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Qu K, Liu D, Sun L, Li M, Xia T, Sun W, Xia Y. De novo assembly and comprehensive analysis of the mitochondrial genome of Taxus wallichiana reveals different repeats mediate recombination to generate multiple conformations. Genomics 2024; 116:110900. [PMID: 39067796 DOI: 10.1016/j.ygeno.2024.110900] [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: 05/05/2024] [Revised: 07/09/2024] [Accepted: 07/20/2024] [Indexed: 07/30/2024]
Abstract
Taxus plants are the exclusive source of paclitaxel, an anticancer drug with significant medicinal and economic value. Interspecies hybridization and gene introgression during evolution have obscured distinctions among Taxus species, complicating their phylogenetic classification. While the chloroplast genome of Taxus wallichiana, a widely distributed species in China, has been sequenced, its mitochondrial genome (mitogenome) remains uncharacterized.We sequenced and assembled the T. wallichiana mitogenome using BGI short reads and Nanopore long reads, facilitating comparisons with other gymnosperm mitogenomes. The T. wallichiana mitogenome spanning 469,949 bp, predominantly forms a circular configuration with a GC content of 50.51%, supplemented by 3 minor configurations mediated by one pair of LRs and two pairs of IntRs. It includes 32 protein-coding genes, 7 tRNA genes, and 3 rRNA genes, several of which exist in multiple copies.We detailed the mitogenome's structure, codon usage, RNA editing, and sequence migration between organelles, constructing a phylogenetic tree to elucidate evolutionary relationships. Unlike typical gymnosperm mitochondria, T. wallichiana shows no evidence of mitochondrial-plastid DNA transfer (MTPT), highlighting its unique genomic architecture. Synteny analysis indicated extensive genomic rearrangements in T. wallichiana, likely driven by recombination among abundant repetitive sequences. This study offers a high-quality T. wallichiana mitogenome, enhancing our understanding of gymnosperm mitochondrial evolution and supporting further cultivation and utilization of Taxus species.
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Affiliation(s)
- Kai Qu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China; National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Dan Liu
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China; National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Limin Sun
- Forestry College of Shandong Agricultural University, Taian 271018, China
| | - Meng Li
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Tiantian Xia
- Shandong Jianzhu University, Jinan 250101, China
| | - Weixia Sun
- Shandong Provincial Center of Forest and Grass Germplasm Resources, Jinan 250102, China
| | - Yufei Xia
- National Engineering Laboratory of Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
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2
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Pan Y, Zhuang Y, Liu T, Chen H, Wang L, Varshney RK, Zhuang W, Wang X. Deciphering peanut complex genomes paves a way to understand its origin and domestication. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2173-2181. [PMID: 37523347 PMCID: PMC10579718 DOI: 10.1111/pbi.14125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 06/12/2023] [Accepted: 07/01/2023] [Indexed: 08/02/2023]
Abstract
Peanut (Arachis) is a key oil and protein crop worldwide with large genome. The genomes of diploid and tetraploid peanuts have been sequenced, which were compared to decipher their genome structures, evolutionary, and life secrets. Genome sequencing efforts showed that different cultivars, although Bt homeologs being more privileged in gene retention and gene expression. This subgenome bias, extended to sequence variation and point mutation, might be related to the long terminal repeat (LTR) explosions after tetraploidization, especially in At subgenomes. Except that, whole-genome sequences revealed many important genes, for example, fatty acids and triacylglycerols pathway, NBS-LRR (nucleotide-binding site-leucine-rich repeats), and seed size decision genes, were enriched after recursive polyploidization. Each ancestral polyploidy, with old ones having occurred hundreds of thousand years ago, has thousands of duplicated genes in extant genomes, contributing to genetic novelty. Notably, although full genome sequences are available, the actual At subgenome ancestor has still been elusive, highlighted with new debate about peanut origin. Although being an orphan crop lagging behind other crops in genomic resources, the genome sequencing achievement has laid a solid foundation for advancing crop enhancement and system biology research of peanut.
