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Gaikwad K, Ramakrishna G, Srivastava H, Saxena S, Kaila T, Tyagi A, Sharma P, Sharma S, Sharma R, Mahla HR, Kumar K, Sv AM, Solanke AU, Kalia P, Rao AR, Rai A, Sharma TR, Singh NK. The chromosome-scale genome assembly of cluster bean provides molecular insight into edible gum (galactomannan) biosynthesis family genes. Sci Rep 2023; 13:9941. [PMID: 37336893 DOI: 10.1038/s41598-023-33762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 04/18/2023] [Indexed: 06/21/2023] Open
Abstract
Cluster bean (Cyamopsis tetragonoloba (L.) Taub 2n = 14, is commonly known as Guar. Apart from being a vegetable crop, it is an abundant source of a natural hetero-polysaccharide called guar gum or galactomannan. Here, we are reporting a chromosome-scale reference genome assembly of a popular cluster bean cultivar RGC-936, by combining sequencing data from Illumina, 10X Genomics, Oxford Nanopore technologies. An initial assembly of 1580 scaffolds with an N50 value of 7.12 Mb was generated and these scaffolds were anchored to a high density SNP linkage map. Finally, a genome assembly of 550.31 Mb (94% of the estimated genome size of ~ 580 Mb (through flow cytometry) with 58 scaffolds was obtained, including 7 super scaffolds with a very high N50 value of 78.27 Mb. Phylogenetic analysis using single copy orthologs among 12 angiosperms showed that cluster bean shared a common ancestor with other legumes 80.6 MYA. No evidence of recent whole genome duplication event in cluster bean was found in our analysis. Further comparative transcriptomics analyses revealed pod-specific up-regulation of genes encoding enzymes involved in galactomannan biosynthesis. The high-quality chromosome-scale cluster bean genome assembly will facilitate understanding of the molecular basis of galactomannan biosynthesis and aid in genomics-assisted improvement of cluster bean.
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Affiliation(s)
- Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, India.
| | | | | | - Swati Saxena
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Tanvi Kaila
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Priya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - R Sharma
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - H R Mahla
- ICAR-Central Arid Zone Research Institute, Jodhpur, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Amitha Mithra Sv
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | - Pritam Kalia
- Division of Vegetable Sciences, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - A R Rao
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - T R Sharma
- DDG (CS), Indian Council of Agricultural Research, New Delhi, India
| | - N K Singh
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
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2
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Shirasawa K, Moraga R, Ghelfi A, Hirakawa H, Nagasaki H, Ghamkhar K, Barrett BA, Griffiths AG, Isobe SN. An improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny. FRONTIERS IN PLANT SCIENCE 2023; 14:1103857. [PMID: 36875612 PMCID: PMC9975737 DOI: 10.3389/fpls.2023.1103857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data. These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.
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Affiliation(s)
- Kenta Shirasawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Roger Moraga
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
- Tea Break Bioinformatics Limited, Palmerston North, New Zealand
| | - Andrea Ghelfi
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Hideki Hirakawa
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Hideki Nagasaki
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kioumars Ghamkhar
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | - Brent A. Barrett
- AgResearch, Grasslands Research Centre, Palmerston North, New Zealand
| | | | - Sachiko N. Isobe
- Department of Frontier Research and Development, Kazusa DNA Research Institute, Kisarazu, Japan
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3
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Comparative cytogenomics reveals genome reshuffling and centromere repositioning in the legume tribe Phaseoleae. Chromosome Res 2022; 30:477-492. [PMID: 35715657 DOI: 10.1007/s10577-022-09702-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 01/25/2023]
Abstract
The tribe Phaseoleae includes several legume crops with assembled genomes. Comparative genomic studies have evidenced the preservation of large genomic blocks among legumes, although chromosome dynamics during Phaseoleae evolution has not been investigated. We conducted a comparative genomic analysis to define an informative genomic block (GB) system and to reconstruct the ancestral Phaseoleae karyotype (APK). We identified GBs based on the orthologous genes between Phaseolus vulgaris and Vigna unguiculata and searched for GBs in different genomes of the Phaseolinae (P. lunatus) and Glycininae (Amphicarpaea edgeworthii) subtribes and Spatholobus suberectus (sister to Phaseolinae and Glycininae), using Medicago truncatula as the outgroup. We also used oligo-FISH probes of two P. vulgaris chromosomes to paint the orthologous chromosomes of two non-sequenced Phaseolinae species. We inferred the APK as having n = 11 and 19 GBs (A to S), hypothesizing five chromosome fusions that reduced the ancestral legume karyotype to n = 11. We identified the rearrangements among the APK and the subtribes and species, with extensive centromere repositioning in Phaseolus. We also reconstructed the chromosome number reduction in S. suberectus. The development of the GB system and the proposed APK provide useful approaches for future comparative genomic analyses of legume species.
