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Lian Q, Huettel B, Walkemeier B, Mayjonade B, Lopez-Roques C, Gil L, Roux F, Schneeberger K, Mercier R. A pan-genome of 69 Arabidopsis thaliana accessions reveals a conserved genome structure throughout the global species range. Nat Genet 2024; 56:982-991. [PMID: 38605175 PMCID: PMC11096106 DOI: 10.1038/s41588-024-01715-9] [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: 05/24/2023] [Accepted: 03/11/2024] [Indexed: 04/13/2024]
Abstract
Although originally primarily a system for functional biology, Arabidopsis thaliana has, owing to its broad geographical distribution and adaptation to diverse environments, developed into a powerful model in population genomics. Here we present chromosome-level genome assemblies of 69 accessions from a global species range. We found that genomic colinearity is very conserved, even among geographically and genetically distant accessions. Along chromosome arms, megabase-scale rearrangements are rare and typically present only in a single accession. This indicates that the karyotype is quasi-fixed and that rearrangements in chromosome arms are counter-selected. Centromeric regions display higher structural dynamics, and divergences in core centromeres account for most of the genome size variations. Pan-genome analyses uncovered 32,986 distinct gene families, 60% being present in all accessions and 40% appearing to be dispensable, including 18% private to a single accession, indicating unexplored genic diversity. These 69 new Arabidopsis thaliana genome assemblies will empower future genetic research.
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Affiliation(s)
- Qichao Lian
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck-Genome-centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Birgit Walkemeier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Baptiste Mayjonade
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | | | - Lisa Gil
- INRAE, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microbes-Environnement, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, CNRS, Université de Toulouse, Castanet-Tolosan, France
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Faculty of Biology, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
| | - Raphael Mercier
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.
- Cluster of Excellence on Plant Sciences, Heinrich-Heine University, Düsseldorf, Germany.
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2
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Jiang J, Xu YC, Zhang ZQ, Chen JF, Niu XM, Hou XH, Li XT, Wang L, Zhang YE, Ge S, Guo YL. Forces driving transposable element load variation during Arabidopsis range expansion. THE PLANT CELL 2024; 36:840-862. [PMID: 38036296 PMCID: PMC10980350 DOI: 10.1093/plcell/koad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 12/02/2023]
Abstract
Genetic load refers to the accumulated and potentially life-threatening deleterious mutations in populations. Understanding the mechanisms underlying genetic load variation of transposable element (TE) insertion, a major large-effect mutation, during range expansion is an intriguing question in biology. Here, we used 1,115 global natural accessions of Arabidopsis (Arabidopsis thaliana) to study the driving forces of TE load variation during its range expansion. TE load increased with range expansion, especially in the recently established Yangtze River basin population. Effective population size, which explains 62.0% of the variance in TE load, high transposition rate, and selective sweeps contributed to TE accumulation in the expanded populations. We genetically mapped and identified multiple candidate causal genes and TEs, and revealed the genetic architecture of TE load variation. Overall, this study reveals the variation in TE genetic load during Arabidopsis expansion and highlights the causes of TE load variation from the perspectives of both population genetics and quantitative genetics.
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Affiliation(s)
- Juan Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Zhi-Qin Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jia-Fu Chen
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiao-Min Niu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xing-Hui Hou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Xin-Tong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Wang
- Agricultural Synthetic Biology Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
| | - Yong E Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents & Key Laboratory of the Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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3
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Pianezza R, Scarpa A, Narayanan P, Signor S, Kofler R. Spoink, a LTR retrotransposon, invaded D. melanogaster populations in the 1990s. PLoS Genet 2024; 20:e1011201. [PMID: 38530818 DOI: 10.1371/journal.pgen.1011201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/27/2024] [Indexed: 03/28/2024] Open
Abstract
During the last few centuries D. melanogaster populations were invaded by several transposable elements, the most recent of which was thought to be the P-element between 1950 and 1980. Here we describe a novel TE, which we named Spoink, that has invaded D. melanogaster. It is a 5216nt LTR retrotransposon of the Ty3/gypsy superfamily. Relying on strains sampled at different times during the last century we show that Spoink invaded worldwide D. melanogaster populations after the P-element between 1983 and 1993. This invasion was likely triggered by a horizontal transfer from the D. willistoni group, much as the P-element. Spoink is probably silenced by the piRNA pathway in natural populations and about 1/3 of the examined strains have an insertion into a canonical piRNA cluster such as 42AB. Given the degree of genetic investigation of D. melanogaster it is perhaps surprising that Spoink was able to invade unnoticed.
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Affiliation(s)
- Riccardo Pianezza
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Almorò Scarpa
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
- Vienna Graduate School of Population Genetics, Vetmeduni Vienna, Vienna, Austria
| | - Prakash Narayanan
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Sarah Signor
- Biological Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Robert Kofler
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria
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4
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Escamilla DM, Dietz N, Bilyeu K, Hudson K, Rainey KM. Genome-wide association study reveals GmFulb as candidate gene for maturity time and reproductive length in soybeans (Glycine max). PLoS One 2024; 19:e0294123. [PMID: 38241340 PMCID: PMC10798547 DOI: 10.1371/journal.pone.0294123] [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: 04/06/2023] [Accepted: 10/25/2023] [Indexed: 01/21/2024] Open
Abstract
The ability of soybean [Glycine max (L.) Merr.] to adapt to different latitudes is attributed to genetic variation in major E genes and quantitative trait loci (QTLs) determining flowering time (R1), maturity (R8), and reproductive length (RL). Fully revealing the genetic basis of R1, R8, and RL in soybeans is necessary to enhance genetic gains in soybean yield improvement. Here, we performed a genome-wide association analysis (GWA) with 31,689 single nucleotide polymorphisms (SNPs) to detect novel loci for R1, R8, and RL using a soybean panel of 329 accessions with the same genotype for three major E genes (e1-as/E2/E3). The studied accessions were grown in nine environments and observed for R1, R8 and RL in all environments. This study identified two stable peaks on Chr 4, simultaneously controlling R8 and RL. In addition, we identified a third peak on Chr 10 controlling R1. Association peaks overlap with previously reported QTLs for R1, R8, and RL. Considering the alternative alleles, significant SNPs caused RL to be two days shorter, R1 two days later and R8 two days earlier, respectively. We identified association peaks acting independently over R1 and R8, suggesting that trait-specific minor effect loci are also involved in controlling R1 and R8. From the 111 genes highly associated with the three peaks detected in this study, we selected six candidate genes as the most likely cause of R1, R8, and RL variation. High correspondence was observed between a modifying variant SNP at position 04:39294836 in GmFulb and an association peak on Chr 4. Further studies using map-based cloning and fine mapping are necessary to elucidate the role of the candidates we identified for soybean maturity and adaptation to different latitudes and to be effectively used in the marker-assisted breeding of cultivars with optimal yield-related traits.
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Affiliation(s)
- Diana M. Escamilla
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
| | - Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, Missouri, United States of America
| | - Kristin Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture (USDA)−Agricultural Research Service (ARS), Columbia, Missouri, United States of America
| | - Karen Hudson
- USDA-ARS Crop Production and Pest Control Research Unit, West Lafayette, Indiana, United States of America
| | - Katy Martin Rainey
- Department of Agronomy, Purdue University, West Lafayette, Indiana, United States of America
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5
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Kreiner JM, Hnatovska S, Stinchcombe JR, Wright SI. Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus. PLoS Genet 2023; 19:e1010865. [PMID: 38150485 PMCID: PMC10775983 DOI: 10.1371/journal.pgen.1010865] [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: 07/12/2023] [Revised: 01/09/2024] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
Genome size variation, largely driven by repeat content, is poorly understood within and among populations, limiting our understanding of its significance for adaptation. Here we characterize intraspecific variation in genome size and repeat content across 186 individuals of Amaranthus tuberculatus, a ubiquitous native weed that shows flowering time adaptation to climate across its range and in response to agriculture. Sequence-based genome size estimates vary by up to 20% across individuals, consistent with the considerable variability in the abundance of transposable elements, unknown repeats, and rDNAs across individuals. The additive effect of this variation has important phenotypic consequences-individuals with more repeats, and thus larger genomes, show slower flowering times and growth rates. However, compared to newly-characterized gene copy number and polygenic nucleotide changes underlying variation in flowering time, we show that genome size is a marginal contributor. Differences in flowering time are reflected by genome size variation across sexes and marginally, habitats, while polygenic variation and a gene copy number variant within the ATP synthesis pathway show consistently stronger environmental clines than genome size. Repeat content nonetheless shows non-neutral distributions across the genome, and across latitudinal and environmental gradients, demonstrating the numerous governing processes that in turn influence quantitative genetic variation for phenotypes key to plant adaptation.
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Affiliation(s)
- Julia M. Kreiner
- Department of Botany, Biodiversity Research Centre, University of British Columbia
- Department of Ecology & Evolutionary Biology, University of Toronto
| | - Solomiya Hnatovska
- Department of Ecology & Evolutionary Biology, University of Toronto
- Department of Molecular Genetics, University of Toronto
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6
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Williams BR, Miller AJ, Edwards CE. How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity. Mol Ecol Resour 2023. [PMID: 37988186 DOI: 10.1111/1755-0998.13897] [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: 12/20/2022] [Revised: 10/20/2023] [Accepted: 11/01/2023] [Indexed: 11/23/2023]
Abstract
Many threatened plants have low genetic diversity, which may reduce their capacity for genetically based adaptation, increasing their extinction risk. Non-genetic variation (e.g. epigenomic modifications such as DNA methylation) and plasticity may facilitate the persistence of threatened plants, yet are rarely incorporated into conservation assessments. We present a case study investigating variation and plasticity in DNA methylation and phenotypic traits in four genetically depauperate species of Leavenworthia (Brassicaceae), including one widespread species and one asexual, threatened species. We grew individuals from several maternal lines and populations per species in contrasting watering treatments, measured phenotypic traits and analysed DNA methylation using whole-genome bisulphite sequencing. We addressed four questions: (1) How do patterns of DNA methylation differ within and among species? (2) Within species, how do phenotypic traits and patterns of DNA methylation vary in response to drought? (3) Does variation in DNA methylation correspond to phenotypic variation? (4) What are the implications for conservation? We found that taxa were epigenomically distinct and that each species exhibited variation in DNA methylation among populations that could be relevant for conservation. Within species, the DNA methylation response to environmental stress corresponded to its phenotypic response. Species differed in their DNA methylation and phenotypic responses to environmental stress, with the extent of plasticity possibly related to species geographic range size. We also found phenotypic and DNA methylation variation in the asexual, threatened species that may be relevant for conservation. Our results suggest that variation in DNA methylation may promote the persistence of genetically depauperate threatened plants, highlighting its potential as a novel conservation target to reduce extinction risk.
