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Session AM. Allopolyploid subgenome identification and implications for evolutionary analysis. Trends Genet 2024; 40:621-631. [PMID: 38637269 DOI: 10.1016/j.tig.2024.03.008] [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: 11/17/2023] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Whole-genome duplications (WGDs) are widespread genomic events in eukaryotes that are hypothesized to contribute to the evolutionary success of many lineages, including flowering plants, Saccharomyces yeast, and vertebrates. WGDs generally can be classified into autopolyploids (ploidy increase descended from one species) or allopolyploids (ploidy increase descended from multiple species). Assignment of allopolyploid progenitor species (called subgenomes in the polyploid) is important to understanding the biology and evolution of polyploids, including the asymmetric subgenome evolution following hybridization (biased fractionation). Here, I review the different methodologies used to identify the ancestors of allopolyploid subgenomes, discuss the advantages and disadvantages of these methods, and outline the implications of how these methods affect the subsequent evolutionary analysis of these genomes.
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Affiliation(s)
- Adam M Session
- Department of Biological Sciences, Binghamton University, Binghamton, NY 13902, USA.
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2
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Karbstein K, Kösters L, Hodač L, Hofmann M, Hörandl E, Tomasello S, Wagner ND, Emerson BC, Albach DC, Scheu S, Bradler S, de Vries J, Irisarri I, Li H, Soltis P, Mäder P, Wäldchen J. Species delimitation 4.0: integrative taxonomy meets artificial intelligence. Trends Ecol Evol 2024:S0169-5347(23)00296-3. [PMID: 38849221 DOI: 10.1016/j.tree.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 10/20/2023] [Accepted: 11/08/2023] [Indexed: 06/09/2024]
Abstract
Although species are central units for biological research, recent findings in genomics are raising awareness that what we call species can be ill-founded entities due to solely morphology-based, regional species descriptions. This particularly applies to groups characterized by intricate evolutionary processes such as hybridization, polyploidy, or asexuality. Here, challenges of current integrative taxonomy (genetics/genomics + morphology + ecology, etc.) become apparent: different favored species concepts, lack of universal characters/markers, missing appropriate analytical tools for intricate evolutionary processes, and highly subjective ranking and fusion of datasets. Now, integrative taxonomy combined with artificial intelligence under a unified species concept can enable automated feature learning and data integration, and thus reduce subjectivity in species delimitation. This approach will likely accelerate revising and unraveling eukaryotic biodiversity.
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Affiliation(s)
- Kevin Karbstein
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany.
| | - Lara Kösters
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Ladislav Hodač
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany
| | - Martin Hofmann
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany
| | - Elvira Hörandl
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Salvatore Tomasello
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Natascha D Wagner
- University of Göttingen, Albrecht-von-Haller Institute for Plant Sciences, Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), 37073 Göttingen, Germany
| | - Brent C Emerson
- Institute of Natural Products and Agrobiology (IPNA-CSIC), Island Ecology and Evolution Research Group, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - Dirk C Albach
- Carl von Ossietzky-Universität Oldenburg, Institute of Biology and Environmental Science, 26129 Oldenburg, Germany
| | - Stefan Scheu
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany; University of Göttingen, Centre of Biodiversity and Sustainable Land Use (CBL), 37073 Göttingen, Germany
| | - Sven Bradler
- University of Göttingen, Johann-Friedrich-Blumenbach Institute of Zoology and Anthropology, 37073 Göttingen, Germany
| | - Jan de Vries
- University of Göttingen, Institute for Microbiology and Genetics, Department of Applied Bioinformatics, 37077 Göttingen, Germany; University of Göttingen, Campus Institute Data Science (CIDAS), 37077 Göttingen, Germany; University of Göttingen, Göttingen Center for Molecular Biosciences (GZMB), Department of Applied Bioinformatics, 37077 Göttingen, Germany
| | - Iker Irisarri
- Leibniz Institute for the Analysis of Biodiversity Change (LIB), Centre for Molecular Biodiversity Research, Phylogenomics Section, Museum of Nature, 20146 Hamburg, Germany
| | - He Li
- Eastern China Conservation Centre for Wild Endangered Plant Resources, Chenshan Botanical Garden, 201602 Shanghai, China
| | - Pamela Soltis
- University of Florida, Florida Museum of Natural History, 32611 Gainesville, USA
| | - Patrick Mäder
