby, Denmark
| | - Robert J Capon
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD 4072, Australia
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9
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Dobbs JT, Caballero JRI, Ata JP, Babiker E, Copes WE, Stewart JE. Genomic and Transcriptomic Comparisons of the Twig Blight Pathogen, Passalora sequoiae, with Mycosphaerellaceae Foliar and Conifer Pathogens. PHYTOPATHOLOGY 2024; 114:732-742. [PMID: 37942864 DOI: 10.1094/phyto-08-23-0271-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Passalora sequoiae is a foliar pathogen to conifer tree species. In this study, we conducted whole-genome and transcriptome analyses on isolates of P. sequoiae collected from symptomatic Leyland cypress leaves from a Christmas tree farm in Mississippi. The objectives for this research were to elucidate the pathogenicity mechanisms of P. sequoiae by characterizing the genome and transcriptome and possibly identify unique and shared predicted genes in comparison with non-conifer/canker and foliar pathogens in the family Mycosphaerellaceae. P. sequoiae was found to be similar to other foliar Mycosphaerellaceae pathogens and likely represents a hemibiotrophic lifestyle based on comparisons across pathogens. The genome and in planta transcriptome highlighted some unique features of P. sequoiae: the significant presence of chitin synthases and fructose-degrading carbohydrate-degrading enzymes, trans-AT PKS genes, and antibiotic gene clusters that were unique to P. sequoiae compared with the other Mycosphaerellaceae species genomes. Several transcripts that were highly expressed in planta were identified as effectors, yet the functions were not characterized. These targets provide ample resources to continue to characterize pathogen-conifer host interactions in conifer foliar pathogens. Furthermore, this research helps build genomic resources for an important plant pathogen on Leyland cypress that will further our ability to develop novel management practices that could begin with breeding for resistance.
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Affiliation(s)
- John T Dobbs
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
| | | | - Jessa P Ata
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
- Department of Forest Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Ebrahiem Babiker
- Thad Cochran Southern Horticultural Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, U.S.A
| | - Warren E Copes
- Thad Cochran Southern Horticultural Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Beltsville, MD, U.S.A
| | - Jane E Stewart
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, U.S.A
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10
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Pankey MS, Gochfeld DJ, Gastaldi M, Macartney KJ, Clayshulte Abraham A, Slattery M, Lesser MP. Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin. Mol Ecol 2024; 33:e17321. [PMID: 38529721 DOI: 10.1111/mec.17321] [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: 05/31/2023] [Accepted: 03/07/2024] [Indexed: 03/27/2024]
Abstract
Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.
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Affiliation(s)
- M S Pankey
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - D J Gochfeld
- National Center for Natural Products Research and Environmental Toxicology, University of Mississippi, University, Mississippi, USA
| | - M Gastaldi
- Escuela Superior de Ciencias Marinas-Universidad Nacional del Comahue, San Antonio Oeste, Río Negro, Argentina
| | - K J Macartney
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - A Clayshulte Abraham
- Division of Environmental Toxicology, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
| | - M Slattery
- Division of Environmental Toxicology, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
- Division of Pharmacognosy, Department of BioMolecular Sciences, University of Mississippi, University, Mississippi, USA
| | - M P Lesser
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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11
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Marcet-Houben M, Cruz F, Gómez-Garrido J, Alioto TS, Nunez-Rodriguez JC, Mesanza N, Gut M, Iturritxa E, Gabaldon T. Genomics of the expanding pine pathogen Lecanosticta acicola reveals patterns of ongoing genetic admixture. mSystems 2024; 9:e0092823. [PMID: 38364101 PMCID: PMC10949461 DOI: 10.1128/msystems.00928-23] [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: 09/07/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Lecanosticta acicola is the causal agent for brown spot needle blight that affects pine trees across the northern hemisphere. Based on marker genes and microsatellite data, two distinct lineages have been identified that were introduced into Europe on two separate occasions. Despite their overall distinct geographic distribution, they have been found to coexist in regions of northern Spain and France. Here, we present the first genome-wide study of Lecanosticta acicola, including assembly of the reference genome and a population genomics analysis of 70 natural isolates from northern Spain. We show that most of the isolates belong to the southern lineage but show signs of introgression with northern lineage isolates, indicating mating between the two lineages. We also identify phenotypic differences between the two lineages based on the activity profiles of 20 enzymes, with introgressed strains being more phenotypically similar to members of the southern lineage. In conclusion, we show undergoing genetic admixture between the two main lineages of L. acicola in a region of recent expansion. IMPORTANCE Lecanosticta acicola is a fungal pathogen causing severe defoliation, growth reduction, and even death in more than 70 conifer species. Despite the increasing incidence of this species, little is known about its population dynamics. Two divergent lineages have been described that have now been found together in regions of France and Spain, but it is unknown how these mixed populations evolve. Here we present the first reference genome for this important plant pathogenic fungi and use it to study the population genomics of 70 isolates from an affected forest in the north of Spain. We find signs of introgression between the two main lineages, indicating that active mating is occurring in this region which could propitiate the appearance of novel traits in this species. We also study the phenotypic differences across this population based on enzymatic activities on 20 compounds.
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Affiliation(s)
- Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jéssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Tyler S. Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Juan Carlos Nunez-Rodriguez
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Nebai Mesanza
- Instituto Vasco de Investigación y Desarrollo Agrario (BRTA), Arkaute, Araba, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eugenia Iturritxa
- Instituto Vasco de Investigación y Desarrollo Agrario (BRTA), Arkaute, Araba, Spain
| | - Toni Gabaldon
- Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Centro de Investigación Biomédica En Red de Enfermedades Infecciosas (CIBERINFEC), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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12
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Jin D, Li C, Chen X, Wang Y, Al-Rasheid KAS, Stover NA, Shao C, Zhang T. Decryption of the survival "black box": gene family expansion promotes the encystment in ciliated protists. BMC Genomics 2024; 25:286. [PMID: 38500030 PMCID: PMC10946202 DOI: 10.1186/s12864-024-10207-3] [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: 12/12/2023] [Accepted: 03/11/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Encystment is an important survival strategy extensively employed by microbial organisms to survive unfavorable conditions. Single-celled ciliated protists (ciliates) are popular model eukaryotes for studying encystment, whereby these cells degenerate their ciliary structures and develop cyst walls, then reverse the process under more favorable conditions. However, to date, the evolutionary basis and mechanism for encystment in ciliates is largely unknown. With the rapid development of high-throughput sequencing technologies, genome sequencing and comparative genomics of ciliates have become effective methods to provide insights into above questions. RESULTS Here, we profiled the MAC genome of Pseudourostyla cristata, a model hypotrich ciliate for encystment studies. Like other hypotrich MAC genomes, the P. cristata MAC genome is extremely fragmented with a single gene on most chromosomes, and encodes introns that are generally small and lack a conserved branch point for pre-mRNA splicing. Gene family expansion analyses indicate that multiple gene families involved in the encystment are expanded during the evolution of P. cristata. Furthermore, genomic comparisons with other five representative hypotrichs indicate that gene families of phosphorelay sensor kinase, which play a role in the two-component signal transduction system that is related to encystment, show significant expansion among all six hypotrichs. Additionally, cyst wall-related chitin synthase genes have experienced structural changes that increase them from single-exon to multi-exon genes during evolution. These genomic features potentially promote the encystment in hypotrichs and enhance their ability to survive in adverse environments during evolution. CONCLUSIONS We systematically investigated the genomic structure of hypotrichs and key evolutionary phenomenon, gene family expansion, for encystment promotion in ciliates. In summary, our results provided insights into the evolutionary mechanism of encystment in ciliates.
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Affiliation(s)
- Didi Jin
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Chao Li
- Key Laboratory of Evolution & Marine Biodiversity (Ministry of Education), and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209, China
- Suzhou Research Institute, Shandong University, Suzhou, 215123, China
| | - Yurui Wang
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Khaled A S Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Naomi A Stover
- Department of Biology, Bradley University, Peoria, 61625, USA
| | - Chen Shao
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Tengteng Zhang
- Laboratory of Biodiversity and Evolution of Protozoa in Wetland, College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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13
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Billman ZP, Kovacs SB, Wei B, Kang K, Cissé OH, Miao EA. Caspase-1 activates gasdermin A in non-mammals. eLife 2024; 12:RP92362. [PMID: 38497531 PMCID: PMC10948149 DOI: 10.7554/elife.92362] [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: 03/19/2024] Open
Abstract
Gasdermins oligomerize to form pores in the cell membrane, causing regulated lytic cell death called pyroptosis. Mammals encode five gasdermins that can trigger pyroptosis: GSDMA, B, C, D, and E. Caspase and granzyme proteases cleave the linker regions of and activate GSDMB, C, D, and E, but no endogenous activation pathways are yet known for GSDMA. Here, we perform a comprehensive evolutionary analysis of the gasdermin family. A gene duplication of GSDMA in the common ancestor of caecilian amphibians, reptiles, and birds gave rise to GSDMA-D in mammals. Uniquely in our tree, amphibian, reptile, and bird GSDMA group in a separate clade than mammal GSDMA. Remarkably, GSDMA in numerous bird species contain caspase-1 cleavage sites like YVAD or FASD in the linker. We show that GSDMA from birds, amphibians, and reptiles are all cleaved by caspase-1. Thus, GSDMA was originally cleaved by the host-encoded protease caspase-1. In mammals the caspase-1 cleavage site in GSDMA is disrupted; instead, a new protein, GSDMD, is the target of caspase-1. Mammal caspase-1 uses exosite interactions with the GSDMD C-terminal domain to confer the specificity of this interaction, whereas we show that bird caspase-1 uses a stereotypical tetrapeptide sequence to confer specificity for bird GSDMA. Our results reveal an evolutionarily stable association between caspase-1 and the gasdermin family, albeit a shifting one. Caspase-1 repeatedly changes its target gasdermin over evolutionary time at speciation junctures, initially cleaving GSDME in fish, then GSDMA in amphibians/reptiles/birds, and finally GSDMD in mammals.