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Affiliation(s)
- Brigette R Williams
- Missouri Botanical Garden, Center for Conservation and Sustainable Development, St. Louis, Missouri, USA
- Department of Biology, Saint Louis University, St. Louis, Missouri, USA
| | - Allison J Miller
- Department of Biology, Saint Louis University, St. Louis, Missouri, USA
- Donald Danforth Plant Science Center, St. Louis, Missouri, USA
| | - Christine E Edwards
- Missouri Botanical Garden, Center for Conservation and Sustainable Development, St. Louis, Missouri, USA
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7
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Wang W, Zhang X, Garcia S, Leitch AR, Kovařík A. Intragenomic rDNA variation - the product of concerted evolution, mutation, or something in between? Heredity (Edinb) 2023; 131:179-188. [PMID: 37402824 PMCID: PMC10462631 DOI: 10.1038/s41437-023-00634-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/12/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023] Open
Abstract
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
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Affiliation(s)
- Wencai Wang
- Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Xianzhi Zhang
- Department of Horticulture, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Sònia Garcia
- Institut Botànic de Barcelona, IBB (CSIC - Ajuntament de Barcelona), Barcelona, Spain
| | - Andrew R Leitch
- School of Biological and Behavioral Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Aleš Kovařík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61200, Czech Republic.
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8
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Hoffmann G, Shukla A, López-González S, Hafrén A. Cauliflower mosaic virus disease spectrum uncovers novel susceptibility factor NCED9 in Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4751-4764. [PMID: 37249342 PMCID: PMC10433934 DOI: 10.1093/jxb/erad204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 05/26/2023] [Indexed: 05/31/2023]
Abstract
Viruses are intimately linked with their hosts and especially dependent on gene-for-gene interactions to establish successful infections. On the host side, defence mechanisms such as tolerance and resistance can occur within the same species, leading to differing virus accumulation in relation to symptomology and plant fitness. The identification of novel resistance genes against viruses and susceptibility factors is an important part of understanding viral patho-genesis and securing food production. The model plant Arabidopsis thaliana displays a wide symptom spectrum in response to RNA virus infections, and unbiased genome-wide association studies have proven a powerful tool to identify novel disease-genes. In this study we infected natural accessions of A. thaliana with the pararetrovirus cauliflower mosaic virus (CaMV) to study the phenotypic variations between accessions and their correlation with virus accumulation. Through genome-wide association mapping of viral accumulation differences, we identified several susceptibility factors for CaMV, the strongest of which was the abscisic acid synthesis gene NCED9. Further experiments confirmed the importance of abscisic acid homeostasis and its disruption for CaMV disease.
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Affiliation(s)
- Gesa Hoffmann
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Aayushi Shukla
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Silvia López-González
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Anders Hafrén
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
- Linnean Center for Plant Biology, 75007 Uppsala, Sweden
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9
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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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10
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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11
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Delorme-Hinoux V, Mbodj A, Brando S, De Bures A, Llauro C, Covato F, Garrigue J, Guisset C, Borrut J, Mirouze M, Reichheld JP, Sáez-Vásquez J. 45S rDNA Diversity In Natura as One Step towards Ribosomal Heterogeneity in Arabidopsis thaliana. PLANTS (BASEL, SWITZERLAND) 2023; 12:2722. [PMID: 37514338 PMCID: PMC10386311 DOI: 10.3390/plants12142722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]
Abstract
The keystone of ribosome biogenesis is the transcription of 45S rDNA. The Arabidopsis thaliana genome contains hundreds of 45S rDNA units; however, they are not all transcribed. Notably, 45S rDNA units contain insertions/deletions revealing the existence of heterogeneous rRNA genes and, likely, heterogeneous ribosomes for rRNAs. In order to obtain an overall picture of 45S rDNA diversity sustaining the synthesis of rRNAs and, subsequently, of ribosomes in natura, we took advantage of 320 new occurrences of Arabidopsis thaliana as a metapopulation named At66, sampled from 0 to 1900 m of altitude in the eastern Pyrenees in France. We found that the 45S rDNA copy number is very dynamic in natura and identified new genotypes for both 5' and 3' External Transcribed Spacers (ETS). Interestingly, the highest 5'ETS genotype diversity is found in altitude while the highest 3'ETS genotype diversity is found at sea level. Structural analysis of 45S rDNA also shows conservation in natura of specific 5'ETS and 3'ETS sequences/features required to control rDNA expression and the processing of rRNAs. In conclusion, At66 is a worthwhile natural laboratory, and unraveled 45S rDNA diversity represents an interesting starting material to select subsets for rDNA transcription and alter the rRNA composition of ribosomes both intra- and inter-site.
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Affiliation(s)
- Valérie Delorme-Hinoux
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Association Charles Flahault, 66350 Toulouges, France
| | - Assane Mbodj
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Institut de Recherche pour le Développement (IRD), ECOBIO, 34000 Montpellier, France
| | - Sophie Brando
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Anne De Bures
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Christel Llauro
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
| | - Fabrice Covato
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | - Joseph Garrigue
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | - Claude Guisset
- Association Charles Flahault, 66350 Toulouges, France
- FRNC, Fédération des Réserves Naturelles Catalanes, 66500 Prades, France
| | | | - Marie Mirouze
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- EMR LGDP/MANGO, Mechanisms of Adaptation and Genomics, IRD-CNRS-UPVD, 66860 Perpignan, France
- Institut de Recherche pour le Développement (IRD), ECOBIO, 34000 Montpellier, France
| | - Jean-Philippe Reichheld
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
| | - Julio Sáez-Vásquez
- Université de Perpignan Via Domitia (UPVD), Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
- Centre National de la Recherche Scientifique, Laboratoire Génome et Développement des Plantes (LGDP), UMR 5096, 66860 Perpignan, France
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12
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Kolesnikova UK, Scott AD, Van de Velde JD, Burns R, Tikhomirov NP, Pfordt U, Clarke AC, Yant L, Seregin AP, Vekemans X, Laurent S, Novikova PY. Transition to Self-compatibility Associated With Dominant S-allele in a Diploid Siberian Progenitor of Allotetraploid Arabidopsis kamchatica Revealed by Arabidopsis lyrata Genomes. Mol Biol Evol 2023; 40:msad122. [PMID: 37432770 PMCID: PMC10335350 DOI: 10.1093/molbev/msad122] [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: 07/13/2023] Open
Abstract
A transition to selfing can be beneficial when mating partners are scarce, for example, due to ploidy changes or at species range edges. Here, we explain how self-compatibility evolved in diploid Siberian Arabidopsis lyrata, and how it contributed to the establishment of allotetraploid Arabidopsis kamchatica. First, we provide chromosome-level genome assemblies for two self-fertilizing diploid A. lyrata accessions, one from North America and one from Siberia, including a fully assembled S-locus for the latter. We then propose a sequence of events leading to the loss of self-incompatibility in Siberian A. lyrata, date this independent transition to ∼90 Kya, and infer evolutionary relationships between Siberian and North American A. lyrata, showing an independent transition to selfing in Siberia. Finally, we provide evidence that this selfing Siberian A. lyrata lineage contributed to the formation of the allotetraploid A. kamchatica and propose that the selfing of the latter is mediated by the loss-of-function mutation in a dominant S-allele inherited from A. lyrata.
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Affiliation(s)
- Uliana K Kolesnikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Alison Dawn Scott
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Jozefien D Van de Velde
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Robin Burns
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
| | - Nikita P Tikhomirov
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Ursula Pfordt
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Andrew C Clarke
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington, United Kingdom
| | - Levi Yant
- Future Food Beacon of Excellence and School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Alexey P Seregin
- Herbarium (MW), Faculty of Biology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Xavier Vekemans
- University Lille, CNRS, UMR 8198—Evo-Eco-Paleo, Lille, France
| | - Stefan Laurent
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Polina Yu Novikova
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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13
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Morton EA, Hall AN, Cuperus JT, Queitsch C. Substantial rDNA copy number reductions alter timing of development and produce variable tissue-specific phenotypes in C. elegans. Genetics 2023; 224:iyad039. [PMID: 36919976 PMCID: PMC10474940 DOI: 10.1093/genetics/iyad039] [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: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
The genes that encode ribosomal RNAs are present in several hundred copies in most eukaryotes. These vast arrays of repetitive ribosomal DNA (rDNA) have been implicated not just in ribosome biogenesis, but also aging, cancer, genome stability, and global gene expression. rDNA copy number is highly variable among and within species; this variability is thought to associate with traits relevant to human health and disease. Here we investigate the phenotypic consequences of multicellular life at the lower bounds of rDNA copy number. We use the model Caenorhabditis elegans, which has previously been found to complete embryogenesis using only maternally provided ribosomes. We find that individuals with rDNA copy number reduced to ∼5% of wild type are capable of further development with variable penetrance. Such individuals are sterile and exhibit severe morphological defects, particularly in post-embryonically dividing tissues such as germline and vulva. Developmental completion and fertility are supported by an rDNA copy number ∼10% of wild type, with substantially delayed development. Worms with rDNA copy number reduced to ∼33% of wild type display a subtle developmental timing defect that was absent in worms with higher copy numbers. Our results support the hypothesis that rDNA requirements vary across tissues and indicate that the minimum rDNA copy number for fertile adulthood is substantially less than the lowest naturally observed total copy number. The phenotype of individuals with severely reduced rDNA copy number is highly variable in penetrance and presentation, highlighting the need for continued investigation into the biological consequences of rDNA copy number variation.
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Affiliation(s)
| | - Ashley N Hall
- Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53726, USA
- Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA
| | - Josh T Cuperus
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Christine Queitsch
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
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14
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Gupta S, Harkess A, Soble A, Van Etten M, Leebens-Mack J, Baucom RS. Interchromosomal linkage disequilibrium and linked fitness cost loci associated with selection for herbicide resistance. THE NEW PHYTOLOGIST 2023; 238:1263-1277. [PMID: 36721257 DOI: 10.1111/nph.18782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
The adaptation of weeds to herbicide is both a significant problem in agriculture and a model of rapid adaptation. However, significant gaps remain in our knowledge of resistance controlled by many loci and the evolutionary factors that influence the maintenance of resistance. Here, using herbicide-resistant populations of the common morning glory (Ipomoea purpurea), we perform a multilevel analysis of the genome and transcriptome to uncover putative loci involved in nontarget-site herbicide resistance (NTSR) and to examine evolutionary forces underlying the maintenance of resistance in natural populations. We found loci involved in herbicide detoxification and stress sensing to be under selection and confirmed that detoxification is responsible for glyphosate (RoundUp) resistance using a functional assay. We identified interchromosomal linkage disequilibrium (ILD) among loci under selection reflecting either historical processes or additive effects leading to the resistance phenotype. We further identified potential fitness cost loci that were strongly linked to resistance alleles, indicating the role of genetic hitchhiking in maintaining the cost. Overall, our work suggests that NTSR glyphosate resistance in I. purpurea is conferred by multiple genes which are potentially maintained through generations via ILD, and that the fitness cost associated with resistance in this species is likely a by-product of genetic hitchhiking.