- Technical University of Ilmenau, Institute for Computer and Systems Engineering, 98693 Ilmenau, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Friedrich Schiller University Jena, Faculty of Biological Sciences, Institute of Ecology and Evolution, Philosophenweg 16, 07743 Jena, Germany
| | - Jana Wäldchen
- Max Planck Institute for Biogeochemistry, Department of Biogeochemical Integration, 07745 Jena, Germany; German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
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3
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Skubic M, Záveská E, Frajman B. Meeting in Liguria: hybridisation between Apennine endemic Euphorbia barrelieri and western Mediterranean E. nicaeensis led to the allopolyploid origin of E. ligustica. Mol Phylogenet Evol 2023; 185:107805. [PMID: 37127112 DOI: 10.1016/j.ympev.2023.107805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/17/2023] [Accepted: 04/25/2023] [Indexed: 05/03/2023]
Abstract
The Mediterranean Basin is renowned for its extremely rich biota and is considered as one of the 25 Global Biodiversity Hotspots, but its diversity is not homogeneously distributed. Outstanding in the number of (endemic) species are the Ligurian Alps (Italy). At the foot of the Ligurian Alps, little above the Mediterranean Sea, a disjunct occurrence of Italian endemic Euphorbia barrelieri was reported. Using an array of integrative methods ranging from cytogenetic (chromosome number and relative genome size estimation), over phylogenetic approaches (plastid, ITS and RAD sequencing) to multivariate morphometrics we disentangled the origin of these populations that were shown to be tetraploid. We performed phylogenetic analyses of the nuclear ITS and plastid regions of a broad taxonomic sampling of Euphorbia sect. Pithyusa to identify possible species involved in the origin of the tetraploid populations and then applied various analyses of RADseq data to identify the putative parental species. Our results have shown that the Ligurian populations of E. barrelieri are of allotetraploid origin that involved E. barrelieri and western Mediterranean E. nicaeensis as parental species. We thus describe a new species, E. ligustica, and hypothesise that its adaptation to similar environments in which E. barrelieri occurs, triggered development of similar morphology, whereas its genetic composition appears to be closer to that of E. nicaeensis. Our study emphasises the importance of polyploidisation for plant diversification, highlights the value of the Ligurian Alps as a hotspot of biodiversity and endemism and underlines the importance of integrative taxonomic approaches in uncovering cryptic diversity.
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Affiliation(s)
- Maruša Skubic
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria; Department of Agronomy, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva ulica 101, 1000 Ljubljana, Slovenia
| | - Eliška Záveská
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, 25243 Průhonice, Czech Republic
| | - Božo Frajman
- Department of Botany, University of Innsbruck, Sternwartestrasse 15, 6020 Innsbruck, Austria.
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4
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Karbstein K, Tomasello S, Hodač L, Wagner N, Marinček P, Barke BH, Paetzold C, Hörandl E. Untying Gordian knots: unraveling reticulate polyploid plant evolution by genomic data using the large Ranunculus auricomus species complex. THE NEW PHYTOLOGIST 2022; 235:2081-2098. [PMID: 35633497 DOI: 10.1111/nph.18284] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Speciation via hybridization and polyploidization is a major evolutionary force in plant evolution but is still poorly understood for neopolyploid groups. Challenges are attributed to high heterozygosity, low genetic divergence, and missing information on progenitors, ploidy, and reproduction. We study the large Eurasian Ranunculus auricomus species complex and use a comprehensive workflow integrating reduced-representation sequencing (RRS) genomic data to unravel reticulate evolution, genome diversity and composition of polyploids. We rely on 97 312 restriction site-associated DNA sequencing (RAD-Seq) loci, 576 targeted nuclear genes (48 phased), and 71 plastid regions derived from 78 polyploid apomictic taxa and four diploid and one tetraploid putative sexual progenitor species. We applied (phylo)genomic structure, network, and single nucleotide polymorphism (SNP)-origin analyses. Results consistently showed only 3-5 supported and geographically structured polyploid genetic groups, each containing extant sexual and one unknown progenitor species. Combined analyses demonstrated predominantly allopolyploid origins, each involving 2-3 different diploid sexual progenitor species. Young allotetraploids were characterized by subgenome dominance and nonhybrid SNPs, suggesting substantial post-origin but little lineage-specific evolution. The biodiversity of neopolyploid complexes can result from multiple hybrid origins involving different progenitors and substantial post-origin evolution (e.g. homoeologous exchanges, hybrid segregation, gene flow). Reduced-representation sequencing genomic data including multi-approach information is efficient to delimit shallow reticulate relationships.