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Affiliation(s)
- Yuxin Pan
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Yuhui Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tao Liu
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
| | - Hua Chen
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Lihui Wang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, and Centre for Crop & Food InnovationFood Futures InstituteMurdoch UniversityMurdochWest AustraliaAustralia
| | - Weijian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell BiologyOil Crops Research InstituteState Key Laboratory of Ecological Pest Control for Fujian and Taiwan CropsFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiyin Wang
- Center for Genomics and Computational BiologyCollege of Life Science, and College of ScienceNorth China University of Science and TechnologyTangshanHebeiChina
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3
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Samoluk SS, Vaio M, Ortíz AM, Chalup LMI, Robledo G, Bertioli DJ, Seijo G. Comparative repeatome analysis reveals new evidence on genome evolution in wild diploid Arachis (Fabaceae) species. PLANTA 2022; 256:50. [PMID: 35895167 DOI: 10.1007/s00425-022-03961-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Opposing changes in the abundance of satellite DNA and long terminal repeat (LTR) retroelements are the main contributors to the variation in genome size and heterochromatin amount in Arachis diploids. The South American genus Arachis (Fabaceae) comprises 83 species organized in nine taxonomic sections. Among them, section Arachis is characterized by species with a wide genome and karyotype diversity. Such diversity is determined mainly by the amount and composition of repetitive DNA. Here we performed computational analysis on low coverage genome sequencing to infer the dynamics of changes in major repeat families that led to the differentiation of genomes in diploid species (x = 10) of genus Arachis, focusing on section Arachis. Estimated repeat content ranged from 62.50 to 71.68% of the genomes. Species with different genome composition tended to have different landscapes of repeated sequences. Athila family retrotransposons were the most abundant and variable lineage among Arachis repeatomes, with peaks of transpositional activity inferred at different times in the evolution of the species. Satellite DNAs (satDNAs) were less abundant, but differentially represented among species. High rates of evolution of an AT-rich superfamily of satDNAs led to the differential accumulation of heterochromatin in Arachis genomes. The relationship between genome size variation and the repetitive content is complex. However, largest genomes presented a higher accumulation of LTR elements and lower contents of satDNAs. In contrast, species with lowest genome sizes tended to accumulate satDNAs in detriment of LTR elements. Phylogenetic analysis based on repetitive DNA supported the genome arrangement of section Arachis. Altogether, our results provide the most comprehensive picture on the repeatome dynamics that led to the genome differentiation of Arachis species.
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Affiliation(s)
- Sergio S Samoluk
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina.
| | - Magdalena Vaio
- Laboratory of Plant Genome Evolution and Domestication, Department of Plant Biology, Faculty of Agronomy, University of the Republic, Montevideo, Uruguay
| | - Alejandra M Ortíz
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Laura M I Chalup
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
| | - Germán Robledo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (UNNE-CONICET), Facultad de Ciencias Agrarias, Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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4
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Zhang Y, Chai M, Zhang X, Yang G, Yao X, Song H. The fate of drought-related genes after polyploidization in Arachis hypogaea cv. Tifrunner. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1249-1259. [PMID: 35910439 PMCID: PMC9334475 DOI: 10.1007/s12298-022-01198-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/25/2022] [Accepted: 06/06/2022] [Indexed: 06/03/2023]
Abstract
Drought stress affects plant growth and development. Cultivated peanut (Arachis hypogaea) was formed by a cross between A. duranensis and A. ipaensis. The drought tolerance of A. duranensis and A. ipaensis is reportedly stronger than that of cultivated peanut. However, there has been little study of drought tolerance genes in Arachis. In this study, we compared drought tolerance genes between A. hypogaea cv. Tifrunner and its diploid donors. We have observed that polyploidization does not generate more drought tolerance genes in A. hypogaea cv. Tifrunner but promotes the loss of many ancient drought tolerance genes. Although putative drought tolerance genes occurred on gene duplication events in A. hypogaea cv. Tifrunner, most copies lacked drought tolerance. These findings suggest that the loss of drought tolerance genes in A. hypogaea cv. Tifrunner could possibly result in weaker drought tolerance. In addition, we have observed that the three Arachis species stochastically lost putative drought tolerance genes. The evolution of drought tolerance genes could possibly have correlated with environmental changes. Our results enhance the current understanding of drought tolerance and polyploidy evolution in Arachis species. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01198-0.
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Affiliation(s)
- Yongli Zhang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Maofeng Chai
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Xiaojun Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
| | - Xiang Yao
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Nanjing, China
| | - Hui Song
- Grassland Agri-Husbandry Research Center, College of Grassland Science, Qingdao Agricultural University, Qingdao, China
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5
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Faizullah L, Morton JA, Hersch-Green EI, Walczyk AM, Leitch AR, Leitch IJ. Exploring environmental selection on genome size in angiosperms. TRENDS IN PLANT SCIENCE 2021; 26:1039-1049. [PMID: 34219022 DOI: 10.1016/j.tplants.2021.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Accepted: 06/02/2021] [Indexed: 05/22/2023]
Abstract
Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.
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Affiliation(s)
- Lubna Faizullah
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Joseph A Morton
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK; School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK
| | - Erika I Hersch-Green
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Angela M Walczyk
- Department of Biological Sciences, Michigan Technological University, Houghton, MI, USA
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, UK.
| | - Ilia J Leitch
- Character Evolution Team, Royal Botanic Gardens, Kew, Richmond, Surrey, UK.
