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Liang Q, Muñoz-Amatriaín M, Shu S, Lo S, Wu X, Carlson JW, Davidson P, Goodstein DM, Phillips J, Janis NM, Lee EJ, Liang C, Morrell PL, Farmer AD, Xu P, Close TJ, Lonardi S. A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.). THE PLANT GENOME 2024; 17:e20319. [PMID: 36946261 DOI: 10.1002/tpg2.20319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/19/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.
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Affiliation(s)
- Qihua Liang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Joseph W Carlson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick Davidson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nadia M Janis
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Elaine J Lee
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Chenxi Liang
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | | | - Pei Xu
- Key Lab of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
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2
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Botkin JR, Farmer AD, Young ND, Curtin SJ. Genome assembly of Medicago truncatula accession SA27063 provides insight into spring black stem and leaf spot disease resistance. BMC Genomics 2024; 25:204. [PMID: 38395768 PMCID: PMC10885650 DOI: 10.1186/s12864-024-10112-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Medicago truncatula, model legume and alfalfa relative, has served as an essential resource for advancing our understanding of legume physiology, functional genetics, and crop improvement traits. Necrotrophic fungus, Ascochyta medicaginicola, the causal agent of spring black stem (SBS) and leaf spot is a devasting foliar disease of alfalfa affecting stand survival, yield, and forage quality. Host resistance to SBS disease is poorly understood, and control methods rely on cultural practices. Resistance has been observed in M. truncatula accession SA27063 (HM078) with two recessively inherited quantitative-trait loci (QTL), rnpm1 and rnpm2, previously reported. To shed light on host resistance, we carried out a de novo genome assembly of HM078. The genome, referred to as MtHM078 v1.0, is comprised of 23 contigs totaling 481.19 Mbp. Notably, this assembly contains a substantial amount of novel centromere-related repeat sequences due to deep long-read sequencing. Genome annotation resulted in 98.4% of BUSCO fabales proteins being complete. The assembly enabled sequence-level analysis of rnpm1 and rnpm2 for gene content, synteny, and structural variation between SBS-resistant accession SA27063 (HM078) and SBS-susceptible accession A17 (HM101). Fourteen candidate genes were identified, and some have been implicated in resistance to necrotrophic fungi. Especially interesting candidates include loss-of-function events in HM078 because they fit the inverse gene-for-gene model, where resistance is recessively inherited. In rnpm1, these include a loss-of-function in a disease resistance gene due to a premature stop codon, and a 10.85 kbp retrotransposon-like insertion disrupting a ubiquitin conjugating E2. In rnpm2, we identified a frameshift mutation causing a loss-of-function in a glycosidase, as well as a missense and frameshift mutation altering an F-box family protein. This study generated a high-quality genome of HM078 and has identified promising candidates, that once validated, could be further studied in alfalfa to enhance disease resistance.
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Affiliation(s)
- Jacob R Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN, 55108, USA.
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA.
- Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN, 55108, USA.
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, 55108, USA.
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3
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Ringelberg JJ, Koenen EJ, Sauter B, Aebli A, Rando JG, Iganci JR, de Queiroz LP, Murphy DJ, Gaudeul M, Bruneau A, Luckow M, Lewis GP, Miller JT, Simon MF, Jordão LS, Morales M, Bailey CD, Nageswara-Rao M, Nicholls JA, Loiseau O, Pennington RT, Dexter KG, Zimmermann NE, Hughes CE. Precipitation is the main axis of tropical plant phylogenetic turnover across space and time. SCIENCE ADVANCES 2023; 9:eade4954. [PMID: 36800419 PMCID: PMC10957106 DOI: 10.1126/sciadv.ade4954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Early natural historians-Comte de Buffon, von Humboldt, and De Candolle-established environment and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, a pantropical plant clade of c. 3500 species, we show that the water availability gradient from deserts to rain forests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.