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Affiliation(s)
- Kevin Karbstein
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
- Georg-August University School of Science (GAUSS), University of Göttingen, 37073, Göttingen, Germany
| | - Salvatore Tomasello
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Ladislav Hodač
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
- Department of Biogeochemical Integration, Max Planck Institute for Biogeochemistry, 07745, Jena, Germany
| | - Natascha Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Pia Marinček
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Birthe Hilkka Barke
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
| | - Claudia Paetzold
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325, Frankfurt (Main), Germany
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Albrecht-von-Haller Institute for Plant Sciences, University of Göttingen, 37073, Göttingen, Germany
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5
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Hörandl E. Novel Approaches for Species Concepts and Delimitation in Polyploids and Hybrids. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11020204. [PMID: 35050093 PMCID: PMC8781807 DOI: 10.3390/plants11020204] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 05/08/2023]
Abstract
Hybridization and polyploidization are important processes for plant evolution. However, classification of hybrid or polyploid species has been notoriously difficult because of the complexity of processes and different evolutionary scenarios that do not fit with classical species concepts. Polyploid complexes are formed via combinations of allopolyploidy, autopolyploidy and homoploid hybridization with persisting sexual reproduction, resulting in many discrete lineages that have been classified as species. Polyploid complexes with facultative apomixis result in complicated net-work like clusters, or rarely in agamospecies. Various case studies illustrate the problems that apply to traditional species concepts to hybrids and polyploids. Conceptual progress can be made if lineage formation is accepted as an inevitable consequence of meiotic sex, which is established already in the first eukaryotes as a DNA restoration tool. The turnaround of the viewpoint that sex forms species as lineages helps to overcome traditional thinking of species as "units". Lineage formation and self-sustainability is the prerequisite for speciation and can also be applied to hybrids and polyploids. Species delimitation is aided by the improved recognition of lineages via various novel -omics methods, by understanding meiosis functions, and by recognizing functional phenotypes by considering morphological-physiological-ecological adaptations.
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Affiliation(s)
- Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, 37073 Göttingen, Germany
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6
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Schiavinato M, Bodrug‐Schepers A, Dohm JC, Himmelbauer H. Subgenome evolution in allotetraploid plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:672-688. [PMID: 33547826 PMCID: PMC8251528 DOI: 10.1111/tpj.15190] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 05/02/2023]
Abstract
Polyploidization is a well-known speciation and adaptation mechanism. Traces of former polyploidization events were discovered within many genomes, and especially in plants. Allopolyploidization by interspecific hybridization between two species is common. Among hybrid plants, many are domesticated species of agricultural interest and many of their genomes and of their presumptive parents have been sequenced. Hybrid genomes remain challenging to analyse because of the presence of multiple subgenomes. The genomes of hybrids often undergo rearrangement and degradation over time. Based on 10 hybrid plant genomes from six different genera, with hybridization dating from 10,000 to 5 million years ago, we assessed subgenome degradation, subgenomic intermixing and biased subgenome fractionation. The restructuring of hybrid genomes does not proceed proportionally with the age of the hybrid. The oldest hybrids in our data set display completely different fates: whereas the subgenomes of the tobacco plant Nicotiana benthamiana are in an advanced stage of degradation, the subgenomes of quinoa (Chenopodium quinoa) are exceptionally well conserved by structure and sequence. We observed statistically significant biased subgenome fractionation in seven out of 10 hybrids, which had different ages and subgenomic intermixing levels. Hence, we conclude that no correlation exists between biased fractionation and subgenome intermixing. Lastly, domestication may encourage or hinder subgenome intermixing, depending on the evolutionary context. In summary, comparative analysis of hybrid genomes and their presumptive parents allowed us to determine commonalities and differences between their evolutionary fates. In order to facilitate the future analysis of further hybrid genomes, we automated the analysis steps within manticore, which is publicly available at https://github.com/MatteoSchiavinato/manticore.git.