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Wang J, Yuan M, Feng Y, Zhang Y, Bao S, Hao Y, Ding Y, Gao X, Yu Z, Xu Q, Zhao J, Zhu Q, Wang P, Wu C, Wang J, Li Y, Xu C, Wang J. A common whole-genome paleotetraploidization in Cucurbitales. PLANT PHYSIOLOGY 2022; 190:2430-2448. [PMID: 36053177 PMCID: PMC9706448 DOI: 10.1093/plphys/kiac410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/10/2022] [Indexed: 06/01/2023]
Abstract
Cucurbitales are an important order of flowering plants known for encompassing edible plants of economic and medicinal value and numerous ornamental plants of horticultural value. By reanalyzing the genomes of two representative families (Cucurbitaceae and Begoniaceae) in Cucurbitales, we found that the previously identified Cucurbitaceae common paleotetraploidization that occurred shortly after the core-eudicot-common hexaploidization event is shared by Cucurbitales, including Begoniaceae. We built a multigenome alignment framework for Cucurbitales by identifying orthologs and paralogs and systematically redating key evolutionary events in Cucurbitales. Notably, characterizing the gene retention levels and genomic fractionation patterns between subgenomes generated from different polyploidizations in Cucurbitales suggested the autopolyploid nature of the Begoniaceae common tetraploidization and the allopolyploid nature of the Cucurbitales common tetraploidization and the Cucurbita-specific tetraploidization. Moreover, we constructed the ancestral Cucurbitales karyotype comprising 17 proto-chromosomes, confirming that the most recent common ancestor of Cucurbitaceae contained 15 proto-chromosomes and rejecting the previous hypothesis for an ancestral Cucurbitaceae karyotype with 12 proto-chromosomes. In addition, we found that the polyploidization and tandem duplication events promoted the expansion of gene families involved in the cucurbitacin biosynthesis pathway; however, gene loss and chromosomal rearrangements likely limited the expansion of these gene families.
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Affiliation(s)
- Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Min Yuan
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yan Zhang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Shoutong Bao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qiang Xu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Junxin Zhao
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Qianwen Zhu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Ping Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Chunyang Wu
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, Norch China University of Science and Technology, Tangshan 063000, China
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Jiang L, Lin M, Wang H, Song H, Zhang L, Huang Q, Chen R, Song C, Li G, Cao Y. Haplotype-resolved genome assembly of Bletilla striata (Thunb.) Reichb.f. to elucidate medicinal value. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1340-1353. [PMID: 35785503 DOI: 10.1111/tpj.15892] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Bletilla striata, commonly known as baiji, is a species used in traditional Chinese medicine; it is highly regarded for its medicinal applications and therefore has high economic value. Here, we report a high-quality haplotype-resolved genome of B. striata, haplotype A (2.37 Gb, with a scaffold N50 of 146.39 Mb and a contig N50 of 1.65 Mb) and haplotype B (2.43 Gb, with a scaffold N50 of 150.22 Mb and a contig N50 of 1.66 Mb), assembled from high-fidelity (HiFi) reads and chromosome conformation capture (Hi-C) reads. We find evidence that B. striata has undergone two whole-genome duplication (WGD) events: an ancient WGD event shared by most monocots and a recent WGD event unique to all orchids. We also reconstructed the ancestral orchid karyotype (AOK) of 18 ancient chromosomes and the evolutionary trajectories of 16 modern B. striata chromosomes. Comparative genomic analysis suggests that the expanded gene families of B. striata might play important roles in secondary metabolite biosynthesis and environmental adaptation. By combining genomic and transcriptomic data, we identified the 10 core members from nine gene families that were probably involved in B. striata polysaccharide (BSP) biosynthesis. Based on virus-induced gene silencing (VIGS) and yeast two-hybrid experiments, we present an MYB transcription factor (TF), BsMYB2, that can regulate BSP biosynthesis by directly interacting with eight key BSP-related genes: sacA1, HK1, scrK1, scrK2, GPI1, manA1, GMPP1 and UGP2_1. Our study will enhance the understanding of orchid evolution and accelerate the molecular-assisted breeding of B. striata for improving traits of medicinal value.
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Affiliation(s)
- Lan Jiang
- Key Laboratory of Non-coding RNA Transformation Research of Anhui Higher Education Institution, Yijishan Hospital of Wannan Medical College, Wuhu, 241000, China
| | - Mengfei Lin
- Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang, 330224, Jiangxi, China
| | - Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Hui Song
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | - Lin Zhang
- School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan, 430065, China
| | - Qingyu Huang
- College of Life Sciences, Anhui Normal University, Wuhu, 241000, China
| | - Renrui Chen
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Guohui Li
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu'an, 237012, China
| | - Yunpeng Cao
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, 430074, China
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6
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Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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7
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Redsun S, Hokin S, Cameron CT, Cleary AM, Berendzen J, Dash S, Brown AV, Wilkey A, Campbell JD, Huang W, Kalberer SR, Weeks NT, Cannon SB, Farmer AD. Doing Genetic and Genomic Biology Using the Legume Information System and Associated Resources. Methods Mol Biol 2022; 2443:81-100. [PMID: 35037201 DOI: 10.1007/978-1-0716-2067-0_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In this chapter, we introduce the main components of the Legume Information System ( https://legumeinfo.org ) and several associated resources. Additionally, we provide an example of their use by exploring a biological question: is there a common molecular basis, across legume species, that underlies the photoperiod-mediated transition from vegetative to reproductive development, that is, days to flowering? The Legume Information System (LIS) holds genetic and genomic data for a large number of crop and model legumes and provides a set of online bioinformatic tools designed to help biologists address questions and tasks related to legume biology. Such tasks include identifying the molecular basis of agronomic traits; identifying orthologs/syntelogs for known genes; determining gene expression patterns; accessing genomic datasets; identifying markers for breeding work; and identifying genetic similarities and differences among selected accessions. LIS integrates with other legume-focused informatics resources such as SoyBase ( https://soybase.org ), PeanutBase ( https://peanutbase.org ), and projects of the Legume Federation ( https://legumefederation.org ).