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6
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Bertioli DJ, Clevenger J, Godoy IJ, Stalker HT, Wood S, Santos JF, Ballén-Taborda C, Abernathy B, Azevedo V, Campbell J, Chavarro C, Chu Y, Farmer AD, Fonceka D, Gao D, Grimwood J, Halpin N, Korani W, Michelotto MD, Ozias-Akins P, Vaughn J, Youngblood R, Moretzsohn MC, Wright GC, Jackson SA, Cannon SB, Scheffler BE, Leal-Bertioli SCM. Legacy genetics of Arachis cardenasii in the peanut crop shows the profound benefits of international seed exchange. Proc Natl Acad Sci U S A 2021; 118:e2104899118. [PMID: 34518223 PMCID: PMC8463892 DOI: 10.1073/pnas.2104899118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2021] [Indexed: 12/26/2022] Open
Abstract
The narrow genetics of most crops is a fundamental vulnerability to food security. This makes wild crop relatives a strategic resource of genetic diversity that can be used for crop improvement and adaptation to new agricultural challenges. Here, we uncover the contribution of one wild species accession, Arachis cardenasii GKP 10017, to the peanut crop (Arachis hypogaea) that was initiated by complex hybridizations in the 1960s and propagated by international seed exchange. However, until this study, the global scale of the dispersal of genetic contributions from this wild accession had been obscured by the multiple germplasm transfers, breeding cycles, and unrecorded genetic mixing between lineages that had occurred over the years. By genetic analysis and pedigree research, we identified A. cardenasii-enhanced, disease-resistant cultivars in Africa, Asia, Oceania, and the Americas. These cultivars provide widespread improved food security and environmental and economic benefits. This study emphasizes the importance of wild species and collaborative networks of international expertise for crop improvement. However, it also highlights the consequences of the implementation of a patchwork of restrictive national laws and sea changes in attitudes regarding germplasm that followed in the wake of the Convention on Biological Diversity. Today, the botanical collections and multiple seed exchanges which enable benefits such as those revealed by this study are drastically reduced. The research reported here underscores the vital importance of ready access to germplasm in ensuring long-term world food security.
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Affiliation(s)
- David J Bertioli
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602;
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Josh Clevenger
- HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806
| | | | - H T Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
| | - Shona Wood
- Centre for Crop Health, University of Southern Queensland, Toowoomba QLD, Australia 4370
| | - Joáo F Santos
- Instituto Agronômico, Campinas, SP, Brazil 13075-630
| | | | - Brian Abernathy
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA 30602
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Vania Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India 502324
| | - Jacqueline Campbell
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA 50011
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA 31793
| | | | - Daniel Fonceka
- AGAP (Amélioration Génétique et Adaptation des Plantes Méditerranéennes et Tropicales), Univ Montpellier, CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), INRAE (Institut National de la Recherche Agronomique), Montpellier SupAgro, Montpellier, France 34090
- CIRAD (Centre de coopération Internationale en Recherche Agronomique pour le Développement), UMR AGAP (Amélioration Génétique et Adaptation des Plantes méditerranéennes et tropicales), Thies BP, Senegal 3320
| | - Dongying Gao
- Small Grains and Potato Germplasm Research Unit, United States Department of Agriculture (USDA)-ARS, Aberdeen, ID 83210
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806
| | - Neil Halpin
- Queensland Department of Agriculture and Fisheries, Bundaberg Research Facility, QLD, Australia 4670
| | - Walid Korani
- HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806
| | - Marcos D Michelotto
- Agência Paulista de Tecnologia dos Agronegócios, Polo Regional Centro Norte, Pindorama, São Paulo, Brazil 15830-000
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602
- Department of Horticulture, University of Georgia, Tifton, GA 31793
| | - Justin Vaughn
- Genomics and Bioinformatics Research Unit, USDA-ARS, Athens, GA 30602
| | - Ramey Youngblood
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS 39762
| | - Marcio C Moretzsohn
- Embrapa (Empresa Brasileira de Pesquisa Agropecuária) Genetic Resources and Biotechnology, PqEB, W5 Norte Final, Brasília, DF, Brazil 70770-917
| | - Graeme C Wright
- Peanut Company of Australia Pty Ltd, Kingaroy, QLD, Australia 4610
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, QLD, Australia 4072
| | - Scott A Jackson