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Affiliation(s)
- Matteo Schiavinato
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Alexandrina Bodrug‐Schepers
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Juliane C. Dohm
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life Sciences (BOKU)Institute of Computational BiologyMuthgasse 18Vienna1190Austria
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7
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Wagner ND, He L, Hörandl E. Phylogenomic Relationships and Evolution of Polyploid Salix Species Revealed by RAD Sequencing Data. FRONTIERS IN PLANT SCIENCE 2020; 11:1077. [PMID: 32765560 PMCID: PMC7379873 DOI: 10.3389/fpls.2020.01077] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 06/30/2020] [Indexed: 05/19/2023]
Abstract
Polyploidy is common in the genus Salix. However, little is known about the origin, parentage and genomic composition of polyploid species because of a lack of suitable molecular markers and analysis tools. We established a phylogenomic framework including species of all described sections of Eurasian shrub willows. We analyzed the genomic composition of seven polyploid willow species in comparison to putative diploid parental species to draw conclusions on their origin and the effects of backcrossing and post-origin evolution. We applied recently developed programs like SNAPP, HyDe, and SNiPloid to establish a bioinformatic pipeline for unravelling the complexity of polyploid genomes. RAD sequencing revealed 23,393 loci and 320,010 high quality SNPs for the analysis of relationships of 35 species of Eurasian shrub willows (Salix subg. Chamaetia/Vetrix). Polyploid willow species appear to be predominantly of allopolyploid origin. More ancient allopolyploidization events were observed for two hexaploid and one octoploid species, while our data suggested a more recent allopolyploid origin for the included tetraploids and identified putative parental taxa. SNiPloid analyses disentangled the different genomic signatures resulting from hybrid origin, backcrossing, and secondary post-origin evolution in the polyploid species. Our RAD sequencing data demonstrate that willow genomes are shaped by ancient and recent reticulate evolution, polyploidization, and post-origin divergence of species.
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Affiliation(s)
- Natascha D. Wagner
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
| | - Li He
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), University of Goettingen, Göttingen, Germany
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8
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Hu G, Grover CE, Arick MA, Liu M, Peterson DG, Wendel JF. Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids. Brief Bioinform 2020; 22:1819-1835. [PMID: 32219306 PMCID: PMC7986634 DOI: 10.1093/bib/bbaa035] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/06/2020] [Accepted: 02/24/2020] [Indexed: 12/29/2022] Open
Abstract
Polyploidy is a widespread phenomenon throughout eukaryotes. Due to the coexistence of duplicated genomes, polyploids offer unique challenges for estimating gene expression levels, which is essential for understanding the massive and various forms of transcriptomic responses accompanying polyploidy. Although previous studies have explored the bioinformatics of polyploid transcriptomic profiling, the causes and consequences of inaccurate quantification of transcripts from duplicated gene copies have not been addressed. Using transcriptomic data from the cotton genus (Gossypium) as an example, we present an analytical workflow to evaluate a variety of bioinformatic method choices at different stages of RNA-seq analysis, from homoeolog expression quantification to downstream analysis used to infer key phenomena of polyploid expression evolution. In general, EAGLE-RC and GSNAP-PolyCat outperform other quantification pipelines tested, and their derived expression dataset best represents the expected homoeolog expression and co-expression divergence. The performance of co-expression network analysis was less affected by homoeolog quantification than by network construction methods, where weighted networks outperformed binary networks. By examining the extent and consequences of homoeolog read ambiguity, we illuminate the potential artifacts that may affect our understanding of duplicate gene expression, including an overestimation of homoeolog co-regulation and the incorrect inference of subgenome asymmetry in network topology. Taken together, our work points to a set of reasonable practices that we hope are broadly applicable to the evolutionary exploration of polyploids.