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Affiliation(s)
- Jens J. Ringelberg
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Erik J. M. Koenen
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Benjamin Sauter
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Anahita Aebli
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
| | - Juliana G. Rando
- Programa de Pós Graduação em Ciências Ambientais, Centro das Ciências Biológicas e da Saúde, Universidade Federal do Oeste da Bahia, Rua Prof. José Seabra de Lemos, 316, Bairro Recanto dos Pássaros, 47808-021 Barreiras-BA, Brazil
| | - João R. Iganci
- Instituto de Biologia, Universidade Federal de Pelotas, Campus Universitário Capão do Leão, Travessa André Dreyfus s/n, 96010-900 Capão do Leão-RS, Brazil
- Programa de Pós-Graduação em Botânica, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, 91501-970 Porto Alegre-RS, Brazil
| | - Luciano P. de Queiroz
- Departamento Ciências Biológicas, Universidade Estadual de Feira de Santana, Avenida Transnordestina s/n, Novo Horizonte, 44036-900 Feira de Santana-BA, Brazil
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, Birdwood Ave., Melbourne, VIC 3004, Australia
- School of Biological, Earth and Environmental Sciences, Faculty of Science, University of New South Wales, Sydney, NSW 2052, Australia
- School of BioSciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Myriam Gaudeul
- Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA, 57 rue Cuvier, CP 39, 75231 Paris, Cedex 05, France
| | - 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
| | - Melissa Luckow
- School of Integrative Plant Science, Plant Biology Section, Cornell University, 215 Garden Avenue, Roberts Hall 260, Ithaca, NY 14853, USA
| | - Gwilym P. Lewis
- Accelerated Taxonomy Department, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3AE, UK
| | - Joseph T. Miller
- Global Biodiversity Information Facility, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Marcelo F. Simon
- Embrapa Recursos Genéticos e Biotecnologia, 70770-901 Brasília-DF, Brazil
| | - Lucas S. B. Jordão
- Programa de Pós-Graduação em Botânica, Instituto de Pesquisas Jardim Botânico do Rio de Janeiro, 22460-030 Rua Pacheco Leão-RJ, Brazil
| | - Matías Morales
- Instituto de Recursos Biológicos, CIRN-CNIA, Instituto Nacional de Tecnología Agropecuaria (INTA), Hurlingham 1686, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1425FQB Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Agronomía y Ciencias Agroalimentarias, Universidad de Morón, B1708JPD Morón, Buenos Aires, Argentina
| | - C. Donovan Bailey
- Department of Biology, New Mexico State University, Las Cruces, NM 88001, USA
| | - Madhugiri Nageswara-Rao
- United States Department of Agriculture - Agricultural Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL 33158, USA
| | - James A. Nicholls
- Australian National Insect Collection, CSIRO, Clunies Ross Street, Acton, ACT 2601, Australia
| | - Oriane Loiseau
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
| | - R. Toby Pennington
- Department of Geography, University of Exeter, Laver Building, North Park Road, Exeter EX4 4QE, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Kyle G. Dexter
- School of Geosciences, University of Edinburgh, Old College, South Bridge, Edinburgh EH8 9YL, UK
- Tropical Diversity Section, Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, UK
| | - Niklaus E. Zimmermann
- Department of Environmental System Science, ETH Zürich, Universitätstrasse 16, 8092 Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Zürcherstrasse 111, 8903 Birmensdorf, Switzerland
| | - Colin E. Hughes
- Department of Systematic and Evolutionary Botany, University of Zurich, Zollikerstrasse 107, CH 8008 Zurich, Switzerland
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McLay TGB, Murphy DJ, Holmes GD, Mathews S, Brown GK, Cantrill DJ, Udovicic F, Allnutt TR, Jackson CJ. A genome resource for Acacia, Australia's largest plant genus. PLoS One 2022; 17:e0274267. [PMID: 36240205 PMCID: PMC9565413 DOI: 10.1371/journal.pone.0274267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 08/24/2022] [Indexed: 11/05/2022] Open
Abstract
Acacia (Leguminosae, Caesalpinioideae, mimosoid clade) is the largest and most widespread genus of plants in the Australian flora, occupying and dominating a diverse range of environments, with an equally diverse range of forms. For a genus of its size and importance, Acacia currently has surprisingly few genomic resources. Acacia pycnantha, the golden wattle, is a woody shrub or tree occurring in south-eastern Australia and is the country's floral emblem. To assemble a genome for A. pycnantha, we generated long-read sequences using Oxford Nanopore Technology, 10x Genomics Chromium linked reads, and short-read Illumina sequences, and produced an assembly spanning 814 Mb, with a scaffold N50 of 2.8 Mb, and 98.3% of complete Embryophyta BUSCOs. Genome annotation predicted 47,624 protein-coding genes, with 62.3% of the genome predicted to comprise transposable elements. Evolutionary analyses indicated a shared genome duplication event in the Caesalpinioideae, and conflict in the relationships between Cercis (subfamily Cercidoideae) and subfamilies Caesalpinioideae and Papilionoideae (pea-flowered legumes). Comparative genomics identified a suite of expanded and contracted gene families in A. pycnantha, and these were annotated with both GO terms and KEGG functional categories. One expanded gene family of particular interest is involved in flowering time and may be associated with the characteristic synchronous flowering of Acacia. This genome assembly and annotation will be a valuable resource for all studies involving Acacia, including the evolution, conservation, breeding, invasiveness, and physiology of the genus, and for comparative studies of legumes.