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA 50011
| | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, US Department of Agriculture Agricultural Research Service, Stoneville, MS 38776
| | - Soraya C M Leal-Bertioli
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602;
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
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Wang X, Morton JA, Pellicer J, Leitch IJ, Leitch AR. Genome downsizing after polyploidy: mechanisms, rates and selection pressures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1003-1015. [PMID: 34077584 DOI: 10.1111/tpj.15363] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 05/20/2023]
Abstract
An analysis of over 10 000 plant genome sizes (GSs) indicates that most species have smaller genomes than expected given the incidence of polyploidy in their ancestries, suggesting selection for genome downsizing. However, comparing ancestral GS with the incidence of ancestral polyploidy suggests that the rate of DNA loss following polyploidy is likely to have been very low (4-70 Mb/million years, 4-482 bp/generation). This poses a problem. How might such small DNA losses be visible to selection, overcome the power of genetic drift and drive genome downsizing? Here we explore that problem, focussing on the role that double-strand break (DSB) repair pathways (non-homologous end joining and homologous recombination) may have played. We also explore two hypotheses that could explain how selection might favour genome downsizing following polyploidy: to reduce (i) nitrogen (N) and phosphate (P) costs associated with nucleic acid synthesis in the nucleus and the transcriptome and (ii) the impact of scaling effects of GS on cell size, which influences CO2 uptake and water loss. We explore the hypothesis that losses of DNA must be fastest in early polyploid generations. Alternatively, if DNA loss is a more continuous process over evolutionary time, then we propose it is a byproduct of selection elsewhere, such as limiting the damaging activity of repetitive DNA. If so, then the impact of GS on photosynthesis, water use efficiency and/or nutrient costs at the nucleus level may be emergent properties, which have advantages, but not ones that could have been selected for over generational timescales.
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Affiliation(s)
- Xiaotong Wang
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Joseph A Morton
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Jaume Pellicer
- Royal Botanic Gardens, Kew, Surrey, TW9 3AB, UK
- Institut Botànic de Barcelona (IBB, CSIC-Ajuntament de Barcelona), Passeig del Migdia sn, Barcelona, 08038, Spain
| | | | - Andrew R Leitch
- Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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Heitkam T, Schulte L, Weber B, Liedtke S, Breitenbach S, Kögler A, Morgenstern K, Brückner M, Tröber U, Wolf H, Krabel D, Schmidt T. Comparative Repeat Profiling of Two Closely Related Conifers ( Larix decidua and Larix kaempferi) Reveals High Genome Similarity With Only Few Fast-Evolving Satellite DNAs. Front Genet 2021; 12:683668. [PMID: 34322154 PMCID: PMC8312256 DOI: 10.3389/fgene.2021.683668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/25/2021] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic genomes, cycles of repeat expansion and removal lead to large-scale genomic changes and propel organisms forward in evolution. However, in conifers, active repeat removal is thought to be limited, leading to expansions of their genomes, mostly exceeding 10 giga base pairs. As a result, conifer genomes are largely littered with fragmented and decayed repeats. Here, we aim to investigate how the repeat landscapes of two related conifers have diverged, given the conifers' accumulative genome evolution mode. For this, we applied low-coverage sequencing and read clustering to the genomes of European and Japanese larch, Larix decidua (Lamb.) Carrière and Larix kaempferi (Mill.), that arose from a common ancestor, but are now geographically isolated. We found that both Larix species harbored largely similar repeat landscapes, especially regarding the transposable element content. To pin down possible genomic changes, we focused on the repeat class with the fastest sequence turnover: satellite DNAs (satDNAs). Using comparative bioinformatics, Southern, and fluorescent in situ hybridization, we reveal the satDNAs' organizational patterns, their abundances, and chromosomal locations. Four out of the five identified satDNAs are widespread in the Larix genus, with two even present in the more distantly related Pseudotsuga and Abies genera. Unexpectedly, the EulaSat3 family was restricted to L. decidua and absent from L. kaempferi, indicating its evolutionarily young age. Taken together, our results exemplify how the accumulative genome evolution of conifers may limit the overall divergence of repeats after speciation, producing only few repeat-induced genomic novelties.