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Affiliation(s)
- Sonal Gupta
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, 10003, USA
| | - Alex Harkess
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Anah Soble
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
| | - Megan Van Etten
- Biology Department, Pennsylvania State University, Dunmore, PA, 18512, USA
| | - James Leebens-Mack
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Regina S Baucom
- Ecology and Evolutionary Biology Department, University of Michigan, 4034 Biological Sciences Building, Ann Arbor, MI, 48109, USA
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15
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Jaegle B, Pisupati R, Soto-Jiménez LM, Burns R, Rabanal FA, Nordborg M. Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity. Genome Biol 2023; 24:44. [PMID: 36895055 PMCID: PMC9999624 DOI: 10.1186/s13059-023-02875-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/13/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND It is apparent that genomes harbor much structural variation that is largely undetected for technical reasons. Such variation can cause artifacts when short-read sequencing data are mapped to a reference genome. Spurious SNPs may result from mapping of reads to unrecognized duplicated regions. Calling SNP using the raw reads of the 1001 Arabidopsis Genomes Project we identified 3.3 million (44%) heterozygous SNPs. Given that Arabidopsis thaliana (A. thaliana) is highly selfing, and that extensively heterozygous individuals have been removed, we hypothesize that these SNPs reflected cryptic copy number variation. RESULTS The heterozygosity we observe consists of particular SNPs being heterozygous across individuals in a manner that strongly suggests it reflects shared segregating duplications rather than random tracts of residual heterozygosity due to occasional outcrossing. Focusing on such pseudo-heterozygosity in annotated genes, we use genome-wide association to map the position of the duplicates. We identify 2500 putatively duplicated genes and validate them using de novo genome assemblies from six lines. Specific examples included an annotated gene and nearby transposon that transpose together. We also demonstrate that cryptic structural variation produces highly inaccurate estimates of DNA methylation polymorphism. CONCLUSIONS Our study confirms that most heterozygous SNP calls in A. thaliana are artifacts and suggest that great caution is needed when analyzing SNP data from short-read sequencing. The finding that 10% of annotated genes exhibit copy-number variation, and the realization that neither gene- nor transposon-annotation necessarily tells us what is actually mobile in the genome suggests that future analyses based on independently assembled genomes will be very informative.
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Affiliation(s)
- Benjamin Jaegle
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | - Rahul Pisupati
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
| | | | - Robin Burns
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria
- Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | | | - Magnus Nordborg
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Vienna, Austria.
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16
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Lopez FB, McKeown PC, Fort A, Brychkova G, Spillane C. The boys are back in town: Rethinking the function of ribosomal DNA repeats in the genomic era. MOLECULAR PLANT 2023; 16:514-516. [PMID: 36680344 DOI: 10.1016/j.molp.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 01/06/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Affiliation(s)
- Francesca B Lopez
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland.
| | - Peter C McKeown
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, University of Galway, H91 REW4 Galway, Ireland.
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17
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Hu Y, Wang X, Xu Y, Yang H, Tong Z, Tian R, Xu S, Yu L, Guo Y, Shi P, Huang S, Yang G, Shi S, Wei F. Molecular mechanisms of adaptive evolution in wild animals and plants. SCIENCE CHINA. LIFE SCIENCES 2023; 66:453-495. [PMID: 36648611 PMCID: PMC9843154 DOI: 10.1007/s11427-022-2233-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 01/18/2023]
Abstract
Wild animals and plants have developed a variety of adaptive traits driven by adaptive evolution, an important strategy for species survival and persistence. Uncovering the molecular mechanisms of adaptive evolution is the key to understanding species diversification, phenotypic convergence, and inter-species interaction. As the genome sequences of more and more non-model organisms are becoming available, the focus of studies on molecular mechanisms of adaptive evolution has shifted from the candidate gene method to genetic mapping based on genome-wide scanning. In this study, we reviewed the latest research advances in wild animals and plants, focusing on adaptive traits, convergent evolution, and coevolution. Firstly, we focused on the adaptive evolution of morphological, behavioral, and physiological traits. Secondly, we reviewed the phenotypic convergences of life history traits and responding to environmental pressures, and the underlying molecular convergence mechanisms. Thirdly, we summarized the advances of coevolution, including the four main types: mutualism, parasitism, predation and competition. Overall, these latest advances greatly increase our understanding of the underlying molecular mechanisms for diverse adaptive traits and species interaction, demonstrating that the development of evolutionary biology has been greatly accelerated by multi-omics technologies. Finally, we highlighted the emerging trends and future prospects around the above three aspects of adaptive evolution.
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Affiliation(s)
- Yibo Hu
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xiaoping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yongchao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hui Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zeyu Tong
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Ran Tian
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
| | - Yalong Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Peng Shi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Shuangquan Huang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Lab of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Fuwen Wei
- CAS Key Lab of Animal Ecology and Conservation Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
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18
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Pašakinskienė I. Festuca pratensis-like Subgenome Reassembly from a "Chromosomal Cocktail" in the Intergeneric Festulolium (Poaceae) Hybrid: A Rare Chromoanagenesis Event in Grasses. PLANTS (BASEL, SWITZERLAND) 2023; 12:984. [PMID: 36903845 PMCID: PMC10005718 DOI: 10.3390/plants12050984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Festuca and Lolium grass species are used for Festulolium hybrid variety production where they display trait complementarities. However, at the genome level, they show antagonisms and a broad scale of rearrangements. A rare case of an unstable hybrid, a donor plant manifesting pronounced variability of its clonal parts, was discovered in the F2 group of 682 plants of Lolium multiflorum × Festuca arundinacea (2n = 6x = 42). Five phenotypically distinct clonal plants were determined to be diploids, having only 14 chromosomes out of the 42 in the donor. GISH defined the diploids as having the basic genome from F. pratensis (2n = 2x = 14), one of the progenitors of F. arundinacea (2n = 6x = 42), with minor components from L. multiflorum and another subgenome, F. glaucescens. The 45S rDNA position on two chromosomes also corresponded to the variant of F. pratensis in the F. arundinacea parent. In the highly unbalanced donor genome, F. pratensis was the least represented, but the most involved in numerous recombinant chromosomes. Specifically, FISH highlighted 45S rDNA-containing clusters involved in the formation of unusual chromosomal associations in the donor plant, suggesting their active role in karyotype realignment. The results of this study show that F. pratensis chromosomes have a particular fundamental drive for restructuring, which prompts the disassembly/reassembly processes. The finding of F. pratensis "escaping" and rebuilding itself from the chaotic "chromosomal cocktail" of the donor plant points to a rare chromoanagenesis event and extends the view of plant genome plasticity.
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Affiliation(s)
- Izolda Pašakinskienė
- Life Sciences Centre, Vilnius University, Saulėtekio 7, 10221 Vilnius, Lithuania;
- Botanical Garden of Vilnius University, Kairėnų 43, 10239 Vilnius, Lithuania
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19
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Wu H, Su W, Shi M, Xue X, Ren H, Wang Y, Zhao A, Li D, Liu M. Genomic C-Value Variation Analysis in Jujube ( Ziziphus jujuba Mill.) in the Middle Yellow River Basin. PLANTS (BASEL, SWITZERLAND) 2023; 12:858. [PMID: 36840207 PMCID: PMC9962250 DOI: 10.3390/plants12040858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
Chinese jujube (Ziziphus jujuba Mill.) originated in the Yellow River basin (YRB) of the Shanxi-Shaanxi region. The genomic C-value is a crucial indicator for plant breeding and germplasm evaluation. In this study, we used flow cytometry to determine the genomic C-values of jujube germplasms in the YRB of the Shanxi-Shaanxi region and evaluated their differences in different sub-regions. Of the 29 sub-regions, the highest and lowest variations were in Linxian and Xiaxian, respectively. The difference between jujube germplasms was highly significant (F = 14.89, p < 0.0001) in Linxian. Cluster analysis showed that both cluster 2 and 4 belonged to Linxian, which were clearly separated from other taxa but were cross-distributed in them. Linxian County is an important gene exchange center in the YRB of the Shanxi-Shaanxi region. Principal component analysis showed that cluster 1 had low genomic C-values and single-fruit weights and cluster 2 had high genomic C-values and vitamin C contents. The genomic C-value was correlated with single-fruit weight and vitamin C content. In addition, the genomic C-value was used to predict fruit agronomic traits, providing a reference for shortening the breeding cycle and genetic diversity-related studies of jujube germplasm.
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Affiliation(s)
- Hao Wu
- Shanxi Key Laboratory of Fruit Germplasm Creation and Utilization, Institute of Fruit Trees, Agricultural University of Shanxi, Taiyuan 030031, China
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Wanlong Su
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Meijuan Shi
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Xiaofang Xue
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Haiyan Ren
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Yongkang Wang
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Ailing Zhao
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Dengke Li
- College of Horticulture, Taigu Campus, Agricultural University of Shanxi, Jinzhong 030800, China
| | - Mengjun Liu
- College of Horticulture, Baoding Campus, Agricultural University of Hebei, Baoding 071000, China
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20
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Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data. Methods Mol Biol 2023; 2545:279-295. [PMID: 36720819 DOI: 10.1007/978-1-0716-2561-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Whole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data are attractive. Here we describe two such approaches, where the first is based on distributions of allelic read depth at heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.
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21
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Christenhusz MJ, Twyford AD, Hudson A. The genome sequence of thale cress, Arabidopsis thaliana (Heynh., 1842). Wellcome Open Res 2023. [DOI: 10.12688/wellcomeopenres.18665.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We present a genome assembly of an Arabidopsis thaliana specimen (thale cress; Streptophyta; Magnoliopsida; Brassicales; Brassicaceae). The genome sequence spans 138 megabases. Most of the assembly (98.76%) is scaffolded into five chromosomal pseudomolecules. The mitochondrial and plastid genomes were also assembled and are 368.8 and 154.5 kilobases in length respectively.
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22
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Souilmi Y, Tobler R, Johar A, Williams M, Grey ST, Schmidt J, Teixeira JC, Rohrlach A, Tuke J, Johnson O, Gower G, Turney C, Cox M, Cooper A, Huber CD. Admixture has obscured signals of historical hard sweeps in humans. Nat Ecol Evol 2022; 6:2003-2015. [PMID: 36316412 PMCID: PMC9715430 DOI: 10.1038/s41559-022-01914-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 09/16/2022] [Indexed: 11/06/2022]
Abstract
The role of natural selection in shaping biological diversity is an area of intense interest in modern biology. To date, studies of positive selection have primarily relied on genomic datasets from contemporary populations, which are susceptible to confounding factors associated with complex and often unknown aspects of population history. In particular, admixture between diverged populations can distort or hide prior selection events in modern genomes, though this process is not explicitly accounted for in most selection studies despite its apparent ubiquity in humans and other species. Through analyses of ancient and modern human genomes, we show that previously reported Holocene-era admixture has masked more than 50 historic hard sweeps in modern European genomes. Our results imply that this canonical mode of selection has probably been underappreciated in the evolutionary history of humans and suggest that our current understanding of the tempo and mode of selection in natural populations may be inaccurate.