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Affiliation(s)
- Sven Redsun
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Sam Hokin
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Alan M Cleary
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Sudhansu Dash
- National Center for Genome Resources, Santa Fe, NM, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Andrew Wilkey
- ORISE, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Jacqueline D Campbell
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
- Department of Computer Science, Iowa State University, Ames, IA, USA
| | - Wei Huang
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Scott R Kalberer
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Nathan T Weeks
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA, USA.
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Bayat S, Lysak MA, Mandáková T. Genome structure and evolution in the cruciferous tribe Thlaspideae (Brassicaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1768-1785. [PMID: 34661331 DOI: 10.1111/tpj.15542] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 09/30/2021] [Accepted: 10/11/2021] [Indexed: 06/13/2023]
Abstract
Whole-genome duplications (WGDs) and chromosome rearrangements (CRs) play the key role in driving the diversification and evolution of plant lineages. Although the direct link between WGDs and plant diversification is well documented, relatively few studies focus on the evolutionary significance of CRs. The cruciferous tribe Thlaspideae represents an ideal model system to address the role of large-scale chromosome alterations in genome evolution, as most Thlaspideae species share the same diploid chromosome number (2n = 2x = 14). Here we constructed the genome structure in 12 Thlaspideae species, including field pennycress (Thlaspi arvense) and garlic mustard (Alliaria petiolata). We detected and precisely characterized genus- and species-specific CRs, mostly pericentric inversions, as the main genome-diversifying drivers in the tribe. We reconstructed the structure of seven chromosomes of an ancestral Thlaspideae genome, identified evolutionary stable chromosomes versus chromosomes prone to CRs, estimated the rate of CRs, and uncovered an allohexaploid origin of garlic mustard from diploid taxa closely related to A. petiolata and Parlatoria cakiloidea. Furthermore, we performed detailed bioinformatic analysis of the Thlaspideae repeatomes, and identified repetitive elements applicable as unique species- and genus-specific barcodes and chromosome landmarks. This study deepens our general understanding of the evolutionary role of CRs, particularly pericentric inversions, in plant genome diversification, and provides a robust base for follow-up whole-genome sequencing efforts.
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Affiliation(s)
- Soheila Bayat
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Martin A Lysak
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
| | - Terezie Mandáková
- CEITEC, Masaryk University, Brno, 62500, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, 62500, Czech Republic
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9
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Zhao Q, Meng Y, Wang P, Qin X, Cheng C, Zhou J, Yu X, Li J, Lou Q, Jahn M, Chen J. Reconstruction of ancestral karyotype illuminates chromosome evolution in the genus Cucumis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:1243-1259. [PMID: 34160852 DOI: 10.1111/tpj.15381] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 06/06/2021] [Accepted: 06/19/2021] [Indexed: 05/22/2023]
Abstract
Karyotype dynamics driven by complex chromosome rearrangements constitute a fundamental issue in evolutionary genetics. The evolutionary events underlying karyotype diversity within plant genera, however, have rarely been reconstructed from a computed ancestral progenitor. Here, we developed a method to rapidly and accurately represent extant karyotypes with the genus, Cucumis, using highly customizable comparative oligo-painting (COP) allowing visualization of fine-scale genome structures of eight Cucumis species from both African-origin and Asian-origin clades. Based on COP data, an evolutionary framework containing a genus-level ancestral karyotype was reconstructed, allowing elucidation of the evolutionary events that account for the origin of these diverse genomes within Cucumis. Our results characterize the cryptic rearrangement hotspots on ancestral chromosomes, and demonstrate that the ancestral Cucumis karyotype (n = 12) evolved to extant Cucumis genomes by hybridizations and frequent lineage- and species-specific genome reshuffling. Relative to the African species, the Asian species, including melon (Cucumis melo, n = 12), Cucumis hystrix (n = 12) and cucumber (Cucumis sativus, n = 7), had highly shuffled genomes caused by large-scale inversions, centromere repositioning and chromothripsis-like rearrangement. The deduced reconstructed ancestral karyotype for the genus allowed us to propose evolutionary trajectories and specific events underlying the origin of these Cucumis species. Our findings highlight that the partitioned evolutionary plasticity of Cucumis karyotype is primarily located in the centromere-proximal regions marked by rearrangement hotspots, which can potentially serve as a reservoir for chromosome evolution due to their fragility.