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Affiliation(s)
- Zachary Paul Billman
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Stephen Bela Kovacs
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
- Department of Microbiology and Immunology, University of North Carolina at Chapel HillChapel HillUnited States
| | - Bo Wei
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Kidong Kang
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
| | - Ousmane H Cissé
- Critical Care Medicine Department, National Institutes of Health Clinical CenterBethesdaUnited States
| | - Edward A Miao
- Department of Integrative Immunobiology; Molecular Genetics and Microbiology; Pathology; and Cell Biology, Duke University School of MedicineDurhamUnited States
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14
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Jung H, Zarlenga D, Martin JC, Geldhof P, Hallsworth-Pepin K, Mitreva M. The identification of small molecule inhibitors with anthelmintic activities that target conserved proteins among ruminant gastrointestinal nematodes. mBio 2024; 15:e0009524. [PMID: 38358246 PMCID: PMC10936192 DOI: 10.1128/mbio.00095-24] [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: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Gastrointestinal nematode (GIN) infections are a major concern for the ruminant industry worldwide and result in significant production losses. Naturally occurring polyparasitism and increasing drug resistance that potentiate disease outcomes are observed among the most prevalent GINs of veterinary importance. Within the five major taxonomic clades, clade Va represents a group of GINs that predominantly affect the abomasum or small intestine of ruminants. However, the development of effective broad-spectrum anthelmintics against ruminant clade Va GINs has been challenged by a lack of comprehensive druggable genome resources. Here, we first assembled draft genomes for three clade Va species (Cooperia oncophora, Trichostrongylus colubriformis, and Ostertagia ostertagi) and compared them with closely related ruminant GINs. Genome-wide phylogenetic reconstruction showed a relationship among ruminant GINs structured by taxonomic classification. Orthogroup (OG) inference and functional enrichment analyses identified 220 clade Va-specific and Va-conserved OGs, enriched for functions related to cell cycle and cellular senescence. Further transcriptomic analysis identified 61 taxonomically and functionally conserved clade Va OGs that may function as drug targets for new broad-spectrum anthelmintics. Chemogenomic screening identified 11 compounds targeting homologs of these OGs, thus having potential anthelmintic activity. In in vitro phenotypic assays, three kinase inhibitors (digitoxigenin, K-252a, and staurosporine) exhibited broad-spectrum anthelmintic activities against clade Va GINs by obstructing the motility of exsheathed L3 (xL3) or molting of xL3 to L4. These results demonstrate valuable applications of the new ruminant GIN genomes in gaining better insights into their life cycles and offer a contemporary approach to discovering the next generation of anthelmintics.IMPORTANCEGastrointestinal nematode (GIN) infections in ruminants are caused by parasites that inhibit normal function in the digestive tract of cattle, sheep, and goats, thereby causing morbidity and mortality. Coinfection and increasing drug resistance to current therapeutic agents will continue to worsen disease outcomes and impose significant production losses on domestic livestock producers worldwide. In combination with ongoing therapeutic efforts, advancing the discovery of new drugs with novel modes of action is critical for better controlling GIN infections. The significance of this study is in assembling and characterizing new GIN genomes of Cooperia oncophora, Ostertagia ostertagi, and Trichostrongylus colubriformis for facilitating a multi-omics approach to identify novel, biologically conserved drug targets for five major GINs of veterinary importance. With this information, we were then able to demonstrate the potential of commercially available compounds as new anthelmintics.
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Affiliation(s)
- Hyeim Jung
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Dante Zarlenga
- Animal Parasitic Diseases Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, USA
| | - John C. Martin
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter Geldhof
- Laboratory of Parasitology, Faculty of Veterinary Medicine, University of Ghent, Merelbeke, Belgium
| | | | - Makedonka Mitreva
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, Missouri, USA
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15
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Lin Z, Agarwal V, Cong Y, Pomponi SA, Schmidt EW. Short macrocyclic peptides in sponge genomes. Proc Natl Acad Sci U S A 2024; 121:e2314383121. [PMID: 38442178 PMCID: PMC10945851 DOI: 10.1073/pnas.2314383121] [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: 08/22/2023] [Accepted: 01/19/2024] [Indexed: 03/07/2024] Open
Abstract
Sponges (Porifera) contain many peptide-specialized metabolites with potent biological activities and significant roles in shaping marine ecology. It is well established that symbiotic bacteria produce bioactive "sponge" peptides, both on the ribosome (RiPPs) and nonribosomally. Here, we demonstrate that sponges themselves also produce many bioactive macrocyclic peptides, such as phakellistatins and related proline-rich macrocyclic peptides (PRMPs). Using the Stylissa carteri sponge transcriptome, methods were developed to find sequences encoding 46 distinct RiPP-type core peptides, of which ten encoded previously identified PRMP sequences. With this basis set, the genome and transcriptome of the sponge Axinella corrugata was interrogated to find 35 PRMP precursor peptides encoding 31 unique core peptide sequences. At least 11 of these produced cyclic peptides that were present in the sponge and could be characterized by mass spectrometry, including stylissamides A-D and seven previously undescribed compounds. Precursor peptides were encoded in the A. corrugata genome, confirming their animal origin. The peptides contained signal peptide sequences and highly repetitive recognition sequence-core peptide elements with up to 25 PRMP copies in a single precursor. In comparison to sponges without PRMPs, PRMP sponges are incredibly enriched in potentially secreted polypeptides, with >23,000 individual signal peptide encoding genes found in a single transcriptome. The similarities between PRMP biosynthetic genes and neuropeptides in terms of their biosynthetic logic suggest a fundamental biology linked to circular peptides, possibly indicating a widespread and underappreciated diversity of signaling peptide post-translational modifications across the animal kingdom.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Vinayak Agarwal
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA30332
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA30332
| | - Ying Cong
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
| | - Shirley A. Pomponi
- Harbor Branch Oceanographic Institute, Florida Atlantic University, Fort Pierce, FL34946
| | - Eric W. Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT84112
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16
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Harris W, Choi G, Lee KK, Kim H, Lee YH. High-quality genome resource of a basidiomycetous yeast, Moesziomyces antarcticus isolate RS1, isolated from rice seed. Microbiol Resour Announc 2024; 13:e0084723. [PMID: 38226831 PMCID: PMC10868211 DOI: 10.1128/mra.00847-23] [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: 09/07/2023] [Accepted: 12/20/2023] [Indexed: 01/17/2024] Open
Abstract
Moesziomyces antarcticus (anamorph: Pseudozyma antarctica) is a basidiomycetous yeast in the Ustilaginaceae family and is a core member of the rice seed microbiome. M. antarcticus RS1 was isolated from surface-sterilized rice seeds. This 18.287 Mb draft genome of M. antarcticus RS1 is comprised of a 60.8% GC content and 6,817 protein-coding genes.
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Affiliation(s)
- William Harris
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Gobong Choi
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Republic of Korea
| | - Kiseok Keith Lee
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, USA
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Plant Microbiome Research, Seoul National University, Seoul, Republic of Korea
- Plant Immunity Research Center, Seoul National University, Seoul, Republic of Korea
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17
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Zhuri D, Dusenkalkan F, Tunca Alparslan G, Gurkan H. A Case of Okur-Chung Neurodevelopmental Syndrome with a Novel, de novo Variant on the CSNK2A1 Gene in a Turkish Patient. Mol Syndromol 2024; 15:43-50. [PMID: 38357263 PMCID: PMC10862324 DOI: 10.1159/000530585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 04/02/2023] [Indexed: 02/16/2024] Open
Abstract
Introduction Okur-Chung neurodevelopmental syndrome (OCNDS; #617062) has been associated with heterozygous mutations in the CSNK2A1 gene (*115440) mapped on the chromosome's 20p13 region. Case Presentation The analysis was performed on a 2-year-old patient who was admitted to our genetic diseases evaluation center by his family with a complaint of hypotonia. We detected a heterozygous NM_177559.3 (CSNK2A1):c.1139_1140dupGG (p.Met381GlyfsTer32) variant in the CSNK2A1 gene from a whole-exome sequence analysis. Conclusion The variant that we detected has not been reported in open-access databases to date, so it was evaluated as a novel likely pathogenic variant according to the ACMG-2015 criteria. No variant was detected upon segregation analysis of the patient's parents; therefore, the related variant was evaluated as de novo. In this study, we offer the first report of a pathogenic frameshift variant in the CSNK2A1 gene that has a relationship with OCNDS.
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Affiliation(s)
- Drenushe Zhuri
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Fulya Dusenkalkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
| | - Guzin Tunca Alparslan
- Department of Genetics and Bioengineering, Trakya University Faculty of Engineering, Edirne, Turkey
| | - Hakan Gurkan
- Department of Medical Genetics, Trakya University Faculty of Medicine, Edirne, Turkey
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18
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Bascón-Cardozo K, Bours A, Manthey G, Durieux G, Dutheil JY, Pruisscher P, Odenthal-Hesse L, Liedvogel M. Fine-Scale Map Reveals Highly Variable Recombination Rates Associated with Genomic Features in the Eurasian Blackcap. Genome Biol Evol 2024; 16:evad233. [PMID: 38198800 PMCID: PMC10781513 DOI: 10.1093/gbe/evad233] [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] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Recombination is responsible for breaking up haplotypes, influencing genetic variability, and the efficacy of selection. Bird genomes lack the protein PR domain-containing protein 9, a key determinant of recombination dynamics in most metazoans. Historical recombination maps in birds show an apparent stasis in positioning recombination events. This highly conserved recombination pattern over long timescales may constrain the evolution of recombination in birds. At the same time, extensive variation in recombination rate is observed across the genome and between different species of birds. Here, we characterize the fine-scale historical recombination map of an iconic migratory songbird, the Eurasian blackcap (Sylvia atricapilla), using a linkage disequilibrium-based approach that accounts for population demography. Our results reveal variable recombination rates among and within chromosomes, which associate positively with nucleotide diversity and GC content and negatively with chromosome size. Recombination rates increased significantly at regulatory regions but not necessarily at gene bodies. CpG islands are associated strongly with recombination rates, though their specific position and local DNA methylation patterns likely influence this relationship. The association with retrotransposons varied according to specific family and location. Our results also provide evidence of heterogeneous intrachromosomal conservation of recombination maps between the blackcap and its closest sister taxon, the garden warbler. These findings highlight the considerable variability of recombination rates at different scales and the role of specific genomic features in shaping this variation. This study opens the possibility of further investigating the impact of recombination on specific population-genomic features.
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Affiliation(s)
- Karen Bascón-Cardozo
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Andrea Bours
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Georg Manthey
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
| | - Gillian Durieux
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Julien Y Dutheil
- Department for Theoretical Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Peter Pruisscher
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Department of Zoology, Stockholm University, Stockholm SE-106 91, Sweden
| | - Linda Odenthal-Hesse
- Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Miriam Liedvogel
- MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
- Institute of Avian Research “Vogelwarte Helgoland”, Wilhelmshaven 26386, Germany
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg 26129, Germany
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19
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Lin Z, Li F, Krug PJ, Schmidt EW. The polyketide to fatty acid transition in the evolution of animal lipid metabolism. Nat Commun 2024; 15:236. [PMID: 38172109 PMCID: PMC10764717 DOI: 10.1038/s41467-023-44497-0] [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: 05/30/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Animals synthesize simple lipids using a distinct fatty acid synthase (FAS) related to the type I polyketide synthase (PKS) enzymes that produce complex specialized metabolites. The evolutionary origin of the animal FAS and its relationship to the diversity of PKSs remain unclear despite the critical role of lipid synthesis in cellular metabolism. Recently, an animal FAS-like PKS (AFPK) was identified in sacoglossan molluscs. Here, we explore the phylogenetic distribution of AFPKs and other PKS and FAS enzymes across the tree of life. We found AFPKs widely distributed in arthropods and molluscs (>6300 newly described AFPK sequences). The AFPKs form a clade with the animal FAS, providing an evolutionary link bridging the type I PKSs and the animal FAS. We found molluscan AFPK diversification correlated with shell loss, suggesting AFPKs provide a chemical defense. Arthropods have few or no PKSs, but our results indicate AFPKs contributed to their ecological and evolutionary success by facilitating branched hydrocarbon and pheromone biosynthesis. Although animal metabolism is well studied, surprising new metabolic enzyme classes such as AFPKs await discovery.