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Affiliation(s)
- Tony Heitkam
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Luise Schulte
- Institute of Botany, Technische Universität Dresden, Dresden, Germany.,Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Susan Liedtke
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Sarah Breitenbach
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Anja Kögler
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
| | - Kristin Morgenstern
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | | | - Ute Tröber
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Heino Wolf
- Staatsbetrieb Sachsenforst, Pirna, Germany
| | - Doris Krabel
- Institute of Forest Botany and Forest Zoology, Technische Universität Dresden, Tharandt, Germany
| | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, Dresden, Germany
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9
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Li Z, McKibben MTW, Finch GS, Blischak PD, Sutherland BL, Barker MS. Patterns and Processes of Diploidization in Land Plants. ANNUAL REVIEW OF PLANT BIOLOGY 2021; 72:387-410. [PMID: 33684297 DOI: 10.1146/annurev-arplant-050718-100344] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Most land plants are now known to be ancient polyploids that have rediploidized. Diploidization involves many changes in genome organization that ultimately restore bivalent chromosome pairing and disomic inheritance, and resolve dosage and other issues caused by genome duplication. In this review, we discuss the nature of polyploidy and its impact on chromosome pairing behavior. We also provide an overview of two major and largely independent processes of diploidization: cytological diploidization and genic diploidization/fractionation. Finally, we compare variation in gene fractionation across land plants and highlight the differences in diploidization between plants and animals. Altogether, we demonstrate recent advancements in our understanding of variation in the patterns and processes of diploidization in land plants and provide a road map for future research to unlock the mysteries of diploidization and eukaryotic genome evolution.
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Affiliation(s)
- Zheng Li
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael T W McKibben
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Geoffrey S Finch
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Paul D Blischak
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Brittany L Sutherland
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona 85721, USA; , , , , ,
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10
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Massa AN, Bressano M, Soave JH, Buteler MI, Seijo G, Sobolev VS, Orner VA, Oddino C, Soave SJ, Faustinelli PC, de Blas FJ, Lamb MC, Arias RS. Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study. PeerJ 2021; 9:e10581. [PMID: 33575123 PMCID: PMC7849506 DOI: 10.7717/peerj.10581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.
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Affiliation(s)
- Alicia N Massa
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Marina Bressano
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Juan H Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Guillermo Seijo
- Instituto de Botánica del Nordeste (IBONE, CONICET-UNNE) and Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | | | - Valerie A Orner
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | | | - Sara J Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Francisco J de Blas
- Instituto Multidisciplinario de Biología Vegetal-(IMBIV-CONICET-UNC), Córdoba, Argentina
| | - Marshall C Lamb
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Renee S Arias
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
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11
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Giraud D, Lima O, Huteau V, Coriton O, Boutte J, Kovarik A, Leitch AR, Leitch IJ, Aïnouche M, Salmon A. Evolutionary dynamics of transposable elements and satellite DNAs in polyploid Spartina species. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 302:110671. [PMID: 33288000 DOI: 10.1016/j.plantsci.2020.110671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 09/06/2020] [Indexed: 06/12/2023]
Abstract
Repeated sequences and polyploidy play a central role in plant genome dynamics. Here, we analyze the evolutionary dynamics of repeats in tetraploid and hexaploid Spartina species that diverged during the last 10 million years within the Chloridoideae, one of the poorest investigated grass lineages. From high-throughput genome sequencing, we annotated Spartina repeats and determined what sequence types account for the genome size variation among species. We examined whether differential genome size evolution correlated with ploidy levels and phylogenetic relationships. We also examined the tempo of repeat sequence dynamics associated with allopatric speciation over the last 3-6 million years between hexaploid species that diverged on the American and European Atlantic coasts and tetraploid species from North and South America. The tetraploid S. spartinae, whose phylogenetic placement has been debated, exhibits a similar repeat content as hexaploid species, suggesting common ancestry. Genome expansion or contraction resulting from repeat dynamics seems to be explained mostly by the contrasting divergence times between species, rather than by genome changes triggered by ploidy level change per se. One 370 bp satellite may be exhibiting 'meiotic drive' and driving chromosome evolution in S. alterniflora. Our results provide crucial insights for investigating the genetic and epigenetic consequences of such differential repeat dynamics on the ecology and distribution of the meso- and neopolyploid Spartina species.
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Affiliation(s)
- Delphine Giraud
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Oscar Lima
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Virginie Huteau
- Plateforme de cytogénétique moléculaire végétale, INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Olivier Coriton
- Plateforme de cytogénétique moléculaire végétale, INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Julien Boutte
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France; INRAE, Université de Rennes 1, Agrocampus Ouest, IGEPP, F-35650, Le Rheu, France.
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, CZ-61265, Czech Republic.
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK.
| | - Ilia J Leitch
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, TW9 3DS, UK.
| | - Malika Aïnouche
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
| | - Armel Salmon
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, F-35042, Rennes Cedex, France.