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Affiliation(s)
- Yassine Souilmi
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
| | - Raymond Tobler
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australian Capital Territory, Australia.
| | - Angad Johar
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Cardiovascular Diseases, Mayo Clinic, Rochester, MN, USA.
| | - Matthew Williams
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Shane T Grey
- Transplantation Immunology Group, Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Clinical School, Faculty of Medicine, UNSW, Darlinghurst, New South Wales, Australia
| | - Joshua Schmidt
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - João C Teixeira
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Adam Rohrlach
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jonathan Tuke
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, South Australia, Australia
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Olivia Johnson
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia
| | - Chris Turney
- Chronos 14Carbon-Cycle Facility and Earth and Sustainability Science Research Centre, University of New South Wales, Sydney, New South Wales, Australia
| | - Murray Cox
- Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Alan Cooper
- South Australian Museum, Adelaide, South Australia, Australia.
- BlueSky Genetics, Ashton, South Australia, Australia.
| | - Christian D Huber
- Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia, Australia.
- Department of Biology, Penn State University, University Park, PA, USA.
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23
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Lee DJ, Kwon T, Lee HJ, Oh YH, Kim JH, Lee TH. NGSpop: A desktop software that supports population studies by identifying sequence variations from next-generation sequencing data. PLoS One 2022; 17:e0260908. [PMCID: PMC9671411 DOI: 10.1371/journal.pone.0260908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 10/29/2022] [Indexed: 11/18/2022] Open
Abstract
Next-generation sequencing (NGS) is widely used in all areas of genetic research, such as genetic disease diagnosis and breeding, and it can produce massive amounts of data. The identification of sequence variants is an important step when processing large NGS datasets; however, currently, the process is complicated, repetitive, and requires concentration, which can be taxing on the researcher. Therefore, to support researchers who are not familiar enough with bioinformatics to identify sequence variations regularly from large datasets, we have developed a fully automated desktop software, NGSpop. NGSpop includes functionalities for all the variant calling and visualization procedures used when processing NGS data, such as quality control, mapping, filtering details, and variant calling. In the variant calling step, the user can select the GATK or DeepVariant algorithm for variant calling. These algorithms can be executed using pre-set pipelines and options or customized with the user-specified options. NGSpop is implemented using JavaFX (version 1.8) and can thus be run on Unix-like operating systems such as Ubuntu Linux (version 16.04, 18.0.4). Although several pipelines and visualization tools are available for NGS data analysis, most integrated environments do not support batch processes; thus, variant detection cannot be automated for population-level studies. The NGSpop software developed in this study has an easy-to-use interface and helps in rapid analysis of multiple NGS data from population studies. According to a benchmark test, it effectively reduced the carbon footprint in bioinformatics analysis by expending the least central processing unit heat and power. Additionally, this software makes it possible to use the GATK and DeepVariant algorithms more flexibly and efficiently than other programs by allowing users to choose between the algorithms. As a limitation, NGSpop currently supports only the sequencing reads in fastq format produced by the Illumina platform. NGSpop is freely available at https://sourceforge.net/projects/ngspop/.
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Affiliation(s)
- Dong-Jun Lee
- Genomics Division, National Institute of Agricultural Science, Jeonju, Republic of Korea
- * E-mail:
| | - Taesoo Kwon
- Corporate R&D Center, Cloud9, Cheongju-si, Republic of Korea
| | - Hye-Jin Lee
- Genomics Division, National Institute of Agricultural Science, Jeonju, Republic of Korea
| | - Yun-Ho Oh
- Genomics Division, National Institute of Agricultural Science, Jeonju, Republic of Korea
| | - Jin-Hyun Kim
- Genomics Division, National Institute of Agricultural Science, Jeonju, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Science, Jeonju, Republic of Korea
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24
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Leppälä J, Gaupels F, Xu E, Morales LO, Durner J, Brosché M. Ozone and nitrogen dioxide regulate similar gene expression responses in Arabidopsis but natural variation in the extent of cell death is likely controlled by different genetic loci. FRONTIERS IN PLANT SCIENCE 2022; 13:994779. [PMID: 36340361 PMCID: PMC9627343 DOI: 10.3389/fpls.2022.994779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
High doses of ozone (O3) and nitrogen dioxide (NO2) cause damage and cell death in plants. These two gases are among the most harmful air pollutants for ecosystems and therefore it is important to understand how plant resistance or sensitivity to these gases work at the molecular level and its genetic control. We compared transcriptome data from O3 and NO2 fumigations to other cell death related treatments, as well as individual marker gene transcript level in different Arabidopsis thaliana accessions. Our analysis revealed that O3 and NO2 trigger very similar gene expression responses that include genes involved in pathogen resistance, cell death and ethylene signaling. However, we also identified exceptions, for example RBOHF encoding a reactive oxygen species producing RESPIRATORY BURST OXIDASE PROTEIN F. This gene had increased transcript levels by O3 but decreased transcript levels by NO2, showing that plants can identify each of the gases separately and activate distinct signaling pathways. To understand the genetics, we conducted a genome wide association study (GWAS) on O3 and NO2 tolerance of natural Arabidopsis accessions. Sensitivity to both gases seem to be controlled by several independent small effect loci and we did not find an overlap in the significantly associated regions. Further characterization of the GWAS candidate loci identified new regulators of O3 and NO2 induced cell death including ABH1, a protein that functions in abscisic acid signaling, mRNA splicing and miRNA processing. The GWAS results will facilitate further characterization of the control of programmed cell death and differences between oxidative and nitrosative stress in plants.
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Affiliation(s)
- Johanna Leppälä
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Frank Gaupels
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Enjun Xu
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Luis O. Morales
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Jörg Durner
- Institute of Biochemical Plant Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Mikael Brosché
- Organismal and Evolutionary Biology Research Programme, Viikki Plant Science Centre, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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25
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Arteaga N, Méndez‐Vigo B, Fuster‐Pons A, Savic M, Murillo‐Sánchez A, Picó FX, Alonso‐Blanco C. Differential environmental and genomic architectures shape the natural diversity for trichome patterning and morphology in different Arabidopsis organs. PLANT, CELL & ENVIRONMENT 2022; 45:3018-3035. [PMID: 35289421 PMCID: PMC9541492 DOI: 10.1111/pce.14308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Despite the adaptive and taxonomic relevance of the natural diversity for trichome patterning and morphology, the molecular and evolutionary mechanisms underlying these traits remain mostly unknown, particularly in organs other than leaves. In this study, we address the ecological, genetic and molecular bases of the natural variation for trichome patterning and branching in multiple organs of Arabidopsis (Arabidopsis thaliana). To this end, we characterized a collection of 191 accessions and carried out environmental and genome-wide association (GWA) analyses. Trichome amount in different organs correlated negatively with precipitation in distinct seasons, thus suggesting a precise fit between trichome patterning and climate throughout the Arabidopsis life cycle. In addition, GWA analyses showed small overlapping between the genes associated with different organs, indicating partly independent genetic bases for vegetative and reproductive phases. These analyses identified a complex locus on chromosome 2, where two adjacent MYB genes (ETC2 and TCL1) displayed differential effects on trichome patterning in several organs. Furthermore, analyses of transgenic lines carrying different natural alleles demonstrated that TCL1 accounts for the variation for trichome patterning in all organs, and for stem trichome branching. By contrast, two other MYB genes (TRY and GL1), mainly showed effects on trichome patterning or branching, respectively.
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Affiliation(s)
- Noelia Arteaga
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Belén Méndez‐Vigo
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Alberto Fuster‐Pons
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Marija Savic
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Alba Murillo‐Sánchez
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - F. Xavier Picó
- Departamento de Ecología Integrativa, Estación Biológica de Doñana (EBD)Consejo Superior de Investigaciones Científicas (CSIC)SevillaSpain
| | - Carlos Alonso‐Blanco
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
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26
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LaRue T, Lindner H, Srinivas A, Exposito-Alonso M, Lobet G, Dinneny JR. Uncovering natural variation in root system architecture and growth dynamics using a robotics-assisted phenomics platform. eLife 2022; 11:76968. [PMID: 36047575 PMCID: PMC9499532 DOI: 10.7554/elife.76968] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022] Open
Abstract
The plant kingdom contains a stunning array of complex morphologies easily observed above-ground, but more challenging to visualize below-ground. Understanding the magnitude of diversity in root distribution within the soil, termed root system architecture (RSA), is fundamental in determining how this trait contributes to species adaptation in local environments. Roots are the interface between the soil environment and the shoot system and therefore play a key role in anchorage, resource uptake, and stress resilience. Previously, we presented the GLO-Roots (Growth and Luminescence Observatory for Roots) system to study the RSA of soil-grown Arabidopsis thaliana plants from germination to maturity (Rellán-Álvarez et al., 2015). In this study, we present the automation of GLO-Roots using robotics and the development of image analysis pipelines in order to examine the temporal dynamic regulation of RSA and the broader natural variation of RSA in Arabidopsis, over time. These datasets describe the developmental dynamics of two independent panels of accessions and reveal highly complex and polygenic RSA traits that show significant correlation with climate variables of the accessions’ respective origins.
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Affiliation(s)
- Therese LaRue
- Department of Biology, Stanford University, Stanford, United States
| | - Heike Lindner
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | - Ankit Srinivas
- Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
| | | | - Guillaume Lobet
- Agrosphere Institute, Forschungszentrum Jülich, Jülich, Germany
| | - José R Dinneny
- Department of Biology, Stanford University, Stanford, United States
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27
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Hou X, Wang D, Cheng Z, Wang Y, Jiao Y. A near-complete assembly of an Arabidopsis thaliana genome. MOLECULAR PLANT 2022; 15:1247-1250. [PMID: 35655433 DOI: 10.1016/j.molp.2022.05.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/24/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Affiliation(s)
- Xueren Hou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Depeng Wang
- GrandOmics Biosciences, Beijing 102200, China
| | - Zhukuan Cheng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Wang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing 100871, China.
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28
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Becher H, Sampson J, Twyford AD. Measuring the Invisible: The Sequences Causal of Genome Size Differences in Eyebrights ( Euphrasia) Revealed by k-mers. FRONTIERS IN PLANT SCIENCE 2022; 13:818410. [PMID: 35968114 PMCID: PMC9372453 DOI: 10.3389/fpls.2022.818410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Genome size variation within plant taxa is due to presence/absence variation, which may affect low-copy sequences or genomic repeats of various frequency classes. However, identifying the sequences underpinning genome size variation is challenging because genome assemblies commonly contain collapsed representations of repetitive sequences and because genome skimming studies by design miss low-copy number sequences. Here, we take a novel approach based on k-mers, short sub-sequences of equal length k, generated from whole-genome sequencing data of diploid eyebrights (Euphrasia), a group of plants that have considerable genome size variation within a ploidy level. We compare k-mer inventories within and between closely related species, and quantify the contribution of different copy number classes to genome size differences. We further match high-copy number k-mers to specific repeat types as retrieved from the RepeatExplorer2 pipeline. We find genome size differences of up to 230Mbp, equivalent to more than 20% genome size variation. The largest contributions to these differences come from rDNA sequences, a 145-nt genomic satellite and a repeat associated with an Angela transposable element. We also find size differences in the low-copy number class (copy number ≤ 10×) of up to 27 Mbp, possibly indicating differences in gene space between our samples. We demonstrate that it is possible to pinpoint the sequences causing genome size variation within species without the use of a reference genome. Such sequences can serve as targets for future cytogenetic studies. We also show that studies of genome size variation should go beyond repeats if they aim to characterise the full range of genomic variants. To allow future work with other taxonomic groups, we share our k-mer analysis pipeline, which is straightforward to run, relying largely on standard GNU command line tools.