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Affiliation(s)
- Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Feng Li
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA
| | - Patrick J Krug
- Department of Biological Sciences, California State University, Los Angeles, CA, 90032, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, 84112, USA.
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20
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Nachtweide S, Romoth L, Stanke M. Comparative Genome Annotation. Methods Mol Biol 2024; 2802:165-187. [PMID: 38819560 DOI: 10.1007/978-1-0716-3838-5_7] [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] [Indexed: 06/01/2024]
Abstract
Newly sequenced genomes are being added to the tree of life at an unprecedented fast pace. A large proportion of such new genomes are phylogenetically close to previously sequenced and annotated genomes. In other cases, whole clades of closely related species or strains ought to be annotated simultaneously. Often, in subsequent studies, differences between the closely related species or strains are in the focus of research when the shared gene structures prevail. We here review methods for comparative structural genome annotation. The reviewed methods include classical approaches such as the alignment of protein sequences or protein profiles against the genome and comparative gene prediction methods that exploit a genome alignment to annotate either a single target genome or all input genomes simultaneously. We discuss how the methods depend on the phylogenetic placement of genomes, give advice on the choice of methods, and examine the consistency between gene structure annotations in an example. Furthermore, we provide practical advice on genome annotation in general.
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Affiliation(s)
| | | | - Mario Stanke
- Institute for Mathematics and Computer Science, Greifswald, Germany.
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21
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Calamari ZT, Song A, Cohen E, Akter M, Roy RD, Hallikas O, Christensen MM, Li P, Marangoni P, Jernvall J, Klein OD. Conserved and derived expression patterns and positive selection on dental genes reveal complex evolutionary context of ever-growing rodent molars. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572015. [PMID: 38187646 PMCID: PMC10769287 DOI: 10.1101/2023.12.18.572015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Background Continuously growing teeth are an important innovation in mammalian evolution, yet genetic regulation of continuous growth by stem cells remains incompletely understood. Dental stem cells are lost at the onset of tooth root formation, but this loss of continuous crown growth is difficult to study in the mouse because regulatory signaling overlaps with signals that pattern tooth size and shape. Within the voles (Cricetidae, Rodentia, Glires), species have evolved both rooted and unrooted molars that have similar size and shape. We assembled a de novo genome of Myodes glareolus, a vole with high-crowned, rooted molars, and performed genomic and transcriptomic analyses in a broad phylogenetic context of Glires (rodents and lagomorphs) to assess differential selection and evolution in tooth forming genes. Results Our de novo genome recovered 91% of single-copy orthologs for Euarchontoglires and had a total length of 2.44 Gigabases, enabling genomic and transcriptomic analyses. We identified six dental genes undergoing positive selection across Glires and two genes undergoing positive selection in species with unrooted molars, Dspp and Aqp1. Transcriptomics analyses demonstrated conserved patterns of dental gene expression with species-specific variation likely related to developmental timing and morphological differences between mouse and vole molars. Conclusions Our results support ongoing dental gene evolution in rodents with unrooted molars. We identify candidate genes for further functional analyses, particularly Dspp, which plays an important role in mineralizing tissues. Our expression results support conservation of dental genes between voles and model species like mice, while revealing significant effects of overall tooth morphology on gene expression.
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Affiliation(s)
- Zachary T. Calamari
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- The Graduate Center, City University of New York, 365 Fifth Ave, New York, NY 10016, USA
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Division of Paleontology, American Museum of Natural History, Central Park West at 79 Street, New York, NY, 10024, USA
| | - Andrew Song
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- Cornell University, 616 Thurston Ave, Ithaca, NY 14853, USA
| | - Emily Cohen
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
- New York University College of Dentistry, 345 E 34 St, New York, NY 10010
| | - Muspika Akter
- Baruch College, City University of New York, One Bernard Baruch Way, New York, NY 10010, USA
| | - Rishi Das Roy
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Outi Hallikas
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Mona M. Christensen
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Pengyang Li
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
| | - Jukka Jernvall
- Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
- Department of Geosciences and Geography, University of Helsinki, FI-00014 Helsinki, Finland
| | - Ophir D. Klein
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Pediatrics, Cedars-Sinai Guerin Children’s, 8700 Beverly Blvd., Suite 2416, Los Angeles, CA 90048, USA
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22
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Xu MRX, Liao ZY, Brock JR, Du K, Li GY, Chen ZQ, Wang YH, Gao ZN, Agarwal G, Wei KHC, Shao F, Pang S, Platts AE, van de Velde J, Lin HM, Teresi SJ, Bird K, Niederhuth CE, Xu JG, Yu GH, Yang JY, Dai SF, Nelson A, Braasch I, Zhang XG, Schartl M, Edger PP, Han MJ, Zhang HH. Maternal dominance contributes to subgenome differentiation in allopolyploid fishes. Nat Commun 2023; 14:8357. [PMID: 38102128 PMCID: PMC10724154 DOI: 10.1038/s41467-023-43740-y] [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: 02/16/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Teleost fishes, which are the largest and most diverse group of living vertebrates, have a rich history of ancient and recent polyploidy. Previous studies of allotetraploid common carp and goldfish (cyprinids) reported a dominant subgenome, which is more expressed and exhibits biased gene retention. However, the underlying mechanisms contributing to observed 'subgenome dominance' remains poorly understood. Here we report high-quality genomes of twenty-one cyprinids to investigate the origin and subsequent subgenome evolution patterns following three independent allopolyploidy events. We identify the closest extant relatives of the diploid progenitor species, investigate genetic and epigenetic differences among subgenomes, and conclude that observed subgenome dominance patterns are likely due to a combination of maternal dominance and transposable element densities in each polyploid. These findings provide an important foundation to understanding subgenome dominance patterns observed in teleost fishes, and ultimately the role of polyploidy in contributing to evolutionary innovations.
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Affiliation(s)
- Min-Rui-Xuan Xu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Zhen-Yang Liao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jordan R Brock
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kang Du
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA
| | - Guo-Yin Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | | | - Ying-Hao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhong-Nan Gao
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Gaurav Agarwal
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Kevin H-C Wei
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Shao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Southwest University, School of Life Sciences, Chongqing, China
| | | | - Adrian E Platts
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Jozefien van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Hong-Min Lin
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Scott J Teresi
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Kevin Bird
- Department of Horticulture, Michigan State University, East Lansing, MI, USA
| | - Chad E Niederhuth
- Department of Plant Biology, Michigan State University, East Lansing, MI, USA
| | - Jin-Gen Xu
- Jiujiang Academy of Agricultural Sciences, Jiujiang, China
| | - Guo-Hua Yu
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Jian-Yuan Yang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | - Si-Fa Dai
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China
| | | | - Ingo Braasch
- Department of Integrative Biology, Michigan State University, East Lansing, MI, USA
| | - Xiao-Gu Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
| | - Manfred Schartl
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, Bayern, Germany.
| | - Patrick P Edger
- Department of Horticulture, Michigan State University, East Lansing, MI, USA.
| | - Min-Jin Han
- State Key Laboratory of Resource Insects, Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China.
| | - Hua-Hao Zhang
- College of Pharmacy and Life Science, Jiujiang University, Jiujiang, China.
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23
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Xu XW, Sun P, Gao C, Zheng W, Chen S. Assembly of the poorly differentiated Verasper variegatus W chromosome by different sequencing technologies. Sci Data 2023; 10:893. [PMID: 38092799 PMCID: PMC10719390 DOI: 10.1038/s41597-023-02790-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023] Open
Abstract
The assembly of W and Y chromosomes poses significant challenges in vertebrate genome sequencing and assembly. Here, we successfully assembled the W chromosome of Verasper variegatus with a length of 20.48 Mb by combining population and PacBio HiFi sequencing data. It was identified as a young sex chromosome and showed signs of expansion in repetitive sequences. The major component of the expansion was Ty3/Gypsy. The ancestral Osteichthyes karyotype consists of 24 protochromosomes. The sex chromosomes in four Pleuronectiformes species derived from a pair of homologous protochromosomes resulting from a whole-genome duplication event in teleost fish, yet with different sex-determination systems. V. variegatus and Cynoglossus semilaevis adhere to the ZZ/ZW system, while Hippoglossus stenolepis and H. hippoglossus follow the XX/XY system. Interestingly, V. variegatus and H. hippoglossus derived from one protochromosome, while C. semilaevis and H. stenolepis derived from another protochromosome. Our study provides valuable insights into the evolution of sex chromosomes in flatfish and sheds light on the important role of whole-genome duplication in shaping the evolution of sex chromosomes.
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Affiliation(s)
- Xi-Wen Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237, China
| | - Pengchuan Sun
- Key Laboratory for Bio-resources and Eco-environment & Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Chengbin Gao
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Weiwei Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao, 266237, China.
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24
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Liu H, Zhang R, Zhou BF, Shen Z, Chen XY, Gao J, Wang B. Chromosome-scale genome assembly of sweet tea (Lithocarpus polystachyus Rehder). Sci Data 2023; 10:873. [PMID: 38057329 PMCID: PMC10700502 DOI: 10.1038/s41597-023-02791-y] [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: 10/16/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023] Open
Abstract
Lithocarpus, with >320 species, is the second largest genus of Fagaceae. However, the lack of a reference genome limits the molecular biology and functional study of Lithocarpus species. Here, we report the chromosome-scale genome assembly of sweet tea (Lithocarpus polystachyus Rehder), the first Lithocarpus species to be sequenced to date. Sweet tea has a 952-Mb genome, with a 21.4-Mb contig N50 value and 98.6% complete BUSCO score. In addition, the per-base consensus accuracy and completeness of the genome were estimated at 60.6 and 81.4, respectively. Genome annotation predicted 37,396 protein-coding genes, with repetitive sequences accounting for 64.2% of the genome. The genome did not undergo whole-genome duplication after the gamma (γ) hexaploidy event. Phylogenetic analysis showed that sweet tea diverged from the genus Quercus approximately at 59 million years ago. The high-quality genome assembly and gene annotation resources enrich the genomics of sweet tea, and will facilitate functional genomic studies in sweet tea and other Fagaceae species.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China.
| | - Rengang Zhang
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations/Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Biao-Feng Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Zhao Shen
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xue-Yan Chen
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Jie Gao
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden/Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Menglun, 666303, Yunnan, China
| | - Baosheng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops/Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, Guangdong, China.