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Affiliation(s)
- Guanjing Hu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Corrinne E Grover
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Mark A Arick
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Meiling Liu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Daniel G Peterson
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
| | - Jonathan F Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011, USA
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9
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Gautier AT, Chambaud C, Brocard L, Ollat N, Gambetta GA, Delrot S, Cookson SJ. Merging genotypes: graft union formation and scion-rootstock interactions. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:747-755. [PMID: 30481315 DOI: 10.1093/jxb/ery422] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/19/2018] [Indexed: 05/18/2023]
Abstract
Grafting has been utilised for at least the past 7000 years. Historically, grafting has been developed by growers without particular interest beyond the agronomical and ornamental effects, and thus knowledge about grafting has remained largely empirical. Much of the commercial production of fruit, and increasingly vegetables, relies upon grafting with rootstocks to provide resistance to soil-borne pathogens and abiotic stresses as well as to influence scion growth and performance. Although there is considerable agronomic knowledge about the use and selection of rootstocks for many species, we know little of the molecular mechanisms underlying rootstock adaptation to different soil environments and rootstock-conferred modifications of scion phenotypes. Furthermore, the processes involved in the formation of the graft union and graft compatibility are poorly understood despite over a hundred years of scientific study. In this paper, we provide an overview of what is known about grafting and the mechanisms underlying rootstock-scion interactions. We highlight recent studies that have advanced our understanding of graft union formation and outline subjects that require further development.
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Affiliation(s)
- Antoine T Gautier
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Chemin de Leysotte, Villenave d'Ornon, France
| | - Clément Chambaud
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Chemin de Leysotte, Villenave d'Ornon, France
| | - Lysiane Brocard
- Université de Bordeaux, CNRS, INSERM, UMS, INRA, Bordeaux Imaging Center, Plant Imaging Plateform, Villenave d'Ornon, France
| | - Nathalie Ollat
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Chemin de Leysotte, Villenave d'Ornon, France
| | - Gregory A Gambetta
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Chemin de Leysotte, Villenave d'Ornon, France
| | - Serge Delrot
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Chemin de Leysotte, Villenave d'Ornon, France
| | - Sarah J Cookson
- EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, ISVV, Chemin de Leysotte, Villenave d'Ornon, France
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10
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Boutte J, Ferreira de Carvalho J, Rousseau-Gueutin M, Poulain J, Da Silva C, Wincker P, Ainouche M, Salmon A. Reference Transcriptomes and Detection of Duplicated Copies in Hexaploid and Allododecaploid Spartina Species (Poaceae). Genome Biol Evol 2016; 8:3030-3044. [PMID: 27614235 PMCID: PMC5633685 DOI: 10.1093/gbe/evw209] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2016] [Indexed: 01/19/2023] Open
Abstract
In this study, we report the assembly and annotation of five reference transcriptomes for the European hexaploid Spartina species (S. maritima, S. alterniflora and their homoploid hybrids S. x townsendii and S. x neyrautii) and the allododecaploid invasive species S. anglica These transcriptomes were constructed from various leaf and root cDNA libraries that were sequenced using both Roche-454 and Illumina technologies. Considering the high ploidy levels of the Spartina genomes under study, and considering the absence of diploid reference genome and the need of an appropriate analytical strategy, we developed generic bioinformatics tools to (1) detect different haplotypes of each gene within each species and (2) assign a parental origin to haplotypes detected in the hexaploid hybrids and the neo-allopolyploid. The approach described here allows the detection of putative homeologs from sets of short reads. Synonymous substitution rate (KS) comparisons between haplotypes from the hexaploid species revealed the presence of one KS peak (likely resulting from the tetraploid duplication event). The procedure developed in this study can be applied for future differential gene expression or genomics experiments to study the fate of duplicated genes in the invasive allododecaploid S. anglica.