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Affiliation(s)
- Hannes Becher
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Jacob Sampson
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alex D. Twyford
- School of Biological Sciences, Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
- Royal Botanic Garden Edinburgh, Edinburgh, United Kingdom
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29
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Plant genetic effects on microbial hubs impact host fitness in repeated field trials. Proc Natl Acad Sci U S A 2022; 119:e2201285119. [PMID: 35867817 PMCID: PMC9335298 DOI: 10.1073/pnas.2201285119] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent demonstrations of a genetic basis for variation among hosts in the microbiome leave unresolved the question of how commonly host genetic effects influence individual microbes, and whether these effects impact host fitness. We used replicated field studies in the north and south of Sweden to map host genetic effects in microbial community networks using genome-wide association mapping. By focusing on consistent effects across sites, we found effects of genetic variation on important microbial hubs that contributed to plant fitness in a manner robust to the environment. Our results suggest that ongoing efforts to harness host genotype effects on the microbiome for agricultural purposes can be successful and highlight the value of explicitly considering abiotic variation in those efforts. Although complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. In addition, host genetic effects on microbial communities vary widely depending on the environment, obscuring conclusions about which microbes are impacted and which plant functions are important. We characterized the leaf microbiota of 200 Arabidopsis thaliana genotypes in eight field experiments and detected consistent host effects on specific, broadly distributed microbial species (operational taxonomic unit [OTUs]). Host genetic effects disproportionately influenced central ecological hubs, with heritability of particular OTUs declining with their distance from the nearest hub within the microbial network. These host effects could reflect either OTUs preferentially associating with specific genotypes or differential microbial success within them. Host genetics associated with microbial hubs explained over 10% of the variation in lifetime seed production among host genotypes across sites and years. We successfully cultured one of these microbial hubs and demonstrated its growth-promoting effects on plants in sterile conditions. Finally, genome-wide association mapping identified many putatively causal genes with small effects on the relative abundance of microbial hubs across sites and years, and these genes were enriched for those involved in the synthesis of specialized metabolites, auxins, and the immune system. Using untargeted metabolomics, we corroborate the consistent association between variation in specialized metabolites and microbial hubs across field sites. Together, our results reveal that host genetic variation impacts the microbial communities in consistent ways across environments and that these effects contribute to fitness variation among host genotypes.
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30
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Chen Z, Guan Y, Han M, Guo Y, Zhang J, Guo Z, Sun G, Yan X. Altitudinal Patterns in Adaptive Evolution of Genome Size and Inter-Genome Hybridization Between Three Elymus Species From the Qinghai–Tibetan Plateau. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.923967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genome size variation and hybridization occur frequently within or between plant species under diverse environmental conditions, which enrich species diversification and drive the evolutionary process. Elymus L. is the largest genus in Triticeae with five recognized basic genomes (St, H, P, W, and Y). However, the data on population cytogenetics of Elymus species are sparse, especially whether genome hybridization and chromosomal structure can be affected by altitude are still unknown. In order to explore the relationship between genome sizes, we studied interspecific hybridization and altitude of Elymus species at population genetic and cytological levels. Twenty-seven populations at nine different altitudes (2,800–4,300 m) of three Elymus species, namely, hexaploid E. nutans (StHY, 2n = 6x = 42), tetraploid E. burchan-buddae (StY, 2n = 4x = 28), and E. sibiricus (StH, 2n = 4x = 28), were sampled from the Qinghai–Tibetan Plateau (QTP) to estimate whether intraspecific variation could affect the genomic relationships by genomic in situ hybridization (GISH), and quantify the genome size of Elymus among different altitude ecological groups by flow cytometry. The genome size of E. nutans, E. burchan-buddae, and E. sibiricus varied from 12.38 to 22.33, 8.81 to 18.93, and 11.46 to 20.96 pg/2C with the averages of 19.59, 12.39, and 16.85 pg/2C, respectively. The curve regression analysis revealed a strong correlation between altitude and nuclear DNA content in three Elymus species. In addition, the chromosomes of the St and Y genomes demonstrated higher polymorphism than that of the H genome. Larger genome size variations occurred in the mid-altitude populations (3,900–4,300 m) compared with other-altitude populations, suggesting a notable altitudinal pattern in genome size variation, which shaped genome evolution by altitude. This result supports our former hypothesis that genetic richness center at medium altitude is useful and valuable for species adaptation to highland environmental conditions, germplasm utilization, and conservation.
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31
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Genetic diversity analysis and marker-trait associations in Amaranthus species. PLoS One 2022; 17:e0267752. [PMID: 35551526 PMCID: PMC9098028 DOI: 10.1371/journal.pone.0267752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 04/15/2022] [Indexed: 11/26/2022] Open
Abstract
Amaranth (Amaranthus spp.) is a highly nutritious, underutilized vegetable and pseudo-cereal crop. It possesses diverse abiotic stress tolerance traits, is genetically diverse and highly phenotypically plastic, making it an ideal crop to thrive in a rapidly changing climate. Despite considerable genetic diversity there is a lack of detailed characterization of germplasm or population structures. The present study utilized the DArTSeq platform to determine the genetic relationships and population structure between 188 amaranth accessions from 18 agronomically important vegetable, grain, and weedy species. A total of 74, 303 SNP alleles were generated of which 63, 821 were physically mapped to the genome of the grain species A. hypochondriacus. Population structure was inferred in two steps. First, all 188 amaranth accessions comprised of 18 species and second, only 120 A. tricolor accessions. After SNP filtering, a total of 8,688 SNPs were generated on 181 amaranth accessions of 16 species and 9,789 SNPs generated on 118 A. tricolor accessions. Both SNP datasets produced three major sub-populations (K = 3) and generate consistent taxonomic classification of the amaranth sub-genera (Amaranthus Amaranthus, Amaranthus Acnida and Amaranthus albersia), although the accessions were poorly demarcated by geographical origin and morphological traits. A. tricolor accessions were well discriminated from other amaranth species. A genome-wide association study (GWAS) of 10 qualitative traits revealed an association between specific phenotypes and genetic variants within the genome and identified 22 marker trait associations (MTAs) and 100 MTAs (P≤0.01, P≤0.001) on 16 amaranth species and 118 A.tricolor datasets, respectively. The release of SNP markers from this panel has produced invaluable preliminary genetic information for phenotyping and cultivar improvement in amaranth species.
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32
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Castillo-Bravo R, Fort A, Cashell R, Brychkova G, McKeown PC, Spillane C. Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:835219. [PMID: 35330872 PMCID: PMC8940307 DOI: 10.3389/fpls.2022.835219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 05/05/2023]
Abstract
Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.
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33
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Bush SJ, Murren CJ, Urrutia AO, Kover PX. Contrasting gene-level signatures of selection with reproductive fitness. Mol Ecol 2021; 31:1515-1526. [PMID: 34918851 PMCID: PMC9304172 DOI: 10.1111/mec.16329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 11/29/2021] [Accepted: 12/09/2021] [Indexed: 11/30/2022]
Abstract
Selection leaves signatures in the DNA sequence of genes, with many test statistics devised to detect its action. While these statistics are frequently used to support hypotheses about the adaptive significance of particular genes, the effect these genes have on reproductive fitness is rarely quantified experimentally. Consequently, it is unclear how gene-level signatures of selection are associated with empirical estimates of gene effect on fitness. Eukaryotic datasets that permit this comparison are very limited. Using the model plant Arabidopsis thaliana, for which these resources are available, we calculated seven gene-level substitution and polymorphism-based statistics commonly used to infer selection (dN/dS, NI, DOS, Tajima's D, Fu and Li's D*, Fay and Wu's H, and Zeng's E) and, using knockout lines, compared these to gene-level estimates of effect on fitness. We found that consistent with expectations, essential genes were more likely to be classified as negatively selected. By contrast, using 379 Arabidopsis genes for which data was available, we found no evidence that genes predicted to be positively selected had a significantly different effect on fitness than genes evolving more neutrally. We discuss these results in the context of the analytic challenges posed by Arabidopsis, one of the only systems in which this study could be conducted, and advocate for examination in additional systems. These results are relevant to the evaluation of genome-wide studies across species where experimental fitness data is unavailable, as well as highlighting an increasing need for the latter.
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Affiliation(s)
- Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Courtney J Murren
- Department of Biology, College of Charleston, Charleston, SC, USA, 29424
| | - Araxi O Urrutia
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK.,Instituto de Ecologia, UNAM, Ciudad de Mexico, 04510, Mexico
| | - Paula X Kover
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
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Yi C, Wang X, Chen Q, Callahan DL, Fournier-Level A, Whelan J, Jost R. Diverse phosphate and auxin transport loci distinguish phosphate tolerant from sensitive Arabidopsis accessions. PLANT PHYSIOLOGY 2021; 187:2656-2673. [PMID: 34636851 PMCID: PMC8644285 DOI: 10.1093/plphys/kiab441] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/18/2021] [Indexed: 05/11/2023]
Abstract
Phosphorus (P) is an essential element for plant growth often limiting agroecosystems. To identify genetic determinants of performance under variable phosphate (Pi) supply, we conducted genome-wide association studies on five highly predictive Pi starvation response traits in 200 Arabidopsis (Arabidopsis thaliana) accessions. Pi concentration in Pi-limited organs had the strongest, and primary root length had the weakest genetic component. Of 70 trait-associated candidate genes, 17 responded to Pi withdrawal. The PHOSPHATE TRANSPORTER1 gene cluster on chromosome 5 comprises PHT1;1, PHT1;2, and PHT1;3 with known impact on P status. A second locus featured uncharacterized endomembrane-associated auxin efflux carrier encoding PIN-LIKES7 (PILS7) which was more strongly suppressed in Pi-limited roots of Pi-starvation sensitive accessions. In the Col-0 background, Pi uptake and organ growth were impaired in both Pi-limited pht1;1 and two pils7 T-DNA insertion mutants, while Pi -limited pht1;2 had higher biomass and pht1;3 was indistinguishable from wild-type. Copy number variation at the PHT1 locus with loss of the PHT1;3 gene and smaller scale deletions in PHT1;1 and PHT1;2 predicted to alter both protein structure and function suggest diversification of PHT1 is a key driver for adaptation to P limitation. Haplogroup analysis revealed a phosphorylation site in the protein encoded by the PILS7 allele from stress-sensitive accessions as well as additional auxin-responsive elements in the promoter of the "stress tolerant" allele. The former allele's inability to complement the pils7-1 mutant in the Col-0 background implies the presence of a kinase signaling loop controlling PILS7 activity in accessions from P-rich environments, while survival in P-poor environments requires fine-tuning of stress-responsive root auxin signaling.