- South China National Botanical Garden, Chinese Academy of Sciences (CAS), Guangzhou, China.
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25
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Fuchs S, Engelmann S. Small proteins in bacteria - Big challenges in prediction and identification. Proteomics 2023; 23:e2200421. [PMID: 37609810 DOI: 10.1002/pmic.202200421] [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: 05/31/2023] [Revised: 08/03/2023] [Accepted: 08/10/2023] [Indexed: 08/24/2023]
Abstract
Proteins with up to 100 amino acids have been largely overlooked due to the challenges associated with predicting and identifying them using traditional methods. Recent advances in bioinformatics and machine learning, DNA sequencing, RNA and Ribo-seq technologies, and mass spectrometry (MS) have greatly facilitated the detection and characterisation of these elusive proteins in recent years. This has revealed their crucial role in various cellular processes including regulation, signalling and transport, as toxins and as folding helpers for protein complexes. Consequently, the systematic identification and characterisation of these proteins in bacteria have emerged as a prominent field of interest within the microbial research community. This review provides an overview of different strategies for predicting and identifying these proteins on a large scale, leveraging the power of these advanced technologies. Furthermore, the review offers insights into the future developments that may be expected in this field.
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Affiliation(s)
- Stephan Fuchs
- Genome Competence Center (MF1), Department MFI, Robert-Koch-Institut, Berlin, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
- Microbial Proteomics, Helmholtzzentrum für Infektionsforschung GmbH, Braunschweig, Germany
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26
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Davalos-Dehullu E, Baty SM, Fisher RN, Scott PA, Dolby GA, Munguia-Vega A, Cortez D. Chromosome-Level Genome Assembly of the Blacktail Brush Lizard, Urosaurus nigricaudus, Reveals Dosage Compensation in an Endemic Lizard. Genome Biol Evol 2023; 15:evad210. [PMID: 38056449 DOI: 10.1093/gbe/evad210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2023] [Indexed: 12/08/2023] Open
Abstract
Urosaurus nigricaudus is a phrynosomatid lizard endemic to the Baja California Peninsula in Mexico. This work presents a chromosome-level genome assembly and annotation from a male individual. We used PacBio long reads and HiRise scaffolding to generate a high-quality genomic assembly of 1.87 Gb distributed in 327 scaffolds, with an N50 of 279 Mb and an L50 of 3. Approximately 98.4% of the genome is contained in 14 scaffolds, with 6 large scaffolds (334-127 Mb) representing macrochromosomes and 8 small scaffolds (63-22 Mb) representing microchromosomes. Using standard gene modeling and transcriptomic data, we predicted 17,902 protein-coding genes on the genome. The repeat content is characterized by a large proportion of long interspersed nuclear elements that are relatively old. Synteny analysis revealed some microchromosomes with high repeat content are more prone to rearrangements but that both macro- and microchromosomes are well conserved across reptiles. We identified scaffold 14 as the X chromosome. This microchromosome presents perfect dosage compensation where the single X of males has the same expression levels as two X chromosomes in females. Finally, we estimated the effective population size for U. nigricaudus was extremely low, which may reflect a reduction in polymorphism related to it becoming a peninsular endemic.
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Affiliation(s)
- Elizabeth Davalos-Dehullu
- Centro de Ciencias Genómicas, Programa de Biología de Sistemas, UNAM, Cuernavaca, Morelos, Mexico
- Baja GeoGenomics Consortium
| | - Sarah M Baty
- Baja GeoGenomics Consortium
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, California, USA
| | - Peter A Scott
- Natural Sciences Collegium, Eckerd College, St Petersburg, Florida, USA
| | - Greer A Dolby
- Baja GeoGenomics Consortium
- Department of Biology, University of Alabama at Birmingham, Alabama USA
| | - Adrian Munguia-Vega
- Baja GeoGenomics Consortium
- Conservation Genetics Laboratory, The University of Arizona, Tucson, Arizona, USA
- Applied Genomics Lab, La Paz, Baja California Sur, Mexico
| | - Diego Cortez
- Centro de Ciencias Genómicas, Programa de Biología de Sistemas, UNAM, Cuernavaca, Morelos, Mexico
- Baja GeoGenomics Consortium
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27
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Rodriguez Ruiz A, Van Dam AR. Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains. PeerJ 2023; 11:e16276. [PMID: 38025758 PMCID: PMC10676084 DOI: 10.7717/peerj.16276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/20/2023] [Indexed: 12/01/2023] Open
Abstract
PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this article we demonstrate that in this case the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of gene contamination increased with lower coverage. Future work should focus on developing reference free pre-binning approaches for HiFi reads produced from eukaryotic based metagenomic samples.
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Affiliation(s)
- Alfredo Rodriguez Ruiz
- Departamento de Biología, Universidad de Puerto Rico Recinto Universitario de Mayagüez, Mayagüez, Puerto Rico, United States of America
| | - Alex R. Van Dam
- Departamento de Biología, Universidad de Puerto Rico Recinto Universitario de Mayagüez, Mayagüez, Puerto Rico, United States of America
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28
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Ren H, Xu D, Xiao W, Zhou X, Li G, Zou J, Zhang H, Zhang Z, Zhang J, Zheng Y. Chromosome-level genome assembly and annotation of Zicaitai (Brassica rapa var. purpuraria). Sci Data 2023; 10:759. [PMID: 37923891 PMCID: PMC10624672 DOI: 10.1038/s41597-023-02668-0] [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: 07/04/2023] [Accepted: 10/19/2023] [Indexed: 11/06/2023] Open
Abstract
Zicaitai is a seasonal vegetable known for its high anthocyanin content in both stalks and leaves, yet its reference genome has not been published to date. Here, we generated the first chromosome-level genome assembly of Zicaitai using a combination of PacBio long-reads, Illumina short-reads, and Hi-C sequencing techniques. The final genome length is 474.12 Mb with a scaffold N50 length of 43.82 Mb, a BUSCO score of 99.30% and the LAI score of 10.14. Repetitive elements accounted for 60.89% (288.72 Mb) of the genome, and Hi-C data enabled the allocation of 430.87 Mb of genome sequences to ten pseudochromosomes. A total of 42,051 protein-coding genes were successfully predicted using multiple methods, of which 99.74% were functionally annotated. Notably, comparing the genome of Zicaitai with seven other species in the Cruciferae family revealed strong conservation in terms of gene numbers and structures. Overall, the high-quality genome assembly provides a critical resource for studying the genetic basis of important agronomic traits in Zicaitai.
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Affiliation(s)
- Hailong Ren
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
- Crops Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Provincial Key Laboratory of Crop Genetic Improvement, Guangzhou, 510640, China
| | - Donglin Xu
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Wanyu Xiao
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Xianyu Zhou
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Guangguang Li
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Jiwen Zou
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China
| | - Hua Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China.
| | - Zhibin Zhang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
- Zhengzhou Research Base, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Zhengzhou University, Zhengzhou, 450000, China.
| | - Jing Zhang
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China.
| | - Yansong Zheng
- Guangzhou Academy of Agricultural Sciences, Guangzhou, 510308, China.
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Ye H, Fan J, Hou Y, Yue H, Ruan R, Li S, Hu C, Xie Y, Li C. Chromosome-level genome assembly of the largefin longbarbel catfish ( Hemibagrus macropterus). Front Genet 2023; 14:1297119. [PMID: 38028621 PMCID: PMC10646426 DOI: 10.3389/fgene.2023.1297119] [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: 09/19/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
The largefin longbarbel catfish, Hemibagrus macropterus, is an economically important fish species in southwestern China, with males growing faster than females. This study presents a high-quality chromosome-level genome assembly of the largefin longbarbel catfish, generated by integrating Illumina short reads, PacBio HiFi long reads, and Hi-C data. The assembled genome size was 858.5 Mb, with a contig and scaffold N50 of 5.8 Mb and 28.4 Mb, respectively. A total of 656 contigs were successfully anchored to 30 pseudochromosomes with a BUSCO score of 97.7%, consistent with the number of chromosomes analyzed by karyotype. The genome contained 29.5% repeat sequences, and a predicted total of 26,613 protein-coding genes, of which 25,769 (96.8%) were functionally annotated in different databases. Evolutionary analysis showed that H. macropterus was most closely related to H. wyckioides, with a divergence time of approximately 16.3 million years. Chromosomal syntenic relationships among H. macropterus, H. wyckioides, and Pelteobagrus fulvidraco revealed a one-to-one relationship for most chromosomes, except for break, fission, and inversion of some chromosomes. The first high-quality reference genome will not only provide a valuable genetic resource for the study of sex determination mechanisms and genetic breeding of largefin longbarbel catfish, but also contribute to comparative analyses of genome and chromosome evolution within Siluriformes.
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Affiliation(s)
- Huan Ye
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Jiahui Fan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yanling Hou
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Huamei Yue
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Rui Ruan
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Shuang Li
- Chongqing Fishery Sciences Research Institute, Chongqing, China
| | - Chongjiang Hu
- Chongqing Fishery Sciences Research Institute, Chongqing, China
| | - Yong Xie
- Chongqing Fishery Sciences Research Institute, Chongqing, China
| | - Chuangju Li
- Key Laboratory of Freshwater Biodiversity Conservation, Ministry of Agriculture and Rural Affairs, Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
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Ma Y, Li J, Yu H, Teng L, Geng H, Li R, Xing R, Liu S, Li P. Comparative analysis of PacBio and ONT RNA sequencing methods for Nemopilema Nomurai venom identification. Genomics 2023; 115:110709. [PMID: 37739021 DOI: 10.1016/j.ygeno.2023.110709] [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: 05/26/2023] [Revised: 08/28/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Recent studies on marine organisms have made use of third-generation sequencing technologies such as Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT). While these specialized bioinformatics tools have different algorithmic designs and performance capabilities, they offer scalability and can be applied to various datasets. We investigated the effectiveness of PacBio and ONT RNA sequencing methods in identifying the venom of the jellyfish species Nemopilema nomurai. We conducted a detailed analysis of the sequencing data from both methods, focusing on key characteristics such as CD, alternative splicing, long-chain noncoding RNA, simple sequence repeat, transcription factor, and functional transcript annotation. Our findings indicate that ONT generally produced higher raw data quality in the transcriptome analysis, while PacBio generated longer read lengths. PacBio was found to be superior in identifying CDs and long-chain noncoding RNA, whereas ONT was more cost-effective for predicting alternative splicing events, simple sequence repeats, and transcription factors. Based on these results, we conclude that PacBio is the most specific and sensitive method for identifying venom components, while ONT is the most cost-effective method for studying venogenesis, cnidocyst (venom gland) development, and transcription of virulence genes in jellyfish. Our study has implications for future sequencing technologies in marine jellyfish, and highlights the power of full-length transcriptome analysis in discovering potential therapeutic targets for jellyfish dermatitis.