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Affiliation(s)
- Qinzheng Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ya Meng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Panqiao Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaodong Qin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junguo Zhou
- College of Horticulture and landscape, Henan Institute of Science and Technology, Xinxiang, 453000, China
| | - Xiaqing Yu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Molly Jahn
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
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10
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Choi IS, Wojciechowski MF, Ruhlman TA, Jansen RK. In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae). Mol Phylogenet Evol 2021; 163:107236. [PMID: 34147655 DOI: 10.1016/j.ympev.2021.107236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 10/21/2022]
Abstract
Plant specific mitoviruses in the 'genus' Mitovirus (Narnaviridae) and their integrated sequences (non-retroviral endogenous RNA viral elements or NERVEs) have been recently identified in various plant lineages. However, the sparse phylogenetic coverage of complete plant mitochondrial genome (mitogenome) sequences and the non-conserved nature of mitochondrial intergenic regions have hindered comparative studies on mitovirus NERVEs in plants. In this study, 10 new mitogenomes were sequenced from legumes (Fabaceae). Based on comparative genomic analysis of 27 total mitogenomes, we identified mitovirus NERVEs and transposable elements across the family. All legume mitogenomes included NERVEs and total NERVE length varied from ca. 2 kb in the papilionoid Trifolium to 35 kb in the mimosoid Acacia. Most of the NERVE integration sites were in highly variable intergenic regions, however, some were positioned in six cis-spliced mitochondrial introns. In the Acacia mitogenome, there were L1-like transposon sequences including an almost full-length copy with target site duplications (TSDs). The integration sites of NERVEs in four introns showed evidence of L1-like retrotransposition events. Phylogenetic analysis revealed that there were multiple instances of precise deletion of NERVEs between TSDs. This study provides clear evidence that a L1-like retrotransposition mechanism has a long history of contributing to the integration of viral RNA into plant mitogenomes while microhomology-mediated deletion can restore the integration site.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA.
| | | | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA; Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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11
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Lineage-Specific Rewiring of Core Pathways Predating Innovation of Legume Nodules Shapes Symbiotic Efficiency. mSystems 2021; 6:6/2/e01299-20. [PMID: 33850043 PMCID: PMC8547004 DOI: 10.1128/msystems.01299-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The interkingdom coevolution innovated the rhizobium-legume symbiosis. The application of this nitrogen-fixing system in sustainable agriculture is usually impeded by incompatible interactions between partners. However, the progressive evolution of rhizobium-legume compatibility remains elusive. In this work, deletions of rhcV encoding a structural component of the type three secretion system allow related Sinorhizobium strains to nodulate a previously incompatible soybean cultivar (Glycine max). These rhcV mutants show low to medium to high symbiotic efficiency on the same cultivated soybean while being indistinguishable on wild soybean plants (Glycine soja). The dual pantranscriptomics reveals nodule-specific activation of core symbiosis genes of Sinorhizobium and Glycine genes associated with genome duplication events along the chronogram. Unexpectedly, symbiotic efficiency is in line with lineage-dependent transcriptional profiles of core pathways which predate the diversification of Fabaceae and Sinorhizobium. This is supported by further physiological and biochemical experiments. Particularly, low-efficiency nodules show disordered antioxidant activity and low-energy status, which restrict nitrogen fixation activity. Collectively, the ancient core pathways play a crucial role in optimizing the function of later-evolved mutualistic arsenals in the rhizobium-legume coevolution. IMPORTANCE Significant roles of complex extracellular microbiota in environmental adaptation of eukaryotes in ever-changing circumstances have been revealed. Given the intracellular infection ability, facultative endosymbionts can be considered pioneers within complex extracellular microbiota and are ideal organisms for understanding the early stage of interkingdom adaptation. This work reveals that the later innovation of key symbiotic arsenals and the lineage-specific network rewiring in ancient core pathways, predating the divergence of legumes and rhizobia, underline the progressive evolution of rhizobium-legume compatibility. This insight not only is significant for improving the application benefits of rhizobial inoculants in sustainable agriculture but also advances our general understanding of the interkingdom coevolution which is theoretically explored by all host-microbiota interactions.
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12
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Abrouk M, Ahmed HI, Cubry P, Šimoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG. Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 2020; 11:4488. [PMID: 32901040 PMCID: PMC7479619 DOI: 10.1038/s41467-020-18329-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 08/16/2020] [Indexed: 01/24/2023] Open
Abstract
Sustainable food production in the context of climate change necessitates diversification of agriculture and a more efficient utilization of plant genetic resources. Fonio millet (Digitaria exilis) is an orphan African cereal crop with a great potential for dryland agriculture. Here, we establish high-quality genomic resources to facilitate fonio improvement through molecular breeding. These include a chromosome-scale reference assembly and deep re-sequencing of 183 cultivated and wild Digitaria accessions, enabling insights into genetic diversity, population structure, and domestication. Fonio diversity is shaped by climatic, geographic, and ethnolinguistic factors. Two genes associated with seed size and shattering showed signatures of selection. Most known domestication genes from other cereal models however have not experienced strong selection in fonio, providing direct targets to rapidly improve this crop for agriculture in hot and dry environments.