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Affiliation(s)
- Changyu Yi
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Xinchao Wang
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Zhejiang 31008, China
| | - Qian Chen
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Damien L Callahan
- Centre for Chemistry and Biotechnology, School of Life and Environmental Sciences, Deakin University (Burwood Campus), Burwood VIC 3125, Australia
| | | | - James Whelan
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
| | - Ricarda Jost
- Department of Animal, Plant and Soil Sciences and La Trobe Institute for Agriculture and Food (LIAF), ARC Centre of Excellence in Plant Energy Biology, School of Life Sciences, La Trobe University, Bundoora VIC 3086, Australia
- Author for communication:
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35
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2D morphometric analysis of Arabidopsis thaliana nuclei reveals characteristic profiles of different cell types and accessions. Chromosome Res 2021; 30:5-24. [PMID: 34665365 PMCID: PMC8942920 DOI: 10.1007/s10577-021-09673-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/19/2021] [Accepted: 09/22/2021] [Indexed: 11/21/2022]
Abstract
Functional changes of cells upon developmental switches and in response to environmental cues are often reflected in nuclear phenotypes, showing distinctive chromatin states corresponding to transcriptional changes. Such characteristic nuclear shapes have been microscopically monitored and can be quantified after differential staining of euchromatin and heterochromatin domains. Here, we examined several nuclear parameters (size, DNA content, DNA density, chromatin compaction, relative heterochromatin fraction (RHF), and number of chromocenters) in relation to spatial distribution of genes and transposon elements (TEs), using standard 2D fluorescence microscopy. We provide nuclear profiles for different cell types and different accessions of Arabidopsis thaliana. A variable, yet significant, fraction of TEs was found outside chromocenters in all cell types, except for guard cells. The latter cell type features nuclei with the highest level of chromatin compaction, while their chromocenters seem to contain gene-rich regions. The highest number of parameter correlations was found in the accession Cvi, whereas Ler showed only few correlations. This may point at differences in phenotype robustness between accessions. The significantly high association of NOR chromocenters in accessions Ws and Cvi corresponds to their low RHF level.
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Oggenfuss U, Badet T, Wicker T, Hartmann FE, Singh NK, Abraham L, Karisto P, Vonlanthen T, Mundt C, McDonald BA, Croll D. A population-level invasion by transposable elements triggers genome expansion in a fungal pathogen. eLife 2021; 10:e69249. [PMID: 34528512 PMCID: PMC8445621 DOI: 10.7554/elife.69249] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Genome evolution is driven by the activity of transposable elements (TEs). The spread of TEs can have deleterious effects including the destabilization of genome integrity and expansions. However, the precise triggers of genome expansions remain poorly understood because genome size evolution is typically investigated only among deeply divergent lineages. Here, we use a large population genomics dataset of 284 individuals from populations across the globe of Zymoseptoria tritici, a major fungal wheat pathogen. We built a robust map of genome-wide TE insertions and deletions to track a total of 2456 polymorphic loci within the species. We show that purifying selection substantially depressed TE frequencies in most populations, but some rare TEs have recently risen in frequency and likely confer benefits. We found that specific TE families have undergone a substantial genome-wide expansion from the pathogen's center of origin to more recently founded populations. The most dramatic increase in TE insertions occurred between a pair of North American populations collected in the same field at an interval of 25 years. We find that both genome-wide counts of TE insertions and genome size have increased with colonization bottlenecks. Hence, the demographic history likely played a major role in shaping genome evolution within the species. We show that both the activation of specific TEs and relaxed purifying selection underpin this incipient expansion of the genome. Our study establishes a model to recapitulate TE-driven genome evolution over deeper evolutionary timescales.
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Affiliation(s)
- Ursula Oggenfuss
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Badet
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Thomas Wicker
- Institute for Plant and Microbial Biology, University of ZurichZurichSwitzerland
| | - Fanny E Hartmann
- Ecologie Systématique Evolution, Bâtiment 360, Univ. Paris-Sud, AgroParisTech, CNRS, Université Paris-SaclayOrsayFrance
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Nikhil Kumar Singh
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Leen Abraham
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
| | - Petteri Karisto
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Tiziana Vonlanthen
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Christopher Mundt
- Department of Botany and Plant Pathology, Oregon State UniversityCorvallisUnited States
| | - Bruce A McDonald
- Plant Pathology, Institute of Integrative Biology, ETH ZurichZurichSwitzerland
| | - Daniel Croll
- Laboratory of Evolutionary Genetics, Institute of Biology, University of NeuchâtelNeuchatelSwitzerland
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Becher H, Powell RF, Brown MR, Metherell C, Pellicer J, Leitch IJ, Twyford AD. The nature of intraspecific and interspecific genome size variation in taxonomically complex eyebrights. ANNALS OF BOTANY 2021; 128:639-651. [PMID: 34318876 PMCID: PMC8422891 DOI: 10.1093/aob/mcab102] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND AND AIMS Genome size varies considerably across the diversity of plant life. Although genome size is, by definition, affected by genetic presence/absence variants, which are ubiquitous in population sequencing studies, genome size is often treated as an intrinsic property of a species. Here, we studied intra- and interspecific genome size variation in taxonomically complex British eyebrights (Euphrasia, Orobanchaceae). Our aim is to document genome size diversity and investigate underlying evolutionary processes shaping variation between individuals, populations and species. METHODS We generated genome size data for 192 individuals of diploid and tetraploid Euphrasia and analysed genome size variation in relation to ploidy, taxonomy, population affiliation and geography. We further compared the genomic repeat content of 30 samples. KEY RESULTS We found considerable intraspecific genome size variation, and observed isolation-by-distance for genome size in outcrossing diploids. Tetraploid Euphrasia showed contrasting patterns, with genome size increasing with latitude in outcrossing Euphrasia arctica, but with little genome size variation in the highly selfing Euphrasia micrantha. Interspecific differences in genome size and the genomic proportions of repeat sequences were small. CONCLUSIONS We show the utility of treating genome size as the outcome of polygenic variation. Like other types of genetic variation, such as single nucleotide polymorphisms, genome size variation may be affected by ongoing hybridization and the extent of population subdivision. In addition to selection on associated traits, genome size is predicted to be affected indirectly by selection due to pleiotropy of the underlying presence/absence variants.
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Affiliation(s)
- Hannes Becher
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Max R Brown
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Wellcome Trust Genome Campus, Hinxton, Saffron Walden, UK
| | - Chris Metherell
- Botanical Society of Britain and Ireland, Harpenden, Hertfordshire, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Barcelona, Spain
| | | | - Alex D Twyford
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
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38
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Wang B, Yang X, Jia Y, Xu Y, Jia P, Dang N, Wang S, Xu T, Zhao X, Gao S, Dong Q, Ye K. High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads. GENOMICS, PROTEOMICS & BIOINFORMATICS 2021; 20:4-13. [PMID: 34487862 PMCID: PMC9510872 DOI: 10.1016/j.gpb.2021.08.003] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/18/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023]
Abstract
Arabidopsis thaliana is an important and long-established model species for plant molecular biology, genetics, epigenetics, and genomics. However, the latest version of reference genome still contains significant number of missing segments. Here, we report a high-quality and almost complete Col-0 genome assembly with two gaps (Col-XJTU) using combination of Oxford Nanopore Technology ultra-long reads, PacBio high-fidelity long reads, and Hi-C data. The total genome assembly size is 133,725,193 bp, introducing 14.6 Mb of novel sequences compared to the TAIR10.1 reference genome. All five chromosomes of Col-XJTU assembly are highly accurate with consensus quality (QV) scores > 60 (ranging from 62 to 68), which are higher than those of TAIR10.1 reference (QV scores ranging from 45 to 52). We have completely resolved chromosome (Chr) 3 and Chr5 in a telomere-to-telomere manner. Chr4 has been completely resolved except the nucleolar organizing regions, which comprise long repetitive DNA fragments. The Chr1 centromere (CEN1), reportedly around 9 Mb in length, is particularly challenging to assemble due to the presence of tens of thousands of CEN180 satellite repeats. Using the cutting-edge sequencing data and novel computational approaches, we assembled about 4 Mb of sequence for CEN1 and a 3.5-Mb-long CEN2. We investigated the structure and epigenetics of centromeres. We detected four clusters of CEN180 monomers, and found that the centromere-specific histone H3-like protein (CENH3) exhibits a strong preference for CEN180 cluster 3. Moreover, we observed hypomethylation patterns in CENH3-enriched regions. We believe that this high-quality genome assembly, Col-XJTU, would serve as a valuable reference to better understand the global pattern of centromeric polymorphisms, as well as genetic and epigenetic features in plants.
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Affiliation(s)
- Bo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xiaofei Yang
- School of Computer Science and Technology, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China.
| | - Yanyan Jia
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yu Xu
- School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Peng Jia
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Ningxin Dang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Songbo Wang
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Tun Xu
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xixi Zhao
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Shenghan Gao
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China
| | - Quanbin Dong
- Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China
| | - Kai Ye
- MOE Key Laboratory for Intelligent Networks & Network Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, 710049, China; School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, China; School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China; Genome Institute, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China.
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39
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Revisiting a GWAS peak in Arabidopsis thaliana reveals possible confounding by genetic heterogeneity. Heredity (Edinb) 2021; 127:245-252. [PMID: 34226672 PMCID: PMC8405673 DOI: 10.1038/s41437-021-00456-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 06/23/2021] [Accepted: 06/23/2021] [Indexed: 02/06/2023] Open
Abstract
Genome-wide association studies (GWAS) have become a standard approach for exploring the genetic basis of phenotypic variation. However, correlation is not causation, and only a tiny fraction of all associations have been experimentally confirmed. One practical problem is that a peak of association does not always pinpoint a causal gene, but may instead be tagging multiple causal variants. In this study, we reanalyze a previously reported peak associated with flowering time traits in Swedish Arabidopsis thaliana population. The peak appeared to pinpoint the AOP2/AOP3 cluster of glucosinolate biosynthesis genes, which is known to be responsible for natural variation in herbivore resistance. Here we propose an alternative hypothesis, by demonstrating that the AOP2/AOP3 flowering association can be wholly accounted for by allelic variation in two flanking genes with clear roles in regulating flowering: NDX1, a regulator of the main flowering time controller FLC, and GA1, which plays a central role in gibberellin synthesis and is required for flowering under some conditions. In other words, we propose that the AOP2/AOP3 flowering-time association may be yet another example of a spurious, "synthetic" association, arising from trying to fit a single-locus model in the presence of two statistically associated causative loci. We conclude that caution is needed when using GWAS for fine-mapping.