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Affiliation(s)
- Yuzhen Ma
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Jie Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huahua Yu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
| | - Lichao Teng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Geng
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rongfeng Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Ronge Xing
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Song Liu
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China
| | - Pengcheng Li
- Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), No. 1 Wenhai Road, Qingdao 266237, China.
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31
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Brantl S, Ul Haq I. Small proteins in Gram-positive bacteria. FEMS Microbiol Rev 2023; 47:fuad064. [PMID: 38052429 PMCID: PMC10730256 DOI: 10.1093/femsre/fuad064] [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: 10/25/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Small proteins comprising less than 100 amino acids have been often ignored in bacterial genome annotations. About 10 years ago, focused efforts started to investigate whole peptidomes, which resulted in the discovery of a multitude of small proteins, but only a number of them have been characterized in detail. Generally, small proteins can be either membrane or cytosolic proteins. The latter interact with larger proteins, RNA or even metal ions. Here, we summarize our current knowledge on small proteins from Gram-positive bacteria with a special emphasis on the model organism Bacillus subtilis. Our examples include membrane-bound toxins of type I toxin-antitoxin systems, proteins that block the assembly of higher order structures, regulate sporulation or modulate the RNA degradosome. We do not consider antimicrobial peptides. Furthermore, we present methods for the identification and investigation of small proteins.
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Affiliation(s)
- Sabine Brantl
- AG Bakteriengenetik, Matthias-Schleiden-Institut, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
| | - Inam Ul Haq
- AG Bakteriengenetik, Matthias-Schleiden-Institut, Friedrich-Schiller-Universität Jena, Philosophenweg 12, Jena D-07743, Germany
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Chaturvedi A, Li X, Dhandapani V, Marshall H, Kissane S, Cuenca-Cambronero M, Asole G, Calvet F, Ruiz-Romero M, Marangio P, Guigó R, Rago D, Mirbahai L, Eastwood N, Colbourne J, Zhou J, Mallon E, Orsini L. The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome. Nucleic Acids Res 2023; 51:9785-9803. [PMID: 37638757 PMCID: PMC10570034 DOI: 10.1093/nar/gkad685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 07/07/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.
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Affiliation(s)
- Anurag Chaturvedi
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Xiaojing Li
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Vignesh Dhandapani
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Hollie Marshall
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Stephen Kissane
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Maria Cuenca-Cambronero
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- Aquatic Ecology Group, University of Vic - Central University of Catalonia, 08500 Vic, Spain
| | - Giovanni Asole
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Ferriol Calvet
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Marina Ruiz-Romero
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Paolo Marangio
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology (BIST), Barcelona, Catalonia, Spain
| | - Daria Rago
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Leda Mirbahai
- Warwick Medical School, University of Warwick, Coventry CV4 7AL, UK
| | - Niamh Eastwood
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - John K Colbourne
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Jiarui Zhou
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
| | - Eamonn Mallon
- Department of Genetics and Genome Biology, the University of Leicester, Leicester LE1 7RH, UK
| | - Luisa Orsini
- Environmental Genomics Group, School of Biosciences, and Institute for Interdisciplinary Data Science and AI, the University of Birmingham, Birmingham B15 2TT, UK
- The Alan Turing Institute, British Library, London NW1 2DB, UK
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Visagie CM, Magistà D, Ferrara M, Balocchi F, Duong TA, Eichmeier A, Gramaje D, Aylward J, Baker SE, Barnes I, Calhoun S, De Angelis M, Frisvad JC, Hakalova E, Hayes RD, Houbraken J, Grigoriev IV, LaButti K, Leal C, Lipzen A, Ng V, Pangilinan J, Pecenka J, Perrone G, Piso A, Savage E, Spetik M, Wingfield MJ, Zhang Y, Wingfield BD. IMA genome-F18 : The re-identification of Penicillium genomes available in NCBI and draft genomes for Penicillium species from dry cured meat, Penicillium biforme, P. brevicompactum, P. solitum, and P. cvjetkovicii, Pewenomyces kutranfy, Pew. lalenivora, Pew. tapulicola, Pew. kalosus, Teratosphaeria carnegiei, and Trichoderma atroviride SC1. IMA Fungus 2023; 14:21. [PMID: 37803441 PMCID: PMC10559472 DOI: 10.1186/s43008-023-00121-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 10/08/2023] Open
Affiliation(s)
- Cobus M. Visagie
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Donato Magistà
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Massimo Ferrara
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Felipe Balocchi
- Department of Plant and Soil Sciences, FABI, University of Pretoria, Pretoria, South Africa
| | - Tuan A. Duong
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Ales Eichmeier
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - David Gramaje
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Janneke Aylward
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Department of Conservation Ecology and Entomology, Stellenbosch University, Matieland, Private Bag X1, Stellenbosch, 7602 South Africa
| | - Scott E. Baker
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354 USA
- DOE Joint Bioenergy Institute, Emeryville, CA 94608 USA
| | - Irene Barnes
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Sara Calhoun
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Maria De Angelis
- Department of Soil, Plant and Food Sciences, University of Bari “Aldo Moro”, Via G. Amendola 165/a, 70126 Bari, Italy
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark
| | - Eliska Hakalova
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Richard D. Hayes
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California Berkeley, 110 Koshland Hall, Berkeley, CA 94720 USA
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Catarina Leal
- Instituto de Ciencias de la Vid y del Vino (ICVV), Consejo Superior de Investigaciones Científicas - Universidad de la Rioja - Gobierno de La Rioja, Ctra. LO-20 Salida 13, Finca La Grajera, 26071 Logroño, Spain
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Vivian Ng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jasmyn Pangilinan
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Jakub Pecenka
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via G. Amendola 122/O, 70126 Bari, Italy
| | - Anja Piso
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emily Savage
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Milan Spetik
- Mendeleum - Institute of Genetics, Mendel University in Brno, Valticka 334, 691 44 Lednice, Czech Republic
| | - Michael J. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yu Zhang
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA
| | - Brenda D. Wingfield
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
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Baril T, Pym A, Bass C, Hayward A. Transposon accumulation at xenobiotic gene family loci in aphids. Genome Res 2023; 33:1718-1733. [PMID: 37852781 PMCID: PMC10691553 DOI: 10.1101/gr.277820.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/29/2023] [Indexed: 10/20/2023]
Abstract
The evolution of resistance is a major challenge for the sustainable control of pests and pathogens. Thus, a deeper understanding of the evolutionary and genomic mechanisms underpinning resistance evolution is required to safeguard health and food production. Several studies have implicated transposable elements (TEs) in xenobiotic-resistance evolution in insects. However, analyses are generally restricted to one insect species and/or one or a few xenobiotic gene families (XGFs). We examine evidence for TE accumulation at XGFs by performing a comparative genomic analysis across 20 aphid genomes, considering major subsets of XGFs involved in metabolic resistance to insecticides: cytochrome P450s, glutathione S-transferases, esterases, UDP-glucuronosyltransferases, and ABC transporters. We find that TEs are significantly enriched at XGFs compared with other genes. XGFs show similar levels of TE enrichment to those of housekeeping genes. But unlike housekeeping genes, XGFs are not constitutively expressed in germline cells, supporting the selective enrichment of TEs at XGFs rather than enrichment owing to chromatin availability. Hotspots of extreme TE enrichment occur around certain XGFs. We find, in aphids of agricultural importance, particular enrichment of TEs around cytochrome P450 genes with known functions in the detoxification of synthetic insecticides. Our results provide evidence supporting a general role for TEs as a source of genomic variation at host XGFs and highlight the existence of considerable variability in TE content across XGFs and host species. These findings show the need for detailed functional verification analyses to clarify the significance of individual TE insertions and elucidate underlying mechanisms at TE-XGF hotspots.
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Affiliation(s)
- Tobias Baril
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Adam Pym
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Chris Bass
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
| | - Alex Hayward
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Cornwall TR10 9FE, United Kingdom
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Guerra-Guimarães L, Pinheiro C, Oliveira ASF, Mira-Jover A, Valverde J, Guedes FADF, Azevedo H, Várzea V, Muñoz Pajares AJ. The chloroplast protein HCF164 is predicted to be associated with Coffea S H9 resistance factor against Hemileia vastatrix. Sci Rep 2023; 13:16019. [PMID: 37749157 PMCID: PMC10520047 DOI: 10.1038/s41598-023-41950-4] [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: 04/18/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023] Open
Abstract
To explore the connection between chloroplast and coffee resistance factors, designated as SH1 to SH9, whole genomic DNA of 42 coffee genotypes was sequenced, and entire chloroplast genomes were de novo assembled. The chloroplast phylogenetic haplotype network clustered individuals per species instead of SH factors. However, for the first time, it allowed the molecular validation of Coffea arabica as the maternal parent of the spontaneous hybrid "Híbrido de Timor". Individual reads were also aligned on the C. arabica reference genome to relate SH factors with chloroplast metabolism, and an in-silico analysis of selected nuclear-encoded chloroplast proteins (132 proteins) was performed. The nuclear-encoded thioredoxin-like membrane protein HCF164 enabled the discrimination of individuals with and without the SH9 factor, due to specific DNA variants linked to chromosome 7c (from C. canephora-derived sub-genome). The absence of both the thioredoxin domain and redox-active disulphide center in the HCF164 protein, observed in SH9 individuals, raises the possibility of potential implications on redox regulation. For the first time, the identification of specific DNA variants of chloroplast proteins allows discriminating individuals according to the SH profile. This study introduces an unexplored strategy for identifying protein/genes associated with SH factors and candidate targets of H. vastatrix effectors, thereby creating new perspectives for coffee breeding programs.
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Affiliation(s)
- Leonor Guerra-Guimarães
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Carla Pinheiro
- UCIBIO Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
- Associate Laboratory i4HB Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516, Caparica, Portugal.
| | - Ana Sofia F Oliveira
- Center for Computational Chemistry, School of Chemistry, University of Bristol, University Walk, Bristol, BS8 1TS, UK
| | - Andrea Mira-Jover
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain
- Área de Ecología, Departamento de Biología Aplicada, Universidad Miguel Hernández, Elche, Spain
| | - Javier Valverde
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- Estación Biológica de Doñana, Consejo Superior de Investigaciones Científicas (CSIC), Avda. Américo Vespucio 26, 41092, Sevilla, Spain
| | - Fernanda A de F Guedes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Herlander Azevedo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade Do Porto, 4099-002, Porto, Portugal
| | - Vitor Várzea
- CIFC - Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
- LEAF - Linking Landscape, Environment, Agriculture and Food Research Center, Associated Laboratory TERRA, Instituto Superior de Agronomia, Universidade de Lisboa, Tapada da Ajuda, 1349-017, Lisboa, Portugal
| | - Antonio Jesús Muñoz Pajares
- Departamento de Genética, Universidad de Granada, 18071, Granada, Spain.