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Affiliation(s)
- Todd G. B. McLay
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
- School of BioSciences, The University of Melbourne, Parkville, Victoria, Australia
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
| | - Daniel J. Murphy
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Gareth D. Holmes
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | - Sarah Mathews
- Centre for Australian Biodiversity Research, CSIRO, Black Mountain, Australian Capital Territory, Australia
- Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America
| | - Gillian K. Brown
- Queensland Herbarium, Department of Environment and Science, Toowong, Queensland, Australia
| | | | - Frank Udovicic
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
| | | | - Chris J. Jackson
- Royal Botanic Gardens Victoria, South Yarra, Victoria, Australia
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5
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Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
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Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
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6
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Zhong Y, Chen Y, Zheng D, Pang J, Liu Y, Luo S, Meng S, Qian L, Wei D, Dai S, Zhou R. Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia. DNA Res 2022; 29:6570587. [PMID: 35438173 PMCID: PMC9052405 DOI: 10.1093/dnares/dsac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
Cercidoideae, one of the six subfamilies of Leguminosae, contains one genus Cercis with its chromosome number 2n = 14 and all other genera with 2n = 28. An allotetraploid origin hypothesis for the common ancestor of non-Cercis genera in this subfamily has been proposed; however, no chromosome-level genomes from Cercidoideae have been available to test this hypothesis. Here, we conducted a chromosome-level genome assembly of Bauhinia variegata to test this hypothesis. The assembled genome is 326.4 Mb with the scaffold N50 of 22.1 Mb and contains 37,996 protein-coding genes. The Ks distribution between gene pairs in the syntenic regions indicates two whole-genome duplications (WGDs): one is B. variegata-specific, and the other is shared among core eudicots. Although Ks between gene pairs generated by the recent WGD in Bauhinia is greater than that between Bauhinia and Cercis, the WGD was not detected in Cercis, which can be explained by an accelerated evolutionary rate in Bauhinia after divergence from Cercis. Ks distribution and phylogenetic analysis for gene pairs generated by the recent WGD in Bauhinia and their corresponding orthologs in Cercis support the allopolyploidy origin hypothesis of Bauhinia. The genome of B. variegata also provides a genomic resource for dissecting genetic basis of its ornamental traits.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yong Chen
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Danjing Zheng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Jingyi Pang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shukai Luo
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Shiyuan Meng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Lei Qian
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Dan Wei
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Seping Dai
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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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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8
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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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9
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Zhao Y, Zhang R, Jiang KW, Qi J, Hu Y, Guo J, Zhu R, Zhang T, Egan AN, Yi TS, Huang CH, Ma H. Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogen-fixing symbiosis in Fabaceae. MOLECULAR PLANT 2021; 14:748-773. [PMID: 33631421 DOI: 10.1016/j.molp.2021.02.006] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/31/2020] [Accepted: 02/19/2021] [Indexed: 05/20/2023]
Abstract
Fabaceae are the third largest angiosperm family, with 765 genera and ∼19 500 species. They are important both economically and ecologically, and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability. However, resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive, precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae. Here, we report a highly resolved phylogeny using >1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species, along with other datasets, for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera. The subfamilies are maximally supported as monophyletic. The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes, and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae. Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary, marked by mass extinction, and subsequent divergence of most tribe-level clades within ∼15 million years. Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae, including those at the ancestors of Fabaceae and five of the subfamilies, and further analyses supported the Fabaceae ancestral polyploidy. The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switch(es) to rhizobial nodulation followed by multiple losses. Collectively, these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.