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40
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McElroy KE, Müller S, Lamatsch DK, Bankers L, Fields PD, Jalinsky JR, Sharbrough J, Boore JL, Logsdon JM, Neiman M. Asexuality Associated with Marked Genomic Expansion of Tandemly Repeated rRNA and Histone Genes. Mol Biol Evol 2021; 38:3581-3592. [PMID: 33885820 PMCID: PMC8382920 DOI: 10.1093/molbev/msab121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
How does asexual reproduction influence genome evolution? Although is it clear that genomic structural variation is common and important in natural populations, we know very little about how one of the most fundamental of eukaryotic traits-mode of genomic inheritance-influences genome structure. We address this question with the New Zealand freshwater snail Potamopyrgus antipodarum, which features multiple separately derived obligately asexual lineages that coexist and compete with otherwise similar sexual lineages. We used whole-genome sequencing reads from a diverse set of sexual and asexual individuals to analyze genomic abundance of a critically important gene family, rDNA (the genes encoding rRNAs), that is notable for dynamic and variable copy number. Our genomic survey of rDNA in P. antipodarum revealed two striking results. First, the core histone and 5S rRNA genes occur between tandem copies of the 18S-5.8S-28S gene cluster, a unique architecture for these crucial gene families. Second, asexual P. antipodarum harbor dramatically more rDNA-histone copies than sexuals, which we validated through molecular and cytogenetic analysis. The repeated expansion of this genomic region in asexual P. antipodarum lineages following distinct transitions to asexuality represents a dramatic genome structural change associated with asexual reproduction-with potential functional consequences related to the loss of sexual reproduction.
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Affiliation(s)
- Kyle E McElroy
- Ecology, Evolutionary, and Organismal Biology, Iowa State University, Ames, IA, USA
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Stefan Müller
- Institute of Human Genetics, Munich University Hospital, Ludwig-Maximilians University, Munich, Germany
| | - Dunja K Lamatsch
- Research Department for Limnology, University of Innsbruck, Mondsee, Mondsee, Austria
| | - Laura Bankers
- Division of Infectious Diseases, University of Colorado—Anschutz Medical Campus, Aurora, CO, USA
| | - Peter D Fields
- Department of Environmental Sciences, Zoology, University of Basel, Basel, Switzerland
| | | | - Joel Sharbrough
- Biology Department, New Mexico Institute of Mining and Technology, Socorro, NM, USA
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Jeffrey L Boore
- Providence St. Joseph Health and Institute for Systems Biology, Seattle, WA, USA
| | - John M Logsdon
- Department of Biology, University of Iowa, Iowa City, IA, USA
| | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA, USA
- Department of Gender, Women's, and Sexuality Studies, University of Iowa, Iowa City, IA, USA
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41
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Cao C, Kwok D, Edie S, Li Q, Ding B, Kossinna P, Campbell S, Wu J, Greenberg M, Long Q. kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes. Brief Bioinform 2021; 22:5985285. [PMID: 33200776 DOI: 10.1093/bib/bbaa270] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/17/2020] [Accepted: 09/18/2020] [Indexed: 12/31/2022] Open
Abstract
The power of genotype-phenotype association mapping studies increases greatly when contributions from multiple variants in a focal region are meaningfully aggregated. Currently, there are two popular categories of variant aggregation methods. Transcriptome-wide association studies (TWAS) represent a set of emerging methods that select variants based on their effect on gene expressions, providing pretrained linear combinations of variants for downstream association mapping. In contrast to this, kernel methods such as sequence kernel association test (SKAT) model genotypic and phenotypic variance use various kernel functions that capture genetic similarity between subjects, allowing nonlinear effects to be included. From the perspective of machine learning, these two methods cover two complementary aspects of feature engineering: feature selection/pruning and feature aggregation. Thus far, no thorough comparison has been made between these categories, and no methods exist which incorporate the advantages of TWAS- and kernel-based methods. In this work, we developed a novel method called kernel-based TWAS (kTWAS) that applies TWAS-like feature selection to a SKAT-like kernel association test, combining the strengths of both approaches. Through extensive simulations, we demonstrate that kTWAS has higher power than TWAS and multiple SKAT-based protocols, and we identify novel disease-associated genes in Wellcome Trust Case Control Consortium genotyping array data and MSSNG (Autism) sequence data. The source code for kTWAS and our simulations are available in our GitHub repository (https://github.com/theLongLab/kTWAS).
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Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, University of Calgary
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary
| | | | - Qing Li
- Department of Biochemistry & Molecular Biology, University of Calgary
| | - Bowei Ding
- Department of Mathematics & Statistics, University of Calgary
| | - Pathum Kossinna
- Department of Biochemistry & Molecular Biology, University of Calgary
| | | | - Jingjing Wu
- Department of Mathematics & Statistics, University of Calgary
| | | | - Quan Long
- Departments of Biochemistry & Molecular Biology, Medical Genetics and Mathematics & Statistics
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42
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Barragan AC, Weigel D. Plant NLR diversity: the known unknowns of pan-NLRomes. THE PLANT CELL 2021; 33:814-831. [PMID: 33793812 PMCID: PMC8226294 DOI: 10.1093/plcell/koaa002] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 10/23/2020] [Indexed: 05/20/2023]
Abstract
Plants and pathogens constantly adapt to each other. As a consequence, many members of the plant immune system, and especially the intracellular nucleotide-binding site leucine-rich repeat receptors, also known as NOD-like receptors (NLRs), are highly diversified, both among family members in the same genome, and between individuals in the same species. While this diversity has long been appreciated, its true extent has remained unknown. With pan-genome and pan-NLRome studies becoming more and more comprehensive, our knowledge of NLR sequence diversity is growing rapidly, and pan-NLRomes provide powerful platforms for assigning function to NLRs. These efforts are an important step toward the goal of comprehensively predicting from sequence alone whether an NLR provides disease resistance, and if so, to which pathogens.
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Affiliation(s)
- A Cristina Barragan
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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43
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Lopez FB, Fort A, Tadini L, Probst AV, McHale M, Friel J, Ryder P, Pontvianne F, Pesaresi P, Sulpice R, McKeown P, Brychkova G, Spillane C. Gene dosage compensation of rRNA transcript levels in Arabidopsis thaliana lines with reduced ribosomal gene copy number. THE PLANT CELL 2021; 33:1135-1150. [PMID: 33793816 PMCID: PMC8225240 DOI: 10.1093/plcell/koab020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/24/2020] [Indexed: 05/08/2023]
Abstract
The 45S rRNA genes (rDNA) are among the largest repetitive elements in eukaryotic genomes. rDNA consists of tandem arrays of rRNA genes, many of which are transcriptionally silenced. Silent rDNA repeats may act as 'back-up' copies for ribosome biogenesis and have nuclear organization roles. Through Cas9-mediated genome editing in the Arabidopsis thaliana female gametophyte, we reduced 45S rDNA copy number (CN) to a plateau of ∼10%. Two independent lines had rDNA CNs reduced by up to 90% at the T7 generation, named low copy number (LCN) lines. Despite drastic reduction of rDNA copies, rRNA transcriptional rates, and steady-state levels remained the same as wild-type plants. Gene dosage compensation of rRNA transcript levels was associated with reduction of silencing histone marks at rDNA loci and altered Nucleolar Organiser Region 2 organization. Although overall genome integrity of LCN lines appears unaffected, a chromosome segmental duplication occurred in one of the lines. Transcriptome analysis of LCN seedlings identified several shared dysregulated genes and pathways in both independent lines. Cas9 genome editing of rRNA repeats to generate LCN lines provides a powerful technique to elucidate rDNA dosage compensation mechanisms and impacts of low rDNA CN on genome stability, development, and cellular processes.
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Affiliation(s)
- Francesca B Lopez
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Antoine Fort
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Luca Tadini
- Dipartimento di Bioscienze, Universit� degli Studi di Milano, 20133 Milano, Italy
| | - Aline V Probst
- CNRS, GReD, Universit� Clermont Auvergne, INSERM, 63001 Clermont–Ferrand, France
| | - Marcus McHale
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - James Friel
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter Ryder
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Fr�d�ric Pontvianne
- CNRS, Laboratoire G�nome et D�veloppement des Plantes (LGDP), Universit� de Perpignan Via Domitia, Perpignan, France
| | - Paolo Pesaresi
- Dipartimento di Bioscienze, Universit� degli Studi di Milano, 20133 Milano, Italy
| | - Ronan Sulpice
- Systems Biology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Peter McKeown
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Galina Brychkova
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant & AgriBiosciences Research Centre (PABC), Ryan Institute, National University of Ireland Galway, Galway H91 REW4, Ireland
- Author for correspondence:
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44
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Provart NJ, Brady SM, Parry G, Schmitz RJ, Queitsch C, Bonetta D, Waese J, Schneeberger K, Loraine AE. Anno genominis XX: 20 years of Arabidopsis genomics. THE PLANT CELL 2021; 33:832-845. [PMID: 33793861 PMCID: PMC8226293 DOI: 10.1093/plcell/koaa038] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/09/2020] [Indexed: 05/04/2023]
Abstract
Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.
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Affiliation(s)
- Nicholas J Provart
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California, 95616, USA
| | - Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Georgia, 30602, USA
| | - Christine Queitsch
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, Washington, 98195, USA
- Brotman Baty Institute for Precision Medicine, Seattle, Washington, 98195, USA
| | - Dario Bonetta
- Faculty of Science, Ontario Tech University, Oshawa, Ontario, L1G 0C5, Canada
| | - Jamie Waese
- Department of Cell & Systems Biology/Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | - Korbinian Schneeberger
- Department of Chromosome Biology, Max Planck Institute for Plant Breeding Research, D-50829, Cologne, Germany
- Faculty of Biology, LMU Munich, 82152 Munich, Germany
| | - Ann E Loraine
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
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Choi JY, Abdulkina LR, Yin J, Chastukhina IB, Lovell JT, Agabekian IA, Young PG, Razzaque S, Shippen DE, Juenger TE, Shakirov EV, Purugganan MD. Natural variation in plant telomere length is associated with flowering time. THE PLANT CELL 2021; 33:1118-1134. [PMID: 33580702 PMCID: PMC8599780 DOI: 10.1093/plcell/koab022] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 01/14/2021] [Indexed: 05/05/2023]
Abstract
Telomeres are highly repetitive DNA sequences found at the ends of chromosomes that protect the chromosomes from deterioration duringcell division. Here, using whole-genome re-sequencing and terminal restriction fragment assays, we found substantial natural intraspecific variation in telomere length in Arabidopsis thaliana, rice (Oryza sativa), and maize (Zea mays). Genome-wide association study (GWAS) mapping in A. thaliana identified 13 regions with GWAS-significant associations underlying telomere length variation, including a region that harbors the telomerase reverse transcriptase (TERT) gene. Population genomic analysis provided evidence for a selective sweep at the TERT region associated with longer telomeres. We found that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life-history traits and chromosome integrity. Our results point to several possible reasons for this correlation, including the possibility that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier). Our work suggests that chromosomal structure itself might be an adaptive trait associated with plant life-history strategies.