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Affiliation(s)
- Julien Boutte
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Julie Ferreira de Carvalho
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Mathieu Rousseau-Gueutin
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France UMR Institut de Génétique, Environnement et Protection des Plantes, Institut National de la Recherche Agronomique, Le Rheu Cedex, France
| | | | | | | | - Malika Ainouche
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
| | - Armel Salmon
- UMR CNRS 6553 Ecobio, OSUR (Observatoire des Sciences de l'Univers de Rennes), University of Rennes 1, Rennes Cedex, France
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11
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Mora-Ortiz M, Swain MT, Vickers MJ, Hegarty MJ, Kelly R, Smith LMJ, Skøt L. De-novo transcriptome assembly for gene identification, analysis, annotation, and molecular marker discovery in Onobrychis viciifolia. BMC Genomics 2016; 17:756. [PMID: 27671367 PMCID: PMC5037894 DOI: 10.1186/s12864-016-3083-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Sainfoin (Onobrychis viciifolia) is a highly nutritious tannin-containing forage legume. In the diet of ruminants sainfoin can have anti-parasitic effects and reduce methane emissions under in vitro conditions. Many of these benefits have been attributed to condensed tannins or proanthocyanidins in sainfoin. A combination of increased use of industrially produced nitrogen fertilizer, issues with establishment and productivity in the first year and more reliable alternatives, such as red clover led to a decline in the use of sainfoin since the middle of the last century. In recent years there has been a resurgence of interest in sainfoin due to its potential beneficial nutraceutical and environmental attributes. However, genomic resources are scarce, thus hampering progress in genetic analysis and improvement. To address this we have used next generation RNA sequencing technology to obtain the first transcriptome of sainfoin. We used the library to identify gene-based simple sequence repeats (SSRs) and potential single nucleotide polymorphisms (SNPs). RESULTS One genotype from each of five sainfoin accessions was sequenced. Paired-end (PE) sequences were generated from cDNA libraries of RNA extracted from 7 day old seedlings. A combined assembly of 92,772 transcripts was produced de novo using the Trinity programme. About 18,000 transcripts were annotated with at least one GO (gene ontology) term. A total of 63 transcripts were annotated as involved in the tannin biosynthesis pathway. We identified 3786 potential SSRs. SNPs were identified by mapping the reads of the individual assemblies against the combined assembly. After stringent filtering a total of 77,000 putative SNPs were identified. A phylogenetic analysis of single copy number genes showed that sainfoin was most closely related to red clover and Medicago truncatula, while Lotus japonicus, bean and soybean are more distant relatives. CONCLUSIONS This work describes the first transcriptome assembly in sainfoin. The 92 K transcripts provide a rich source of SNP and SSR polymorphisms for future use in genetic studies of this crop. Annotation of genes involved in the condensed tannin biosynthesis pathway has provided the basis for further studies of the genetic control of this important trait in sainfoin.
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Affiliation(s)
- Marina Mora-Ortiz
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 OLE, UK.,Present Address: School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights Campus, Reading, RG6 6AP, UK
| | - Martin T Swain
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Martin J Vickers
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK.,Present Address: The Department of Cell and Developmental Biology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Matthew J Hegarty
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Rhys Kelly
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK
| | - Lydia M J Smith
- National Institute of Agricultural Botany, Huntingdon Road, Cambridge, CB3 OLE, UK
| | - Leif Skøt
- Aberystwyth University, IBERS, Gogerddan, Aberystwyth, Ceredigion, SY23 3EB, UK.
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12
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Guerin C, Joët T, Serret J, Lashermes P, Vaissayre V, Agbessi MDT, Beulé T, Severac D, Amblard P, Tregear J, Durand-Gasselin T, Morcillo F, Dussert S. Gene coexpression network analysis of oil biosynthesis in an interspecific backcross of oil palm. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 87:423-41. [PMID: 27145323 DOI: 10.1111/tpj.13208] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/27/2016] [Accepted: 04/27/2016] [Indexed: 05/25/2023]
Abstract
Global demand for vegetable oils is increasing at a dramatic rate, while our understanding of the regulation of oil biosynthesis in plants remains limited. To gain insights into the mechanisms that govern oil synthesis and fatty acid (FA) composition in the oil palm fruit, we used a multilevel approach combining gene coexpression analysis, quantification of allele-specific expression and joint multivariate analysis of transcriptomic and lipid data, in an interspecific backcross population between the African oil palm, Elaeis guineensis, and the American oil palm, Elaeis oleifera, which display contrasting oil contents and FA compositions. The gene coexpression network produced revealed tight transcriptional coordination of fatty acid synthesis (FAS) in the plastid with sugar sensing, plastidial glycolysis, transient starch storage and carbon recapture pathways. It also revealed a concerted regulation, along with FAS, of both the transfer of nascent FA to the endoplasmic reticulum, where triacylglycerol assembly occurs, and of the production of glycerol-3-phosphate, which provides the backbone of triacylglycerols. Plastid biogenesis and auxin transport were the two other biological processes most tightly connected to FAS in the network. In addition to WRINKLED1, a transcription factor (TF) known to activate FAS genes, two novel TFs, termed NF-YB-1 and ZFP-1, were found at the core of the FAS module. The saturated FA content of palm oil appeared to vary above all in relation to the level of transcripts of the gene coding for β-ketoacyl-acyl carrier protein synthase II. Our findings should facilitate the development of breeding and engineering strategies in this and other oil crops.