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Affiliation(s)
- Michael Abrouk
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hanin Ibrahim Ahmed
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Denisa Šimoníková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Yveline Pailles
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jan Bettgenhaeuser
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Liubov Gapa
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | | | | | - Nagarajan Kathiresan
- Supercomputing Core Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jana Čížková
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Eva Hřibová
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Jaroslav Doležel
- Institute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | | | - Hélène Bergès
- CNRGV Plant Genomics Center, INRAE, Toulouse, France
- Inari Agriculture, One Kendall Square Building 600/700, Cambridge, MA, 02139, USA
| | | | - Mathieu Gueye
- Laboratoire de Botanique, Département de Botanique et Géologie, IFAN Ch. A. Diop/UCAD, Dakar, Senegal
| | - Ndjido A Kane
- Senegalese Agricultural Research Institute, Dakar, Senegal
- Laboratoire Mixte International LAPSE, Dakar, Senegal
| | - Christian Leclerc
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sandrine Causse
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Sylvie Vancoppenolle
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Claire Billot
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université de Montpellier, Cirad, INRAE, Institut Agro, Montpellier, France
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zürich, Switzerland
| | | | - Adeline Barnaud
- DIADE, Univ Montpellier, IRD, Montpellier, France.
- Laboratoire Mixte International LAPSE, Dakar, Senegal.
| | - Simon G Krattinger
- Center for Desert Agriculture, Biological and Environmental Science & Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
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13
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Pootakham W, Nawae W, Naktang C, Sonthirod C, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Somta P, Laosatit K, Tangphatsornruang S. A chromosome-scale assembly of the black gram (Vigna mungo) genome. Mol Ecol Resour 2020; 21:238-250. [PMID: 32794377 DOI: 10.1111/1755-0998.13243] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/05/2020] [Accepted: 08/10/2020] [Indexed: 02/06/2023]
Abstract
Black gram (Vigna mungo) is an important short duration grain legume crop. Black gram seeds provide an inexpensive source of dietary protein. Here, we applied the 10X Genomics linked-read technology to obtain a de novo whole genome assembly of V. mungo cultivated variety Chai Nat 80 (CN80). The preliminary assembly contained 12,228 contigs and had an N50 length of 5.2 Mb. Subsequent scaffolding using the long-range Chicago and HiC techniques yielded the first high-quality, chromosome-level assembly of 499 Mb comprising 11 pseudomolecules. Comparative genomics analyses based on sequence information from single-copy orthologous genes revealed that black gram and mungbean (Vigna radiata) diverged about 2.7 million years ago . The transversion rate (4DTv) analysis in V. mungo revealed no evidence supporting a recent genome-wide duplication event observed in the tetraploid créole bean (Vigna reflexo-pilosa). The proportion of repetitive elements in the black gram genome is slightly lower than the numbers reported for related Vigna species. The majority of long terminal repeat retrotransposons appeared to integrate into the genome within the last five million years. We also examined alternative splicing events in V. mungo using full-length transcript sequences. While intron retention was the most prevalent mode of alternative splicing in several plant species, alternative 3' acceptor site selection represented the majority of events in black gram. Our high-quality genome assembly along with the genomic variation information from the germplasm provides valuable resources for accelerating the development of elite varieties through marker-assisted breeding and for future comparative genomics and phylogenetic studies in legume species.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
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14
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Koenen EJM, Ojeda DI, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Herendeen PS, Bruneau A, Hughes CE. The Origin of the Legumes is a Complex Paleopolyploid Phylogenomic Tangle Closely Associated with the Cretaceous-Paleogene (K-Pg) Mass Extinction Event. Syst Biol 2020; 70:508-526. [PMID: 32483631 PMCID: PMC8048389 DOI: 10.1093/sysbio/syaa041] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/06/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian or early Paleocene and that, apart from the Detarioideae WGD, paleopolyploidy occurred close to the KPB. We conclude that the early evolution of the legumes followed a complex history, in which multiple auto- and/or allopolyploidy events coincided with rapid diversification and in association with the mass extinction event at the KPB, ultimately underpinning the evolutionary success of the Leguminosae in the Cenozoic. [Allopolyploidy; Cretaceous–Paleogene (K–Pg) boundary; Fabaceae, Leguminosae; paleopolyploidy; phylogenomics; whole genome duplication events]
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Affiliation(s)
- Erik J M Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
| | - Dario I Ojeda
- Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium.,Norwegian Institute of Bioeconomy Research, Høgskoleveien 8, 1433 Ås, Norway
| | - Freek T Bakker
- Biosystematics Group, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands
| | - Jan J Wieringa
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Catherine Kidner
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.,School of Biological Sciences, University of Edinburgh, King's Buildings, Mayfield Rd, Edinburgh, EH9 3JU, UK
| | - Olivier J Hardy
- Service Évolution Biologique et Écologie, Faculté des Sciences, Université Libre de Bruxelles, Avenue Franklin Roosevelt 50, 1050, Brussels, Belgium
| | - R Toby Pennington
- Royal Botanic Gardens Edinburgh, 20a Inverleith Row, Edinburgh EH3 5LR, UK.,Geography, University of Exeter, Amory Building, Rennes Drive, Exeter, EX4 4RJ, UK
| | | | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques, Université de Montréal, 4101 Sherbrooke St E, Montreal, QC H1X 2B2, Canada
| | - Colin E Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH-8008, Zurich, Switzerland
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15
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Pootakham W, Sonthirod C, Naktang C, Nawae W, Yoocha T, Kongkachana W, Sangsrakru D, Jomchai N, U-Thoomporn S, Sheedy JR, Buaboocha J, Mekiyanon S, Tangphatsornruang S. De novo assemblies of Luffa acutangula and Luffa cylindrica genomes reveal an expansion associated with substantial accumulation of transposable elements. Mol Ecol Resour 2020; 21:212-225. [PMID: 32841550 DOI: 10.1111/1755-0998.13240] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/30/2020] [Accepted: 08/04/2020] [Indexed: 01/22/2023]
Abstract
Luffa spp. (sponge gourd or ridge gourd) is an economically important vegetable crop widely cultivated in China, India and Southeast Asia. Here, we employed PacBio long-read single-molecule real-time (SMRT) sequencing to perform de novo genome assemblies of two commonly cultivated Luffa species, L. acutangula and L. cylindrica. We obtained preliminary draft genomes of 734.6 Mb and 689.8 Mb with scaffold N50 of 786,130 and 578,616 bases for L. acutangula and L. cylindrica, respectively. We also applied long-range Chicago and HiC techniques to obtain the first chromosome-scale whole-genome assembly of L. acutangula. The final assembly contained 13 pseudomolecules, corresponding to the haploid chromosome number in Luffa spp. (1n = 13, 2n = 26). The sizes of the assembled Luffa genomes are approximately twice as large as the genome assemblies of related Cucurbitaceae. A large proportion of L. acutangula (62.17%; 456.69 Mb) and L. cylindrica (56.78%; 391.65 Mb) genome assemblies contained repetitive elements. Phylogenetic analyses revealed that the substantial accumulation of transposable elements likely contributed to the expansion of the Luffa genomes. We also investigated alternative splicing events in Luffa using full-length transcript sequences obtained from PacBio Isoform Sequencing (Iso-seq). While the predominant form of alternative splicing in most plant species examined was intron retention, alternative 3' acceptor site selection appeared to be a major event observed in Luffa. High-quality genome assemblies for L. acutangula and L. cylindrica reported here provide valuable resources for Luffa breeding and future genetics and comparative genomics studies in Cucurbitaceae.
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Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wanapinun Nawae
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - John R Sheedy
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
| | | | - Supat Mekiyanon
- Chia Tai Company Limited, Phra Khanong District, Bangkok, Thailand
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16
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Nelson MN, Jabbari JS, Turakulov R, Pradhan A, Pazos-Navarro M, Stai JS, Cannon SB, Real D. The First Genetic Map for a Psoraleoid Legume ( Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E973. [PMID: 32752081 PMCID: PMC7463921 DOI: 10.3390/plants9080973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 11/17/2022]
Abstract
We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map comprises 2042 genotyping-by-sequencing (GBS) markers distributed across 10 linkage groups, consistent with the haploid chromosome count for this species (n = 10). Sequence tags from the markers were used to find homologous matches in the genome sequences of the closely related species in the Phaseoleae tribe: soybean, common bean, and cowpea. No tedera linkage groups align in their entirety to chromosomes in any of these phaseoloid species, but there are long stretches of collinearity that could be used in tedera research for gene discovery purposes using the better-resourced phaseoloid species. Using Ks analysis of a tedera transcriptome against five legume genomes provides an estimated divergence time of 17.4 million years between tedera and soybean. Genomic information and resources developed here will be invaluable for breeding tedera varieties for forage and pharmaceutical purposes.
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Affiliation(s)
- Matthew N. Nelson
- CSIRO Agriculture & Food, Floreat, WA 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- Royal Botanic Gardens Kew, Millennium Seed Bank, Ardingly RH17 6TN, UK
| | - Jafar S. Jabbari
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.J.); (R.T.)
| | - Rust Turakulov
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.J.); (R.T.)