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Affiliation(s)
- Jae Young Choi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Liliia R Abdulkina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Jun Yin
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Inna B Chastukhina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - John T Lovell
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Alabama 35806, USA
| | - Inna A Agabekian
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
| | - Pierce G Young
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Samsad Razzaque
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Dorothy E Shippen
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Texas 78712, USA
| | - Eugene V Shakirov
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Republic of Tatarstan 420008, Russia
- Department of Biological Sciences, College of Science, Marshall University, West Virginia 25701, USA
- Department of Biomedical Sciences, Joan C. Edwards School of Medicine, Marshall University, West Virginia 25755, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
| | - Michael D Purugganan
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York 10003, NY, USA
- Author for correspondence: (J.Y.C), (E.V.S.) or (M.D.P.)
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Cytogenomics of Deschampsia P. Beauv. (Poaceae) Species Based on Sequence Analyses and FISH Mapping of CON/COM Satellite DNA Families. PLANTS 2021; 10:plants10061105. [PMID: 34070920 PMCID: PMC8229069 DOI: 10.3390/plants10061105] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/19/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023]
Abstract
The genus Deschampsia P. Beauv. (Poaceae) involves a group of widespread polymorphic species, and many of them are highly tolerant to stressful environmental conditions. Genome diversity and chromosomal phylogeny within the genus are still insufficiently studied. Satellite DNAs, including CON/COM families, are the main components of the plant repeatome, which contribute to chromosome organization. For the first time, using PCR-based (Polymerase Chain Reaction) techniques and sequential BLAST (Basic Local Alignment Search Tool) and MSA (Multiple Sequence Alignment) analyses, we identified and classified CON/COM repeats in genomes of eleven Deschampsia accessions and three accessions from related genera. High homology of CON/COM sequences were revealed in the studied species though differences in single-nucleotide alteration profiles detected in homologous CON/COM regions indicated that they tended to diverge independently. The performed chromosome mapping of 45S rDNA, 5S rDNA, and CON/COM repeats in six Deschampsia species demonstrated interspecific variability in localization of these cytogenetic markers and facilitated the identification of different chromosomal rearrangements. Based on the obtained data, the studied Deschampsia species were distinguished into karyological groups, and MSA-based schematic trees were built, which could clarify the relationships within the genus. Our findings can be useful for further genetic and phylogenetic studies.
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47
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Kim M, Xi H, Park J. Genome-wide comparative analyses of GATA transcription factors among 19 Arabidopsis ecotype genomes: Intraspecific characteristics of GATA transcription factors. PLoS One 2021; 16:e0252181. [PMID: 34038437 PMCID: PMC8153473 DOI: 10.1371/journal.pone.0252181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 05/11/2021] [Indexed: 12/30/2022] Open
Abstract
GATA transcription factors (TFs) are widespread eukaryotic regulators whose DNA-binding domain is a class IV zinc finger motif (CX2CX17-20CX2C) followed by a basic region. Due to the low cost of genome sequencing, multiple strains of specific species have been sequenced: e.g., number of plant genomes in the Plant Genome Database (http://www.plantgenome.info/) is 2,174 originated from 713 plant species. Thus, we investigated GATA TFs of 19 Arabidopsis thaliana genome-widely to understand intraspecific features of Arabidopsis GATA TFs with the pipeline of GATA database (http://gata.genefamily.info/). Numbers of GATA genes and GATA TFs of each A. thaliana genome range from 29 to 30 and from 39 to 42, respectively. Four cases of different pattern of alternative splicing forms of GATA genes among 19 A. thaliana genomes are identified. 22 of 2,195 amino acids (1.002%) from the alignment of GATA domain amino acid sequences display variations across 19 ecotype genomes. In addition, maximally four different amino acid sequences per each GATA domain identified in this study indicate that these position-specific amino acid variations may invoke intraspecific functional variations. Among 15 functionally characterized GATA genes, only five GATA genes display variations of amino acids across ecotypes of A. thaliana, implying variations of their biological roles across natural isolates of A. thaliana. PCA results from 28 characteristics of GATA genes display the four groups, same to those defined by the number of GATA genes. Topologies of bootstrapped phylogenetic trees of Arabidopsis chloroplasts and common GATA genes are mostly incongruent. Moreover, no relationship between geographical distribution and their phylogenetic relationships was found. Our results present that intraspecific variations of GATA TFs in A. thaliana are conserved and evolutionarily neutral along with 19 ecotypes, which is congruent to the fact that GATA TFs are one of the main regulators for controlling essential mechanisms, such as seed germination and hypocotyl elongation.
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Affiliation(s)
- Mangi Kim
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Hong Xi
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Inc., Gangnam-gu, Seoul, Republic of Korea
- InfoBoss Research Center, Gangnam-gu, Seoul, Republic of Korea
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Stelzer CP, Pichler M, Hatheuer A. Linking genome size variation to population phenotypic variation within the rotifer, Brachionus asplanchnoidis. Commun Biol 2021; 4:596. [PMID: 34011946 PMCID: PMC8134563 DOI: 10.1038/s42003-021-02131-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 04/19/2021] [Indexed: 11/17/2022] Open
Abstract
Eukaryotic organisms usually contain much more genomic DNA than expected from their biological complexity. In explaining this pattern, selection-based hypotheses suggest that genome size evolves through selection acting on correlated life history traits, implicitly assuming the existence of phenotypic effects of (extra) genomic DNA that are independent of its information content. Here, we present conclusive evidence of such phenotypic effects within a well-mixed natural population that shows heritable variation in genome size. We found that genome size is positively correlated with body size, egg size, and embryonic development time in a population of the monogonont rotifer Brachionus asplanchnoidis. The effect on embryonic development time was mediated partly by an indirect effect (via egg size), and a direct effect, the latter indicating an increased replication cost of the larger amounts of DNA during mitosis. Our results suggest that selection-based change of genome size can operate in this population, provided it is strong enough to overcome drift or mutational change of genome size.
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Affiliation(s)
| | - Maria Pichler
- University of Innsbruck, Mondseestr. 9, 5310, Mondsee, Austria
| | - Anita Hatheuer
- University of Innsbruck, Mondseestr. 9, 5310, Mondsee, Austria
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Krak K, Caklová P, Kopecký D, Blattner FR, Mahelka V. Horizontally Acquired nrDNAs Persist in Low Amounts in Host Hordeum Genomes and Evolve Independently of Native nrDNA. FRONTIERS IN PLANT SCIENCE 2021; 12:672879. [PMID: 34079572 PMCID: PMC8165317 DOI: 10.3389/fpls.2021.672879] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 04/22/2021] [Indexed: 06/12/2023]
Abstract
Nuclear ribosomal DNA (nrDNA) has displayed extraordinary dynamics during the evolution of plant species. However, the patterns and evolutionary significance of nrDNA array expansion or contraction are still relatively unknown. Moreover, only little is known of the fate of minority nrDNA copies acquired between species via horizontal transfer. The barley genus Hordeum (Poaceae) represents a good model for such a study, as species of section Stenostachys acquired nrDNA via horizontal transfer from at least five different panicoid genera, causing long-term co-existence of native (Hordeum-like) and non-native (panicoid) nrDNAs. Using quantitative PCR, we investigated copy number variation (CNV) of nrDNA in the diploid representatives of the genus Hordeum. We estimated the copy number of the foreign, as well as of the native ITS types (ribotypes), and followed the pattern of their CNV in relation to the genus' phylogeny, species' genomes size and the number of nrDNA loci. For the native ribotype, we encountered an almost 19-fold variation in the mean copy number among the taxa analysed, ranging from 1689 copies (per 2C content) in H. patagonicum subsp. mustersii to 31342 copies in H. murinum subsp. glaucum. The copy numbers did not correlate with any of the genus' phylogeny, the species' genome size or the number of nrDNA loci. The CNV was high within the recognised groups (up to 13.2 × in the American I-genome species) as well as between accessions of the same species (up to 4×). Foreign ribotypes represent only a small fraction of the total number of nrDNA copies. Their copy numbers ranged from single units to tens and rarely hundreds of copies. They amounted, on average, to between 0.1% (Setaria ribotype) and 1.9% (Euclasta ribotype) of total nrDNA. None of the foreign ribotypes showed significant differences with respect to phylogenetic groups recognised within the sect. Stenostachys. Overall, no correlation was found between copy numbers of native and foreign nrDNAs suggesting the sequestration and independent evolution of native and non-native nrDNA arrays. Therefore, foreign nrDNA in Hordeum likely poses a dead-end by-product of horizontal gene transfer events.
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Affiliation(s)
- Karol Krak
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Prague 6, Czechia
| | - Petra Caklová
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
| | - David Kopecký
- Czech Academy of Sciences, Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Olomouc, Czechia
| | - Frank R. Blattner
- Experimental Taxonomy, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
- German Centre of Integrative Biodiversity Research (iDiv) Halle–Jena–Leipzig, Leipzig, Germany
| | - Václav Mahelka
- Czech Academy of Sciences, Institute of Botany, Prùhonice, Czechia
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50
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Campos ACAL, van Dijk WFA, Ramakrishna P, Giles T, Korte P, Douglas A, Smith P, Salt DE. 1,135 ionomes reveal the global pattern of leaf and seed mineral nutrient and trace element diversity in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:536-554. [PMID: 33506585 DOI: 10.1111/tpj.15177] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 01/07/2021] [Accepted: 01/20/2021] [Indexed: 05/06/2023]
Abstract
Soil is a heterogeneous reservoir of essential elements needed for plant growth and development. Plants have evolved mechanisms to balance their nutritional needs based on availability of nutrients. This has led to genetically based variation in the elemental composition, the 'ionome', of plants, both within and between species. We explore this natural variation using a panel of wild-collected, geographically widespread Arabidopsis thaliana accessions from the 1001 Genomes Project including over 1,135 accessions, and the 19 parental accessions of the Multi-parent Advanced Generation Inter-Cross (MAGIC) panel, all with full-genome sequences available. We present an experimental design pipeline for high-throughput ionomic screenings and analyses with improved normalisation procedures to account for errors and variability in conditions often encountered in large-scale, high-throughput data collection. We report quantification of the complete leaf and seed ionome of the entire collection using this pipeline and a digital tool, Ion Explorer, to interact with the dataset. We describe the pattern of natural ionomic variation across the A. thaliana species and identify several accessions with extreme ionomic profiles. It forms a valuable resource for exploratory genetic mapping studies to identify genes underlying natural variation in leaf and seed ionome and genetic adaptation of plants to soil conditions.
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Affiliation(s)
- Ana Carolina A L Campos
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - William F A van Dijk
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Priya Ramakrishna
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Tom Giles
- Digital Research Service and Advanced Data Analysis Centre, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
| | - Pamela Korte
- Gregor Mendel Institute of Molecular Plant Biology, Vienna, Austria
| | - Alex Douglas
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - Pete Smith
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
| | - David E Salt
- Institute of Biological and Environmental Sciences, University of Aberdeen, Cruickshank Building, Aberdeen, AB24 3UU, United Kingdom
- Future Food Beacon of Excellence and School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, United Kingdom
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