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Affiliation(s)
- Chloé Guerin
- PalmElit SAS, Montferrier-sur-Lez, F-34980, France
| | - Thierry Joët
- IRD, UMR DIADE, 911 Av. Agropolis, Montpellier, 34394, France
| | - Julien Serret
- IRD, UMR DIADE, 911 Av. Agropolis, Montpellier, 34394, France
| | | | | | | | | | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, 141 Rue de la Cardonille, Montpellier Cedex 5, 34094, France
| | | | - James Tregear
- IRD, UMR DIADE, 911 Av. Agropolis, Montpellier, 34394, France
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13
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Zohren J, Wang N, Kardailsky I, Borrell JS, Joecker A, Nichols RA, Buggs RJA. Unidirectional diploid-tetraploid introgression among British birch trees with shifting ranges shown by restriction site-associated markers. Mol Ecol 2016; 25:2413-26. [PMID: 27065091 PMCID: PMC4999052 DOI: 10.1111/mec.13644] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 04/05/2016] [Accepted: 04/08/2016] [Indexed: 01/02/2023]
Abstract
Hybridization may lead to introgression of genes among species. Introgression may be bidirectional or unidirectional, depending on factors such as the demography of the hybridizing species, or the nature of reproductive barriers between them. Previous microsatellite studies suggested bidirectional introgression between diploid Betula nana (dwarf birch) and tetraploid B. pubescens (downy birch) and also between B. pubescens and diploid B. pendula (silver birch) in Britain. Here, we analyse introgression among these species using 51 237 variants in restriction site‐associated (RAD) markers in 194 individuals, called with allele dosages in the tetraploids. In contrast to the microsatellite study, we found unidirectional introgression into B. pubescens from both of the diploid species. This pattern fits better with the expected nature of the reproductive barrier between diploids and tetraploids. As in the microsatellite study, introgression into B. pubescens showed clear clines with increasing introgression from B. nana in the north and from B. pendula in the south. Unlike B. pendula alleles, introgression of B. nana alleles was found far from the current area of sympatry or allopatry between B. nana and B. pubescens. This pattern fits a shifting zone of hybridization due to Holocene reduction in the range of B. nana and expansion in the range of B. pubescens.
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Affiliation(s)
- Jasmin Zohren
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Nian Wang
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Igor Kardailsky
- QIAGEN Aarhus A/S, Silkeborgvej 2, Prismet, Aarhus C, 8000, Denmark
| | - James S Borrell
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Anika Joecker
- QIAGEN Aarhus A/S, Silkeborgvej 2, Prismet, Aarhus C, 8000, Denmark
| | - Richard A Nichols
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Richard J A Buggs
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
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14
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Haplotype Detection from Next-Generation Sequencing in High-Ploidy-Level Species: 45S rDNA Gene Copies in the Hexaploid Spartina maritima. G3-GENES GENOMES GENETICS 2015; 6:29-40. [PMID: 26530424 PMCID: PMC4704722 DOI: 10.1534/g3.115.023242] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Gene and whole-genome duplications are widespread in plant nuclear genomes, resulting in sequence heterogeneity. Identification of duplicated genes may be particularly challenging in highly redundant genomes, especially when there are no diploid parents as a reference. Here, we developed a pipeline to detect the different copies in the ribosomal RNA gene family in the hexaploid grass Spartina maritima from next-generation sequencing (Roche-454) reads. The heterogeneity of the different domains of the highly repeated 45S unit was explored by identifying single nucleotide polymorphisms (SNPs) and assembling reads based on shared polymorphisms. SNPs were validated using comparisons with Illumina sequence data sets and by cloning and Sanger (re)sequencing. Using this approach, 29 validated polymorphisms and 11 validated haplotypes were reported (out of 34 and 20, respectively, that were initially predicted by our program). The rDNA domains of S. maritima have similar lengths as those found in other Poaceae, apart from the 5′-ETS, which is approximately two-times longer in S. maritima. Sequence homogeneity was encountered in coding regions and both internal transcribed spacers (ITS), whereas high intragenomic variability was detected in the intergenic spacer (IGS) and the external transcribed spacer (ETS). Molecular cytogenetic analysis by fluorescent in situ hybridization (FISH) revealed the presence of one pair of 45S rDNA signals on the chromosomes of S. maritima instead of three expected pairs for a hexaploid genome, indicating loss of duplicated homeologous loci through the diploidization process. The procedure developed here may be used at any ploidy level and using different sequencing technologies.