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661, Vairão, Portugal.
- Research Unit Modeling Nature, Universidad de Granada, 18071, Granada, Spain.
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Giuseppe A, Raffaella EM. The First Genome-Wide Mildew Locus O Genes Characterization in the Lamiaceae Plant Family. Int J Mol Sci 2023; 24:13627. [PMID: 37686433 PMCID: PMC10487521 DOI: 10.3390/ijms241713627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Powdery mildew (PM) is a widespread plant disease that causes significant economic losses in thousands crops of temperate climates, including Lamiaceae species. Multiple scientific studies describe a peculiar form of PM-resistance associated at the inactivation of specific members of the Mildew Locus O (MLO) gene family, referred to as mlo-resistance. The characterization of Lamiaceae MLO genes, at the genomic level, would be a first step toward their potential use in breeding programs. We carried out a genome-wide characterization of the MLO gene family in 11 Lamiaceae species, providing a manual curated catalog of 324 MLO proteins. Evolutionary history and phylogenetic relationships were studied through maximum likelihood analysis and motif patter reconstruction. Our approach highlighted seven different clades diversified starting from an ancestral MLO domain pattern organized in 18 highly conserved motifs. In addition, 74 Lamiaceae putative PM susceptibility genes, clustering in clade V, were identified. Finally, we performed a codon-based evolutionary analysis, revealing a general high level of purifying selection in the eleven Lamiaceae MLO gene families, and the occurrence of few regions under diversifying selection in candidate susceptibility factors. The results of this work may help to address further biological questions concerning MLOs involved in PM susceptibility. In follow-up studies, it could be investigated whether the silencing or loss-of-function mutations in one or more of these candidate genes may lead to PM resistance.
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Affiliation(s)
- Andolfo Giuseppe
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, Portici, 80055 Naples, Italy
| | - Ercolano Maria Raffaella
- Department of Agricultural Sciences, University of Naples “Federico II”, Via Università 100, Portici, 80055 Naples, Italy
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37
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Guo J, Ren H, Ijaz M, Qi X, Ahmed T, You Y, Li G, Yu Z, Islam MS, Ali HM, Sun L, Li B. The completed genome sequence of Pestalotiopsis versicolor, a pathogenic ascomycete fungus with implications for bayberry production. Genomics 2023; 115:110695. [PMID: 37558012 DOI: 10.1016/j.ygeno.2023.110695] [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: 05/19/2023] [Revised: 07/17/2023] [Accepted: 08/05/2023] [Indexed: 08/11/2023]
Abstract
The pathogenic fungus Pestalotiopsis versicolor is a major etiological agent of fungal twig blight disease affecting bayberry trees. However, the lack of complete genome sequence information for this crucial pathogenic fungus hinders the molecular and genetic investigation of its pathogenic mechanism. To address this knowledge gap, we have generated the complete genome sequence of P. versicolor strain XJ27, employing a combination of Illumina, PacBio, and Hi-C sequencing technologies. This comprehensive genome sequence, comprising 7 chromosomes with an N50 contig size of 7,275,017 bp, a GC content ratio of 50.16%, and a total size of 50.80 Mb, encompasses 13,971 predicted coding genes. By performing comparative genomic analysis between P. versicolor and the genomes of eleven plant-pathogenic fungi, as well as three closely related fungi within the same group, we have gained initial insights into its evolutionary trajectory, particularly through gene family analysis. These findings shed light on the distinctive characteristics and evolutionary history of P. versicolor. Importantly, the availability of this high-quality genetic resource will serve as a foundational tool for investigating the biology, molecular pathogenesis, and virulence of P. versicolor. Furthermore, it will facilitate the development of more potent antifungal medications by uncovering potential vulnerabilities in its genetic makeup.
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Affiliation(s)
- Junning Guo
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haiying Ren
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Munazza Ijaz
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xingjiang Qi
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Temoor Ahmed
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China; Xianghu Laboratory, Hangzhou 311231, China
| | - Yuxin You
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Gang Li
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Zheping Yu
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Mohammad Shafiqul Islam
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hayssam M Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Li Sun
- State Key Laboratory for Managing Biotic and Chemical Treats to the Quality and Safety of Agro-Products, Institute of Horticulture, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Bin Li
- State Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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38
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Anders J, Stadler PF. RNAcode_Web - Convenient identification of evolutionary conserved protein coding regions. J Integr Bioinform 2023; 20:jib-2022-0046. [PMID: 37615674 PMCID: PMC10757073 DOI: 10.1515/jib-2022-0046] [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: 08/25/2022] [Accepted: 02/15/2023] [Indexed: 08/25/2023] Open
Abstract
The differentiation of regions with coding potential from non-coding regions remains a key task in computational biology. Methods such as RNAcode that exploit patterns of sequence conservation for this task have a substantial advantage in classification accuracy in particular for short coding sequences, compared to methods that rely on a single input sequence. However, they require sequence alignments as input. Frequently, suitable multiple sequence alignments are not readily available and are tedious, and sometimes difficult to construct. We therefore introduce here a new web service that provides access to the well-known coding sequence detector RNAcode with minimal user overhead. It requires as input only a single target nucleotide sequence. The service automates the collection, selection, and preparation of homologous sequences from the NCBI database, as well as the construction of the multiple sequence alignment that are needed as input for RNAcode. The service automatizes the entire pre- and postprocessing and thus makes the investigation of specific genomic regions for previously unannotated coding regions, such as small peptides or additional introns, a simple task that is easily accessible to non-expert users. RNAcode_Web is accessible online at rnacode.bioinf.uni-leipzig.de.
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Affiliation(s)
- John Anders
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, D-04107Leipzig, Germany
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16–18, D-04107Leipzig, Germany
- Max-Planck-Institute for Mathematics in the Sciences, Inselstraße 22, D-04103Leipzig, Germany
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090Wien, Austria
- Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA
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39
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Wang Y, Guo X, Zhang X, Chen P, Wang W, Hu S, Ma T, Zhou X, Li D, Yang Y. In Vivo Microevolutionary Analysis of a Fatal Case of Rhinofacial and Disseminated Mycosis Due to Azole-Drug-Resistant Candida Species. J Fungi (Basel) 2023; 9:815. [PMID: 37623586 PMCID: PMC10455694 DOI: 10.3390/jof9080815] [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: 06/27/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
Ten Candida species strains were isolated from the first known fatal case of rhinofacial and rhino-orbital-cerebral candidiasis. Among them, five strains of Candida parapsilosis complex were isolated during the early stage of hospitalization, while five strains of Candida tropicalis were isolated in the later stages of the disease. Using whole-genome sequencing, we distinguished the five strains of C. parapsilosis complex as four Candida metapsilosis strains and one Candida parapsilosis strain. Antifungal susceptibility testing showed that the five strains of C. parapsilosis complex were susceptible to all antifungal drugs, while five C. tropicalis strains had high minimum inhibitory concentrations to azoles, whereas antifungal-drug resistance gene analysis revealed the causes of azole resistance in such strains. For the first time, we analyzed the microevolutionary characteristics of pathogenic fungi in human hosts and inferred the infection time and parallel evolution of C. tropicalis strains. Molecular clock analysis revealed that azole-resistant C. tropicalis infection occurred during the first round of therapy, followed by divergence via parallel evolution in vivo. The presence/absence variations indicated a potential decrease in the virulence of genomes in strains isolated following antifungal drug treatment, despite the absence of observed clinical improvement in the conditions of the patient. These results suggest that genomic analysis could serve as an auxiliary tool in guiding clinical diagnosis and treatment.
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Affiliation(s)
- Yuchen Wang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, Tianjing 300457, China;
| | - Xinran Zhang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Ping Chen
- Division of Dermatology and Mycological Lab, Peking University Third Hospital, Beijing 100191, China
| | - Wenhui Wang
- Division of Dermatology and Mycological Lab, Peking University Third Hospital, Beijing 100191, China
| | - Shan Hu
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Teng Ma
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
| | - Xingchen Zhou
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
- School of Life Science & Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Dongming Li
- Division of Dermatology and Mycological Lab, Peking University Third Hospital, Beijing 100191, China
| | - Ying Yang
- Bioinformatics Center of AMMS, Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing Institute of Microbiology and Epidemiology, Beijing 100850, China; (Y.W.); (X.Z.)
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40
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Wells JN, Chang NC, McCormick J, Coleman C, Ramos N, Jin B, Feschotte C. Transposable elements drive the evolution of metazoan zinc finger genes. Genome Res 2023; 33:1325-1339. [PMID: 37714714 PMCID: PMC10547256 DOI: 10.1101/gr.277966.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 06/15/2023] [Indexed: 09/17/2023]
Abstract
Cys2-His2 zinc finger genes (ZNFs) form the largest family of transcription factors in metazoans. ZNF evolution is highly dynamic and characterized by the rapid expansion and contraction of numerous subfamilies across the animal phylogeny. The forces and mechanisms underlying rapid ZNF evolution remain poorly understood, but there is growing evidence that, in tetrapods, the targeting and repression of lineage-specific transposable elements (TEs) plays a critical role in the evolution of the Krüppel-associated box ZNF (KZNF) subfamily. Currently, it is unknown whether this function and coevolutionary relationship is unique to KZNFs or is a broader feature of metazoan ZNFs. Here, we present evidence that genomic conflict with TEs has been a central driver of the diversification of ZNFs in animals. Sampling from 3221 genome assemblies, we show that the copy number of retroelements correlates with that of ZNFs across at least 750 million years of metazoan evolution. Using computational predictions, we show that ZNFs preferentially bind TEs in diverse animal species. We further investigate the largest ZNF subfamily found in cyprinid fish, which is characterized by a conserved sequence we dubbed the fish N-terminal zinc finger-associated (FiNZ) domain. Zebrafish possess approximately 700 FiNZ-ZNFs, many of which are evolving adaptively under positive selection. Like mammalian KZNFs, most zebrafish FiNZ-ZNFs are expressed at the onset of zygotic genome activation, and blocking their translation using morpholinos during early embryogenesis results in derepression of transcriptionally active TEs. Together, these data suggest that ZNF diversification has been intimately connected to TE expansion throughout animal evolution.