- Research School of Biology & Centre for Biodiversity Analysis, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Aneeta Pradhan
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia;
| | - Maria Pazos-Navarro
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia;
| | - Jacob S. Stai
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50010, USA;
| | - Steven B. Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Daniel Real
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia;
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17
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Xu W, Zhang Q, Yuan W, Xu F, Muhammad Aslam M, Miao R, Li Y, Wang Q, Li X, Zhang X, Zhang K, Xia T, Cheng F. The genome evolution and low-phosphorus adaptation in white lupin. Nat Commun 2020; 11:1069. [PMID: 32103018 PMCID: PMC7044338 DOI: 10.1038/s41467-020-14891-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 02/09/2020] [Indexed: 11/23/2022] Open
Abstract
White lupin (Lupinus albus) is a legume crop that develops cluster roots and has high phosphorus (P)-use efficiency (PUE) in low-P soils. Here, we assemble the genome of white lupin and find that it has evolved from a whole-genome triplication (WGT) event. We then decipher its diploid ancestral genome and reconstruct the three sub-genomes. Based on the results, we further reveal the sub-genome dominance and the genic expression of the different sub-genomes varying in relation to their transposable element (TE) density. The PUE genes in white lupin have been expanded through WGT as well as tandem and dispersed duplications. Furthermore, we characterize four main pathways for high PUE, which include carbon fixation, cluster root formation, soil-P remobilization, and cellular-P reuse. Among these, auxin modulation may be important for cluster root formation through involvement of potential genes LaABCG36s and LaABCG37s. These findings provide insights into the genome evolution and low-P adaptation of white lupin.
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Affiliation(s)
- Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
| | - Qian Zhang
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
| | - Wei Yuan
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Feiyun Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Mehtab Muhammad Aslam
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Rui Miao
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Ying Li
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Qianwen Wang
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Xing Li
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Xin Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Kang Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China
| | - Tianyu Xia
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
| | - Feng Cheng
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops of the Ministry of Agriculture, Sino-Dutch Joint Laboratory of Horticultural Genomics, Beijing, China.
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18
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Hufnagel B, Marques A, Soriano A, Marquès L, Divol F, Doumas P, Sallet E, Mancinotti D, Carrere S, Marande W, Arribat S, Keller J, Huneau C, Blein T, Aimé D, Laguerre M, Taylor J, Schubert V, Nelson M, Geu-Flores F, Crespi M, Gallardo K, Delaux PM, Salse J, Bergès H, Guyot R, Gouzy J, Péret B. High-quality genome sequence of white lupin provides insight into soil exploration and seed quality. Nat Commun 2020; 11:492. [PMID: 31980615 PMCID: PMC6981116 DOI: 10.1038/s41467-019-14197-9] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/19/2019] [Indexed: 12/31/2022] Open
Abstract
White lupin (Lupinus albus L.) is an annual crop cultivated for its protein-rich seeds. It is adapted to poor soils due to the production of cluster roots, which are made of dozens of determinate lateral roots that drastically improve soil exploration and nutrient acquisition (mostly phosphate). Using long-read sequencing technologies, we provide a high-quality genome sequence of a cultivated accession of white lupin (2n = 50, 451 Mb), as well as de novo assemblies of a landrace and a wild relative. We describe a modern accession displaying increased soil exploration capacity through early establishment of lateral and cluster roots. We also show how seed quality may have been impacted by domestication in term of protein profiles and alkaloid content. The availability of a high-quality genome assembly together with companion genomic and transcriptomic resources will enable the development of modern breeding strategies to increase and stabilize white lupin yield. White lupin is an annual crop cultivated for protein rich seeds and can produce cluster roots for efficient phosphate acquisition. Here, the authors generate high quality genome assemblies of a cultivated accession, a landrace, and a wild relative and provides insight into soil exploration and seed quality.
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Affiliation(s)
- Bárbara Hufnagel
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - André Marques
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France.,MPIPZ, Cologne, Germany
| | | | - Laurence Marquès
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Fanchon Divol
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Patrick Doumas
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | - Erika Sallet
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | | | | | | | | | - Jean Keller
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, Castanet Tolosan, France
| | | | - Thomas Blein
- Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
| | | | - Malika Laguerre
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France
| | | | | | | | | | - Martin Crespi
- Institute of Plant Sciences Paris-Saclay, Gif-sur-Yvette, France
| | | | - Pierre-Marc Delaux
- Laboratoire de Recherche en Sciences Végétales (LRSV), Université de Toulouse, CNRS, Castanet Tolosan, France
| | | | | | - Romain Guyot
- IRD, Montpellier, France INRAE / 13 Department of Electronics and Automatization, Universidad Autónoma de Manizales, Manizales, Colombia
| | - Jérôme Gouzy
- LIPM, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - Benjamin Péret
- BPMP, Univ Montpellier, CNRS, INRAE, SupAgro, Montpellier, France.