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15
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Bardil A, Tayalé A, Parisod C. Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:621-31. [PMID: 25823965 DOI: 10.1111/tpj.12837] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 03/18/2015] [Accepted: 03/23/2015] [Indexed: 05/21/2023]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR-RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR-RTs and/or genetic redundancy supports the accumulation of active LTR-RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR-RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR-RT families revealed contrasted dynamics during species diversification. Quiescent LTR-RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR-RT families in autopolyploids further supported that genome shock and redundancy are non-mutually exclusive triggers of LTR-RT proliferation. Although reputed stable, autopolyploid genomes show LTR-RT fractions presenting analogies with polyploids between widely divergent genomes.
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Affiliation(s)
- Amélie Bardil
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Alexandre Tayalé
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
| | - Christian Parisod
- Laboratory of Evolutionary Botany, University of Neuchâtel, Neuchâtel, 2000, Switzerland
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16
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Page JT, Udall JA. Methods for mapping and categorization of DNA sequence reads from allopolyploid organisms. BMC Genet 2015; 16 Suppl 2:S4. [PMID: 25951770 PMCID: PMC4423573 DOI: 10.1186/1471-2156-16-s2-s4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Genome read categorization determines the genome of origin for sequence reads from an allopolyploid organism. Different techniques have been used to perform read categorization, mostly based on homoeo-SNPs identified between extant diploid relatives of allopolyploids. We present a novel technique for read categorization implemented by the software PolyDog. We demonstrate its accuracy and improved categorization relative to other methods. We discuss the situations in which one method or another might be most appropriate.
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17
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Lashermes P, Combes MC, Hueber Y, Severac D, Dereeper A. Genome rearrangements derived from homoeologous recombination following allopolyploidy speciation in coffee. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:674-85. [PMID: 24628823 DOI: 10.1111/tpj.12505] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Revised: 02/26/2014] [Accepted: 03/04/2014] [Indexed: 05/27/2023]
Abstract
Allopolyploidization is widespread and has played a major role in flowering plant diversification. Genomic changes are common consequences of allopolyploidization, but their mechanisms of occurrence and dynamics over time are still poorly understood. Coffea arabica, a recently formed allotetraploid, was chosen as a model to investigate genetic changes in allopolyploid using an approach that exploits next-generation sequencing technologies. Genes affected by putative homoeolog loss were inferred by comparing the numbers of single-nucleotide polymorphisms detected using RNA-seq in individual accessions of C. arabica, and between accessions of its two diploid progenitor species for common sequence positions. Their physical locations were investigated and clusters of genes exhibiting homoeolog loss were identified. To validate these results, genome sequencing data were generated from one accession of C. arabica and further analyzed. Genomic rearrangements involving homoeologous exchanges appear to occur in C. arabica and to be a major source of genetic diversity. At least 5% of the C. arabica genes were inferred to have undergone homoeolog loss. The detection of a large number of homoeologous exchange events (HEEs) shared by all accessions of C. arabica strongly reinforces the assumption of a single allopolyploidization event. Furthermore, HEEs were specific to one or a few accessions, suggesting that HEE accumulates gradually. Our results provide evidence for the important role of HEE in allopolyploid genome evolution.
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Affiliation(s)
- Philippe Lashermes
- IRD, UMR RPB (IRD, CIRAD, Université Montpellier II), 911 avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
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