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Affiliation(s)
- Jonathan N Wells
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
| | - Ni-Chen Chang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - John McCormick
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Caitlyn Coleman
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida 33620, USA
| | - Nathalie Ramos
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
- Department of Genetics and Genomic Sciences, Center for Transformative Disease Modeling, Tisch Cancer Institute, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Bozhou Jin
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14850, USA;
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41
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Jin D, Li C, Chen X, Byerly A, Stover NA, Zhang T, Shao C, Wang Y. Comparative genome analysis of three euplotid protists provides insights into the evolution of nanochromosomes in unicellular eukaryotic organisms. MARINE LIFE SCIENCE & TECHNOLOGY 2023; 5:300-315. [PMID: 37637252 PMCID: PMC10449743 DOI: 10.1007/s42995-023-00175-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/12/2023] [Indexed: 08/29/2023]
Abstract
One of the most diverse clades of ciliated protozoa, the class Spirotrichea, displays a series of unique characters in terms of eukaryotic macronuclear (MAC) genome, including high fragmentation that produces nanochromosomes. However, the genomic diversity and evolution of nanochromosomes and gene families for spirotrich MAC genomes are poorly understood. In this study, we assemble the MAC genome of a representative euplotid (a new model organism in Spirotrichea) species, Euplotes aediculatus. Our results indicate that: (a) the MAC genome includes 35,465 contigs with a total length of 97.3 Mb and a contig N50 of 3.4 kb, and contains 13,145 complete nanochromosomes and 43,194 predicted genes, with the majority of these nanochromosomes containing tiny introns and harboring only one gene; (b) genomic comparisons between E. aediculatus and other reported spirotrichs indicate that average GC content and genome fragmentation levels exhibit interspecific variation, and chromosome breaking sites (CBSs) might be lost during evolution, resulting in the increase of multi-gene nanochromosome; (c) gene families associated with chitin metabolism and FoxO signaling pathway are expanded in E. aediculatus, suggesting their potential roles in environment adaptation and survival strategies of E. aediculatus; and (d) a programmed ribosomal frameshift (PRF) with a conservative motif 5'-AAATAR-3' tends to occur in longer genes with more exons, and PRF genes play an important role in many cellular regulation processes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-023-00175-0.
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Affiliation(s)
- Didi Jin
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Chao Li
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003 China
| | - Xiao Chen
- Laboratory of Marine Protozoan Biodiversity and Evolution, Marine College, Shandong University, Weihai, 264209 China
| | - Adam Byerly
- Department of Computer Science and Information Systems, Bradley University, Peoria, 61625 USA
| | - Naomi A. Stover
- Department of Biology, Bradley University, Peoria, 61625 USA
| | - Tengteng Zhang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Chen Shao
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
| | - Yurui Wang
- Laboratory of Protozoological Biodiversity and Evolution in Wetland, College of Life Sciences, Shaanxi Normal University, Xi’an, 710119 China
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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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43
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Wang Z, Ma X, Zhu J, Zheng B, Yuan R, Lu Z, Shu X, Fang Y, Tian S, Qu Q, Ye X, Tang P, Chen X. Chromosome-level genome assembly of Chouioia cunea Yang, the parasitic wasp of the fall webworm. Sci Data 2023; 10:485. [PMID: 37495588 PMCID: PMC10372138 DOI: 10.1038/s41597-023-02388-5] [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: 04/17/2023] [Accepted: 07/14/2023] [Indexed: 07/28/2023] Open
Abstract
Chouioia cunea Yang 1989 is a parasitic wasp of many lepidopteran insects during their pupal stage, and has been successfully used to control pests such as the fall webworm Hyphantria cunea. Here we reported the chromosome-level genome of C. cunea by using short (MGI-SEQ), long (Oxford Nanopore), chromatin-linked (Hi-C) sequencing reads and transcriptomic data, representing the first chromosome-level genome of parasitic wasps of the family Eulophidae. The total assembly length is 171.99 Mb, containing 6 pesudo-chromosomes with a GC content of 36.89% and the scaffold/contig N50 length of 31.70/26.52 Mb. The BUSCO completeness of the assembly was estimated to be 98.7%. A total of 12,258 protein-coding genes (PCGs), 10,547 3'-UTRs, and 10,671 5'-UTRs were annotated. This high-quality genome is an important step toward a better understanding of the genomes of the Eulophidae (Chalcidoidea), and will serve as a valuable resource for analyses of phylogenetic relationships and the evolution of Hymenoptera.
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Affiliation(s)
- Ziqi Wang
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xingzhou Ma
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiachen Zhu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Boying Zheng
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ruizhong Yuan
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zhaohe Lu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaohan Shu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yu Fang
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiji Tian
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Qiuyu Qu
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiqian Ye
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Pu Tang
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
| | - Xuexin Chen
- State Key Lab of Rice Biology, Zhejiang University, Hangzhou, 310058, China.
- Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China.
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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Wang Q, Bao H, Li Z. Genomic comparison between two Inonotus hispidus strains isolated from growing in different tree species. Front Genet 2023; 14:1221491. [PMID: 37519891 PMCID: PMC10372432 DOI: 10.3389/fgene.2023.1221491] [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: 05/12/2023] [Accepted: 07/03/2023] [Indexed: 08/01/2023] Open
Abstract
Inonotus hispidus mainly growing in broad-leaved trees, including Morus alba, Fraxinus mandshurica, and Ulmus macrocarpa etc. The fruiting body of I. hispidus growing in M. alba (hereafter as MA) is used as a traditional Chinese medicine "Sanghuang". However, differences between the genetic material basis of I. hispidus growing in other tree species have not been reported. Therefore, in this paper, the genomic comparison between MA and I. hispidus growing in F. mandshurica (hereafter as FM) were studied. The whole genome of MA monokaryon was sequenced by Illumina combined with Pac Bio platform. Next, genome assembly, genome component prediction and genome functional annotation were performed. Comparative genomics analysis was performed between FM monokaryon and MA monokaryon, using MA as the reference. The results showed that, MA had 24 contigs with a N50 length of 2.6 Mb. Specifically, 5,342, 6,564, 1,595, 383 and 123 genes were annotated from GO, KEGG, KOG, CAZymes and CYP450, respectively. Moreover, comparative genomics showed that, the coding genes and total number of genes annotated in different databases of FM were higher than that of MA. This study provides a foundation for the medicinal application of FM as MA from the perspective of genetic composition.
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Affiliation(s)
- Qingchun Wang
- Key Laboratory for Development and Utilization of Fungi Traditional Chinese Medicine Resources, Jilin Agricultural University, Changchun, Jilin, China
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, China
| | - Haiying Bao
- Key Laboratory for Development and Utilization of Fungi Traditional Chinese Medicine Resources, Jilin Agricultural University, Changchun, Jilin, China
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, China
| | - Zhijun Li
- Key Laboratory for Development and Utilization of Fungi Traditional Chinese Medicine Resources, Jilin Agricultural University, Changchun, Jilin, China
- Key Laboratory of Edible Fungal Resources and Utilization (North), Ministry of Agriculture and Rural Affairs, Jilin Agricultural University, Changchun, Jilin, China
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Radosavljević I, Križanović K, Šarančić SL, Jakše J. Towards the Investigation of the Adaptive Divergence in a Species of Exceptional Ecological Plasticity: Chromosome-Scale Genome Assembly of Chouardia litardierei (Hyacinthaceae). Int J Mol Sci 2023; 24:10755. [PMID: 37445933 DOI: 10.3390/ijms241310755] [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: 05/24/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
One of the central goals of evolutionary biology is to understand the genomic basis of adaptive divergence. Different aspects of evolutionary processes should be studied through genome-wide approaches, therefore maximizing the investigated genomic space. However, in-depth genome-scale analyses often are restricted to a model or economically important species and their closely related wild congeners with available reference genomes. Here, we present the high-quality chromosome-level genome assembly of Chouardia litardierei, a plant species with exceptional ecological plasticity. By combining PacBio and Hi-C sequencing technologies, we generated a 3.7 Gbp genome with a scaffold N50 size of 210 Mbp. Over 80% of the genome comprised repetitive elements, among which the LTR retrotransposons prevailed. Approximately 86% of the 27,257 predicted genes were functionally annotated using public databases. For the comparative analysis of different ecotypes' genomes, the whole-genome sequencing of two individuals, each from a distinct ecotype, was performed. The detected above-average SNP density within coding regions suggests increased adaptive divergence-related mutation rates, therefore confirming the assumed divergence processes within the group. The constructed genome presents an invaluable resource for future research activities oriented toward the investigation of the genetics underlying the adaptive divergence that is likely unfolding among the studied species' ecotypes.
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Affiliation(s)
- Ivan Radosavljević
- Division of Botany, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9A, HR-10000 Zagreb, Croatia
| | - Krešimir Križanović
- Department of Electronic Systems and Information Processing, Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR-10000 Zagreb, Croatia
| | - Sara Laura Šarančić
- Division of Botany, Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9A, HR-10000 Zagreb, Croatia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
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Wang X, Zhao N, Cai L, Liu N, Zhu J, Yang B. High-quality chromosome-level scaffolds of the plant bug Pachypeltis micranthus provide insights into the availability of Mikania micrantha control. BMC Genomics 2023; 24:339. [PMID: 37340339 DOI: 10.1186/s12864-023-09445-8] [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: 04/03/2023] [Accepted: 06/13/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND The plant bug, Pachypeltis micranthus Mu et Liu (Hemiptera: Miridae), is an effective potential biological control agent for Mikania micrantha H.B.K. (Asteraceae; one of the most notorious invasive weeds worldwide). However, limited knowledge about this species hindered its practical application and research. Accordingly, sequencing the genome of this mirid bug holds great significance in controlling M. micrantha. RESULTS Here, 712.72 Mb high-quality chromosome-level scaffolds of P. micranthus were generated, of which 707.51 Mb (99.27%) of assembled sequences were anchored onto 15 chromosome-level scaffolds with contig N50 of 16.84 Mb. The P. micranthus genome had the highest GC content (42.43%) and the second highest proportion of repetitive sequences (375.82 Mb, 52.73%) than the three other mirid bugs (i.e., Apolygus lucorum, Cyrtorhinus lividipennis, and Nesidiocoris tenuis). Phylogenetic analysis showed that P. micranthus clustered with other mirid bugs and diverged from the common ancestor approximately 200 million years ago. Gene family expansion and/or contraction were analyzed, and significantly expanded gene families associated with P. micranthus feeding and adaptation to M. micrantha were manually identified. Compared with the whole body, transcriptome analysis of the salivary gland revealed that most of the upregulated genes were significantly associated with metabolism pathways and peptidase activity, particularly among cysteine peptidase, serine peptidase, and polygalacturonase; this could be one of the reasons for precisely and highly efficient feeding by the oligophagous bug P. micranthus on M. micrantha. CONCLUSION Collectively, this work provides a crucial chromosome-level scaffolds resource to study the evolutionary adaptation between mirid bug and their host. It is also helpful in searching for novel environment-friendly biological strategies to control M. micrantha.
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Affiliation(s)
- Xiafei Wang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Ning Zhao
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Liqiong Cai
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, China
| | - Naiyong Liu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Jiaying Zhu
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China
| | - Bin Yang
- Key Laboratory of Forest Disaster Warning and Control of Yunnan Province, Southwest Forestry University, Kunming, China.