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12
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Moeglein MK, Chatelet DS, Donoghue MJ, Edwards EJ. Evolutionary dynamics of genome size in a radiation of woody plants. AMERICAN JOURNAL OF BOTANY 2020; 107:1527-1541. [PMID: 33079383 DOI: 10.1002/ajb2.1544] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/06/2020] [Indexed: 05/22/2023]
Abstract
PREMISE Plant genome size ranges widely, providing many opportunities to examine how genome size variation affects plant form and function. We analyzed trends in chromosome number, genome size, and leaf traits for the woody angiosperm clade Viburnum to examine the evolutionary associations, functional implications, and possible drivers of genome size. METHODS Chromosome counts and genome size estimates were mapped onto a Viburnum phylogeny to infer the location and frequency of polyploidization events and trends in genome size evolution. Genome size was analyzed with leaf anatomical and physiological data to evaluate the influence of genome size on plant function. RESULTS We discovered nine independent polyploidization events, two reductions in base chromosome number, and substantial variation in genome size with a slight trend toward genome size reduction in polyploids. We did not find strong relationships between genome size and the functional and morphological traits that have been highlighted at broader phylogenetic scales. CONCLUSIONS Polyploidization events were sometimes associated with rapid radiations, demonstrating that polyploid lineages can be highly successful. Relationships between genome size and plant physiological function observed at broad phylogenetic scales may be largely irrelevant to the evolutionary dynamics of genome size at smaller scales. The view that plants readily tolerate changes in ploidy and genome size, and often do so, appears to apply to Viburnum.
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Affiliation(s)
- Morgan K Moeglein
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520, USA
| | - David S Chatelet
- Biomedical Imaging Unit, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Michael J Donoghue
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520, USA
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, New Haven, CT, 06520, USA
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13
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Mata-Sucre Y, Sader M, Van-Lume B, Gagnon E, Pedrosa-Harand A, Leitch IJ, Lewis GP, Souza G. How diverse is heterochromatin in the Caesalpinia group? Cytogenomic characterization of Erythrostemon hughesii Gagnon & G.P. Lewis (Leguminosae: Caesalpinioideae). PLANTA 2020; 252:49. [PMID: 32918627 DOI: 10.1007/s00425-020-03453-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/27/2020] [Indexed: 05/25/2023]
Abstract
Cytogenomic characterization of Erythrostemon hughesii reveals a heterogeneity of repeats in its subtelomeric heterochromatin. Comparative analyses with other Caesalpinia group species reveal a significant reduction in the abundance of Ty3-gypsy/Chromovirus Tekay retrotransposons during its evolution. In numerically stable karyotypes, repetitive DNA variability is one of the main causes of genome and chromosome variation and evolution. Species from the Caesalpinia group (Leguminosae) are karyotypically characterized by 2n = 24, with small chromosomes and highly variable CMA+ heterochromatin banding patterns that correlate with environmental variables. Erythrostemon hughesii differs from other species of the group examined to date for having subtelomeric CMA+ bands; this contrasts with most species in the group which have proximal bands. Here we analyse the repeatome of E. hughesii using genome skimming and chromosomal mapping approaches to characterize the identity of the most abundant repetitive elements and their physical location. The repetitive fraction of E. hughesii comprises 28.73% of the genome. The most abundant elements were retrotransposons (RT) with long terminal repeats (LTR-RT; 9.76%) and satellite DNAs (7.83%). Within the LTR-RTs, the most abundant lineages were: Ty1/copia-Ale (1%), Ty3/gypsy CRM (0.88%) and Ty3/gypsy Athila (0.75%). Using fluorescent in situ hybridization four satellite DNAs and several LTR-RT elements were shown to be present in most subtelomeric CMA+ bands. These results highlight how the repeatome in E. hughesii, a species from Oaxaca state in Mexico, is clearly distinct from Northeast Brazilian species of the Caesalpinia group, mainly due to its high diversity of repeats in its subtelomeric heterochromatic bands and low amount of LTR-RT Ty3/gypsy-Tekay elements. Comparative sequence analysis of Tekay elements from different species is congruent with a clade-specific origin of this LTR-RT after the divergence of the Caesalpinia group. We hypothesize that repeat-rich heterochromatin may play a role in leading to faster genomic divergence between individuals, increasing speciation and diversification.
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Affiliation(s)
- Yennifer Mata-Sucre
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Mariela Sader
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Brena Van-Lume
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Edeline Gagnon
- Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5NZ, UK
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil
| | - Ilia J Leitch
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gwilym P Lewis
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, TW9 3AB, Surrey, UK
| | - Gustavo Souza
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Federal University of Pernambuco, Rua Nelson Chaves S/N, Cidade Universitaria, Recife, PE, 50670-420, Brazil.