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Choi IS, Schwarz EN, Ruhlman TA, Khiyami MA, Sabir JSM, Hajarah NH, Sabir MJ, Rabah SO, Jansen RK. Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent. BMC PLANT BIOLOGY 2019; 19:448. [PMID: 31653201 PMCID: PMC6814987 DOI: 10.1186/s12870-019-2064-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/02/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Organelle genome studies of Fabaceae, an economically and ecologically important plant family, have been biased towards the plastid genome (plastome). Thus far, less than 15 mitochondrial genome (mitogenome) sequences of Fabaceae have been published, all but four of which belong to the subfamily Papilionoideae, limiting the understanding of size variation and content across the family. To address this, four mitogenomes were sequenced and assembled from three different subfamilies (Cercidoideae, Detarioideae and Caesalpinioideae). RESULTS Phylogenetic analysis based on shared mitochondrial protein coding regions produced a fully resolved and well-supported phylogeny that was completely congruent with the plastome tree. Comparative analyses suggest that two kinds of mitogenome expansions have occurred in Fabaceae. Size expansion of four genera (Tamarindus, Libidibia, Haematoxylum, and Leucaena) in two subfamilies (Detarioideae and Caesalpinioideae) occurred in relatively deep nodes, and was mainly caused by intercellular gene transfer and/or interspecific horizontal gene transfer (HGT). The second, more recent expansion occurred in the Papilionoideae as a result of duplication of native mitochondrial sequences. Family-wide gene content analysis revealed 11 gene losses, four (rps2, 7, 11 and 13) of which occurred in the ancestor of Fabaceae. Losses of the remaining seven genes (cox2, rpl2, rpl10, rps1, rps19, sdh3, sdh4) were restricted to specific lineages or occurred independently in different clades. Introns of three genes (cox2, ccmFc and rps10) showed extensive lineage-specific length variation due to large sequence insertions and deletions. Shared DNA analysis among Fabaceae mitogenomes demonstrated a substantial decay of intergenic spacers and provided further insight into HGT between the mimosoid clade of Caesalpinioideae and the holoparasitic Lophophytum (Balanophoraceae). CONCLUSION This study represents the most exhaustive analysis of Fabaceae mitogenomes so far, and extends the understanding the dynamic variation in size and gene/intron content. The four newly sequenced mitogenomes reported here expands the phylogenetic coverage to four subfamilies. The family has experienced multiple mitogenome size fluctuations in both ancient and recent times. The causes of these size variations are distinct in different lineages. Fabaceae mitogenomes experienced extensive size fluctuation by recruitment of exogenous DNA and duplication of native mitochondrial DNA.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Erika N. Schwarz
- Department of Biological Sciences, St. Edward’s University, Austin, TX 78704 USA
| | - Tracey A. Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
| | - Mohammad A. Khiyami
- King Abdulaziz City for Science and Technology (KACST), Riyadh, 11442 Saudi Arabia
| | - Jamal S. M. Sabir
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Nahid H. Hajarah
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Mernan J. Sabir
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Samar O. Rabah
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
| | - Robert K. Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589 Saudi Arabia
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Wojciechowski MF. Tracing the history of chromosome evolution in legumes using genomics. THE NEW PHYTOLOGIST 2019; 223:1693-1695. [PMID: 31173376 DOI: 10.1111/nph.15926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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21
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Stai JS, Yadav A, Sinou C, Bruneau A, Doyle JJ, Fernández-Baca D, Cannon SB. Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family. FRONTIERS IN PLANT SCIENCE 2019; 10:345. [PMID: 31105714 PMCID: PMC6499179 DOI: 10.3389/fpls.2019.00345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 03/05/2019] [Indexed: 05/02/2023]
Abstract
Based on evolutionary, phylogenomic, and synteny analyses of genome sequences for more than a dozen diverse legume species as well as analysis of chromosome counts across the legume family, we conclude that the genus Cercis provides a plausible model for an early evolutionary form of the legume genome. The small Cercis genus is in the earliest-diverging clade in the earliest-diverging legume subfamily (Cercidoideae). The Cercis genome is physically small, and has accumulated mutations at an unusually slow rate compared to other legumes. Chromosome counts across 477 legume genera, combined with phylogenetic reconstructions and histories of whole-genome duplications, suggest that the legume progenitor had 7 chromosomes - as does Cercis. We propose a model in which a legume progenitor, with 7 chromosomes, diversified into species that would become the Cercidoideae and the remaining legume subfamilies; then speciation in the Cercidoideae gave rise to the progenitor of the Cercis genus. There is evidence for a genome duplication in the remaining Cercidoideae, which is likely due to allotetraploidy involving hybridization between a Cercis progenitor and a second diploid species that existed at the time of the polyploidy event. Outside the Cercidoideae, a set of probably independent whole-genome duplications gave rise to the five other legume subfamilies, at least four of which have predominant counts of 12-14 chromosomes among their early-diverging taxa. An earlier study concluded that independent duplications occurred in the Caesalpinioideae, Detarioideae, and Papilionoideae. We conclude that Cercis may be unique among legumes in lacking evidence of polyploidy, a process that has shaped the genomes of all other legumes thus far investigated.
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Affiliation(s)
- Jacob S. Stai
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA, United States
| | - Akshay Yadav
- Bioinformatics and Computational Biology Graduate Program, Iowa State University, Ames, IA, United States
| | - Carole Sinou
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montreal, QC, Canada
| | - Jeff J. Doyle
- School of Integrative Plant Science, Plant Breeding & Genetics and Plant Biology Sections, Cornell University, Ithaca, NY, United States
| | | | - Steven B. Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture–Agricultural Research Service, Ames, IA, United States
- *Correspondence: Steven B. Cannon,
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