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He Q, Tang S, Zhi H, Chen J, Zhang J, Liang H, Alam O, Li H, Zhang H, Xing L, Li X, Zhang W, Wang H, Shi J, Du H, Wu H, Wang L, Yang P, Xing L, Yan H, Song Z, Liu J, Wang H, Tian X, Qiao Z, Feng G, Guo R, Zhu W, Ren Y, Hao H, Li M, Zhang A, Guo E, Yan F, Li Q, Liu Y, Tian B, Zhao X, Jia R, Feng B, Zhang J, Wei J, Lai J, Jia G, Purugganan M, Diao X. A graph-based genome and pan-genome variation of the model plant Setaria. Nat Genet 2023:10.1038/s41588-023-01423-w. [PMID: 37291196 DOI: 10.1038/s41588-023-01423-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 05/08/2023] [Indexed: 06/10/2023]
Abstract
Setaria italica (foxtail millet), a founder crop of East Asian agriculture, is a model plant for C4 photosynthesis and developing approaches to adaptive breeding across multiple climates. Here we established the Setaria pan-genome by assembling 110 representative genomes from a worldwide collection. The pan-genome is composed of 73,528 gene families, of which 23.8%, 42.9%, 29.4% and 3.9% are core, soft core, dispensable and private genes, respectively; 202,884 nonredundant structural variants were also detected. The characterization of pan-genomic variants suggests their importance during foxtail millet domestication and improvement, as exemplified by the identification of the yield gene SiGW3, where a 366-bp presence/absence promoter variant accompanies gene expression variation. We developed a graph-based genome and performed large-scale genetic studies for 68 traits across 13 environments, identifying potential genes for millet improvement at different geographic sites. These can be used in marker-assisted breeding, genomic selection and genome editing to accelerate crop improvement under different climatic conditions.
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Affiliation(s)
- Qiang He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinfeng Chen
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jun Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hongkai Liang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ornob Alam
- Center for Genomics and Systems Biology, New York University, New York City, NY, USA
| | - Hongbo Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Agronomy, Northwest A & F University, Yangling, China
| | - Lihe Xing
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xukai Li
- College of Life Sciences, Shanxi Agricultural University, Taigu, China
| | - Wei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hailong Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junpeng Shi
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Huilong Du
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding, China
| | - Hongpo Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lu Xing
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Hongshan Yan
- Anyang Academy of Agriculture Sciences, Anyang, China
| | | | - Jinrong Liu
- Anyang Academy of Agriculture Sciences, Anyang, China
| | - Haigang Wang
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Xiang Tian
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Zhijun Qiao
- Center for Agricultural Genetic Resources Research, Shanxi Agricultural University, Taiyuan, China
| | - Guojun Feng
- Research Institute of Cereal Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Ruifeng Guo
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Wenjuan Zhu
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Yuemei Ren
- Institute of High Latitude Crops, Shanxi Agricultural University, Datong, China
| | - Hongbo Hao
- Institute of Dry-Land Farming, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Mingzhe Li
- Institute of Dry-Land Farming, Hebei Academy of Agricultural and Forestry Sciences, Hengshui, China
| | - Aiying Zhang
- Millet Research Institute, Shanxi Agricultural University, Changzhi, China
| | - Erhu Guo
- Millet Research Institute, Shanxi Agricultural University, Changzhi, China
| | - Feng Yan
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Qingquan Li
- Qiqihar Sub-Academy of Heilongjiang Academy of Agricultural Sciences, Qiqihar, China
| | - Yanli Liu
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Bohong Tian
- Cangzhou Academy of Agriculture and Forestry Sciences, Cangzhou, China
| | - Xiaoqin Zhao
- Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Ruiling Jia
- Dingxi Academy of Agricultural Sciences, Dingxi, China
| | - Baili Feng
- College of Agronomy, Northwest A & F University, Yangling, China
| | - Jiewei Zhang
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jianhua Wei
- Beijing Key Laboratory of Agricultural Genetic Resources and Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jinsheng Lai
- State Key Laboratory of Plant Physiology and Biochemistry & National Maize Improvement Center, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
| | - Michael Purugganan
- Center for Genomics and Systems Biology, New York University, New York City, NY, USA.
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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48
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Zhang BL, Chen W, Wang Z, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen J, Yang MM, Wu Y, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu Z, Schierup MH, Cooper DN, Liu J, Zheng YT, Zhang G, Wu DD. Comparative genomics reveals the hybrid origin of a macaque group. SCIENCE ADVANCES 2023; 9:eadd3580. [PMID: 37262187 PMCID: PMC10413639 DOI: 10.1126/sciadv.add3580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 01/25/2023] [Indexed: 06/03/2023]
Abstract
Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates.
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Affiliation(s)
- Bao-Lin Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wu Chen
- Guangzhou Zoo and Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Zefu Wang
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China
| | - Wei Pang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Meng-Ting Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Sheng Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen-Qiang He
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yuan Deng
- BGI-Shenzhen, Shenzhen 518083, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
| | - Long Zhou
- Center for Evolutionary and Organismal Biology and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
| | | | - Min-Min Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Yajiang Wu
- Guangzhou Zoo and Guangzhou Wildlife Research Center, Guangzhou 510070, China
| | - Lu Wang
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, China
| | | | | | - Hélène Meunier
- Centre de Primatologie, de l'Université de Strasbourg, Niederhausbergen, France
- Laboratoire de Neurosciences Cognitives et Adaptatives, UMR 7364, Université de Strasbourg, Strasbourg, France
| | - Fanélie Wanert
- Plateforme SILABE, Université de Strasbourg, Niederhausbergen, France
| | - Lukas Kuderna
- Genome Interpretation Department, Illumina Inc., Foster City, CA, USA
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Dr. Aiguader 88, Barcelona 08003, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, Barcelona 08010, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, Barcelona 08028, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Edifici ICTA-ICP, c/Columnes s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Göttingen, Germany
- Gene Bank of Primates, German Primate Center, Göttingen, Germany
| | - Xiao-Guang Qi
- Shaanxi Key Laboratory for Animal Conservation, College of Life Sciences, Northwest University, Xi’an, China
| | - Ming Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhijin Liu
- College of Life Sciences, Capital Normal University, Beijing 100048, China
| | | | - David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK
| | - Jianquan Liu
- Key Laboratory for Bio-resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology and College of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yong-Tang Zheng
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences, KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Evolutionary and Organismal Biology and Women’s Hospital at Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- National Resource Center for Non-Human Primates, Kunming Primate Research Center and National Research Facility for Phenotypic and Genetic Analysis of Model Animals (Primate Facility), Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650107, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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Li H, Sun P, Wang Y, Zhang Z, Yang J, Suo Y, Han W, Diao S, Li F, Fu J. Allele-aware chromosome-level genome assembly of the autohexaploid Diospyros kaki Thunb. Sci Data 2023; 10:270. [PMID: 37169805 PMCID: PMC10175270 DOI: 10.1038/s41597-023-02175-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/21/2023] [Indexed: 05/13/2023] Open
Abstract
Artificially improving persimmon (Diospyros kaki Thunb.), one of the most important fruit trees, remains challenging owing to the lack of reference genomes. In this study, we generated an allele-aware chromosome-level genome assembly for the autohexaploid persimmon 'Xiaoguotianshi' (Chinese-PCNA type) using PacBio CCS and Hi-C technology. The final assembly contained 4.52 Gb, with a contig N50 value of 5.28 Mb and scaffold N50 value of 44.01 Mb, of which 4.06 Gb (89.87%) of the assembly were anchored onto 90 chromosome-level pseudomolecules comprising 15 homologous groups with 6 allelic chromosomes in each. A total of 153,288 protein-coding genes were predicted, of which 98.60% were functionally annotated. Repetitive sequences accounted for 64.02% of the genome; and 110,480 rRNAs, 12,297 tRNAs, 1,483 miRNAs, and 3,510 snRNA genes were also identified. This genome assembly fills the knowledge gap in the autohexaploid persimmon genome, which is conducive in the study on the regulatory mechanisms underlying the major economically advantageous traits of persimmons and promoting breeding programs.
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Affiliation(s)
- Huawei Li
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, No. 498 Shaoshan South Road, Changsha, 410004, China
| | - Peng Sun
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Yiru Wang
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Jun Yang
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai Chenshan Botanical Garden, 3888 Chenhua Road, Shanghai, 201602, China
| | - Yujing Suo
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Weijuan Han
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Songfeng Diao
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China
| | - Fangdong Li
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
| | - Jianmin Fu
- Research Institute of Non-timber Forestry, Chinese Academy of Forestry, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- Key Laboratory of Non-timber Forest Germplasm Enhancement & Utilization of State Administration of Forestry and Grassland, No. 3 Weiwu Road, Jinshui District, Zhengzhou, 450003, China.
- Henan Key Laboratory of Germplasm Innovation and Utilization of Eco-economic Woody Plant, Pingdingshan University, Pingdingshan, 467000, China.
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Li J, Li S, Su H, Yu M, Xu J, Yi Z. Comprehensive phylogenomic analyses reveal that order Armophorida is most closely related to class Armophorea (Protista, Ciliophora). Mol Phylogenet Evol 2023; 182:107737. [PMID: 36841269 DOI: 10.1016/j.ympev.2023.107737] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/12/2023] [Accepted: 02/19/2023] [Indexed: 02/27/2023]
Abstract
Ciliate species within the class Armophorea are widely distributed in various anaerobic environments, hence they are of great interest to researchers studying evolution and adaptation of eukaryotes to extreme habitats. However, phylogenetic relationships within the class remain largely elusive, most especially assignment of the order Armophorida and classification within the family Metopidae. In this study, we newly sequenced transcriptomes and the SSU rDNA of five armophorean species, Sulfonecta cf. uniserialis (order Armophorida), Nyctotheroides sp. (order Clevelandellida), and Metopus major, M. paraes, and Brachonella contorta (order Metopida). Comprehensive phylogenomic analyses revealed that Armophorea was most closely related to Muranotrichea and Parablepharismea. Our results indicate that the order Armophorida either belongs to Armophorea or represents a new class within APM (Armophorea-Parablepharismea-Muranotrichea). Analyses combining ecological niches and molecular trees showed that APM species might descend from an anaerobic free-living ciliate species. Existing molecular phylogenomic/phylogenetic and morphological evidence indicate that the family Metopidae is non-monophyletic and should be further classified with inclusion of additional lines of evidences. Our results provide new insights into the long-debated relationships within Armophorea.
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Affiliation(s)
- Jia Li
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Song Li
- School of Marine Sciences, Sun Yat-Sen University, Zhuhai 519082, China
| | - Hua Su
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Minjie Yu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Jiahui Xu
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China
| | - Zhenzhen Yi
- Guangzhou Key Laboratory of Subtropical Biodiversity and Biomonitoring, School of Life Science, South China Normal University, Guangzhou 510631, China.
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