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14
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Chen S, Huang X. DNA sequencing: the key to unveiling genome. SCIENCE CHINA-LIFE SCIENCES 2020; 63:1593-1596. [DOI: 10.1007/s11427-020-1709-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 04/24/2020] [Indexed: 01/08/2023]
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15
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Vitales D, Álvarez I, Garcia S, Hidalgo O, Nieto Feliner G, Pellicer J, Vallès J, Garnatje T. Genome size variation at constant chromosome number is not correlated with repetitive DNA dynamism in Anacyclus (Asteraceae). ANNALS OF BOTANY 2020; 125:611-623. [PMID: 31697800 PMCID: PMC7103019 DOI: 10.1093/aob/mcz183] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/06/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND AND AIMS Changes in the amount of repetitive DNA (dispersed and tandem repeats) are considered the main contributors to genome size variation across plant species in the absence of polyploidy. However, the study of repeatome dynamism in groups showing contrasting genomic features and complex evolutionary histories is needed to determine whether other processes underlying genome size variation may have been overlooked. The main aim here was to elucidate which mechanism best explains genome size evolution in Anacyclus (Asteraceae). METHODS Using data from Illumina sequencing, we analysed the repetitive DNA in all species of Anacyclus, a genus with a reticulate evolutionary history, which displays significant genome size and karyotype diversity albeit presenting a stable chromosome number. KEY RESULTS By reconstructing ancestral genome size values, we inferred independent episodes of genome size expansions and contractions during the evolution of the genus. However, analysis of the repeatome revealed a similar DNA repeat composition across species, both qualitative and quantitative. Using comparative methods to study repeatome dynamics in the genus, we found no evidence for repeat activity causing genome size variation among species. CONCLUSIONS Our results, combined with previous cytogenetic data, suggest that genome size differences in Anacyclus are probably related to chromosome rearrangements involving losses or gains of chromosome fragments, possibly associated with homoploid hybridization. These could represent balanced rearrangements that do not disrupt gene dosage in merged genomes, for example via chromosome segment exchanges.
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Affiliation(s)
- Daniel Vitales
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
- For correspondence. Email
| | - Inés Álvarez
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - Sònia Garcia
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
| | - Oriane Hidalgo
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, UK
| | - Gonzalo Nieto Feliner
- Department of Biodiversity and Conservation, Real Jardín Botánico (CSIC), Plaza de Murillo 2, 28014 Madrid, Spain
| | - Jaume Pellicer
- Comparative Plant and Fungal Biology Department, Royal Botanic Gardens, Kew, Richmond, UK
| | - Joan Vallès
- Laboratori de Botànica – Unitat associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, Av. Joan XXIII 27–31, 08028 Barcelona, Catalonia, Spain
| | - Teresa Garnatje
- Institut Botànic de Barcelona (IBB, CSIC-ICUB), Passeig del Migdia sn, 08038 Barcelona, Catalonia, Spain
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16
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Hloušková P, Mandáková T, Pouch M, Trávníček P, Lysak MA. The large genome size variation in the Hesperis clade was shaped by the prevalent proliferation of DNA repeats and rarer genome downsizing. ANNALS OF BOTANY 2019; 124:103-120. [PMID: 31220201 PMCID: PMC6676390 DOI: 10.1093/aob/mcz036] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 02/28/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND AND AIMS Most crucifer species (Brassicaceae) have small nuclear genomes (mean 1C-value 617 Mb). The species with the largest genomes occur within the monophyletic Hesperis clade (Mandáková et al., Plant Physiology174: 2062-2071; also known as Clade E or Lineage III). Whereas most chromosome numbers in the clade are 6 or 7, monoploid genome sizes vary 16-fold (256-4264 Mb). To get an insight into genome size evolution in the Hesperis clade (~350 species in ~48 genera), we aimed to identify, quantify and localize in situ the repeats from which these genomes are built. We analysed nuclear repeatomes in seven species, covering the phylogenetic and genome size breadth of the clade, by low-pass whole-genome sequencing. METHODS Genome size was estimated by flow cytometry. Genomic DNA was sequenced on an Illumina sequencer and DNA repeats were identified and quantified using RepeatExplorer; the most abundant repeats were localized on chromosomes by fluorescence in situ hybridization. To evaluate the feasibility of bacterial artificial chromosome (BAC)-based comparative chromosome painting in Hesperis-clade species, BACs of arabidopsis were used as painting probes. KEY RESULTS Most biennial and perennial species of the Hesperis clade possess unusually large nuclear genomes due to the proliferation of long terminal repeat retrotransposons. The prevalent genome expansion was rarely, but repeatedly, counteracted by purging of transposable elements in ephemeral and annual species. CONCLUSIONS The most common ancestor of the Hesperis clade has experienced genome upsizing due to transposable element amplification. Further genome size increases, dominating diversification of all Hesperis-clade tribes, contrast with the overall stability of chromosome numbers. In some subclades and species genome downsizing occurred, presumably as an adaptive transition to an annual life cycle. The amplification versus purging of transposable elements and tandem repeats impacted the chromosomal architecture of the Hesperis-clade species.
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Affiliation(s)
- Petra Hloušková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Terezie Mandáková
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Milan Pouch
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
| | - Pavel Trávníček
- Institute of Botany, Czech Academy of Sciences, Zámek 1, 252 43 Průhonice, Czech Republic
| | - Martin A Lysak
- CEITEC - Central European Institute of Technology, and Faculty of Science, Masaryk University, Kamenice, Brno, Czech Republic
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17
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Bertioli DJ, Jenkins J, Clevenger J, Dudchenko O, Gao D, Seijo G, Leal-Bertioli SCM, Ren L, Farmer AD, Pandey MK, Samoluk SS, Abernathy B, Agarwal G, Ballén-Taborda C, Cameron C, Campbell J, Chavarro C, Chitikineni A, Chu Y, Dash S, El Baidouri M, Guo B, Huang W, Kim KD, Korani W, Lanciano S, Lui CG, Mirouze M, Moretzsohn MC, Pham M, Shin JH, Shirasawa K, Sinharoy S, Sreedasyam A, Weeks NT, Zhang X, Zheng Z, Sun Z, Froenicke L, Aiden EL, Michelmore R, Varshney RK, Holbrook CC, Cannon EKS, Scheffler BE, Grimwood J, Ozias-Akins P, Cannon SB, Jackson SA, Schmutz J. The genome sequence of segmental allotetraploid peanut Arachis hypogaea. Nat Genet 2019; 51:877-884. [PMID: 31043755 DOI: 10.1038/s41588-019-0405-z] [Citation(s) in RCA: 311] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 03/28/2019] [Indexed: 12/24/2022]
Abstract
Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.
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Affiliation(s)
- David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA. .,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA.
| | - Jerry Jenkins
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Josh Clevenger
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Dongying Gao
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.,FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Soraya C M Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | - Longhui Ren
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, IA, USA
| | | | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sergio S Samoluk
- Instituto de Botánica del Nordeste (CONICET-UNNE), Corrientes, Argentina.,FACENA, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - Brian Abernathy
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Gaurav Agarwal
- Department of Plant Pathology, University of Georgia, Tifton, GA, USA
| | | | | | | | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ye Chu
- Department of Horticulture, University of Georgia, Tifton, GA, USA
| | - Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Moaine El Baidouri
- UMR5096, Laboratoire Génome et Développement des Plantes, CNRS, Perpignan, France.,UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture, Agricultural Research Service, Tifton, GA, USA
| | - Wei Huang
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Kyung Do Kim
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Corporate R&D, LG Chem, Seoul, Republic of Korea
| | - Walid Korani
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Sophie Lanciano
- UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France.,UMR232, Diversité, Adaptation et Développement des Plantes, IRD, Montpellier, France.,UMR232, Diversité, Adaptation et Développement des Plantes, Université de Montpellier, Montpellier, France
| | - Christopher G Lui
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Marie Mirouze
- UMR5096, Laboratoire Génome et Développement des Plantes, Université de Perpignan, Perpignan, France.,UMR232, Diversité, Adaptation et Développement des Plantes, IRD, Montpellier, France.,UMR232, Diversité, Adaptation et Développement des Plantes, Université de Montpellier, Montpellier, France
| | | | - Melanie Pham
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | - Jin Hee Shin
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA.,Corporate R&D, LG Chem, Seoul, Republic of Korea
| | - Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | | | | | - Nathan T Weeks
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA, USA
| | - Xinyou Zhang
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Zheng Zheng
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Ziqi Sun
- Henan Provincial Key Laboratory for Genetic Improvement of Oil Crops, Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, China.,Key Laboratory of Oil Crops in Huanghuaihai Plains, Ministry of Agriculture and Rural Affairs, Zhengzhou, China
| | - Lutz Froenicke
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Erez L Aiden
- The Center for Genome Architecture, Baylor College of Medicine, Houston, TX, USA
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Corley Holbrook
- Crop Genetics and Breeding Research Unit, US Department of Agriculture Agricultural Research Service, Tifton, GA, USA
| | | | - Brian E Scheffler
- Genomics and Bioinformatics Research Unit, US Department of Agriculture Agricultural Research Service, Stoneville, MS, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA
| | - Peggy Ozias-Akins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA.,Department of Horticulture, University of Georgia, Tifton, GA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture Agricultural Research Service, Ames, IA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA. .,Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA. .,Department of Crop and Soil Science, University of Georgia, Athens, GA, USA.
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, USA. .,Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.
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