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Affiliation(s)
- Yiyong Zhao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China; Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China
| | - Kai-Wen Jiang
- Key Laboratory of Biodiversity Conservation in Southwest China, State Forestry Administration, Southwest Forestry University, Kunming 650224, PR China; Ningbo Botanical Garden Herbarium, Ningbo 315201, PR China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Yi Hu
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Jing Guo
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Renbin Zhu
- Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, PR China
| | - Taikui Zhang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China
| | - Ashley N Egan
- Department of Biology, Utah Valley University, Orem, UT 84058, USA
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road, Kunming 650201, China.
| | - Chien-Hsun Huang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center of Genetics and Development, Ministry of Education Key Laboratory of Biodiversity and Ecological Engineering, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 2005 Songhu Road, Shanghai 200433, China.
| | - Hong Ma
- Department of Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA.
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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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11
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Koenen EJM, Ojeda DI, Steeves R, Migliore J, Bakker FT, Wieringa JJ, Kidner C, Hardy OJ, Pennington RT, Bruneau A, Hughes CE. Large-scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near-simultaneous evolutionary origin of all six subfamilies. THE NEW PHYTOLOGIST 2020; 225:1355-1369. [PMID: 31665814 PMCID: PMC6972672 DOI: 10.1111/nph.16290] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/14/2019] [Indexed: 05/02/2023]
Abstract
Phylogenomics is increasingly used to infer deep-branching relationships while revealing the complexity of evolutionary processes such as incomplete lineage sorting, hybridization/introgression and polyploidization. We investigate the deep-branching relationships among subfamilies of the Leguminosae (or Fabaceae), the third largest angiosperm family. Despite their ecological and economic importance, a robust phylogenetic framework for legumes based on genome-scale sequence data is lacking. We generated alignments of 72 chloroplast genes and 7621 homologous nuclear-encoded proteins, for 157 and 76 taxa, respectively. We analysed these with maximum likelihood, Bayesian inference, and a multispecies coalescent summary method, and evaluated support for alternative topologies across gene trees. We resolve the deepest divergences in the legume phylogeny despite lack of phylogenetic signal across all chloroplast genes and the majority of nuclear genes. Strongly supported conflict in the remainder of nuclear genes is suggestive of incomplete lineage sorting. All six subfamilies originated nearly simultaneously, suggesting that the prevailing view of some subfamilies as 'basal' or 'early-diverging' with respect to others should be abandoned, which has important implications for understanding the evolution of legume diversity and traits. Our study highlights the limits of phylogenetic resolution in relation to rapid successive speciation.
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Affiliation(s)
- Erik J. M. Koenen
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107CH‐8008ZurichSwitzerland
| | - Dario I. Ojeda
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
- Norwegian Institute of Bioeconomy ResearchHøgskoleveien 81433ÅsNorway
| | - Royce Steeves
- Institut de Recherche en Biologie Végétale and Département de Sciences BiologiquesUniversité de Montréal4101 Sherbrooke St EMontrealQCH1X 2B2Canada
- Fisheries & Oceans CanadaGulf Fisheries Center343 Université AveMonctonNBE1C 5K4Canada
| | - Jérémy Migliore
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
| | - Freek T. Bakker
- Biosystematics GroupWageningen UniversityDroevendaalsesteeg 16708 PBWageningenthe Netherlands
| | - Jan J. Wieringa
- Naturalis Biodiversity Center, LeidenDarwinweg 22333 CRLeidenthe Netherlands
| | - Catherine Kidner
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- School of Biological SciencesUniversity of EdinburghKing's Buildings, Mayfield RdEdinburghEH9 3JUUK
| | - Olivier J. Hardy
- Service Évolution Biologique et ÉcologieFaculté des SciencesUniversité Libre de BruxellesAvenue Franklin Roosevelt 501050BrusselsBelgium
| | - R. Toby Pennington
- Royal Botanic Gardens Edinburgh20a Inverleith RowEdinburghEH3 5LRUK
- GeographyUniversity of ExeterAmory Building, Rennes DriveExeterEX4 4RJUK
| | - Anne Bruneau
- Institut de Recherche en Biologie Végétale and Département de Sciences BiologiquesUniversité de Montréal4101 Sherbrooke St EMontrealQCH1X 2B2Canada
| | - Colin E. Hughes
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZollikerstrasse 107CH‐8008ZurichSwitzerland
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12
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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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13
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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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14
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Ren L, Huang W, Cannon SB. Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species. THE NEW PHYTOLOGIST 2019; 223:2090-2103. [PMID: 30834536 DOI: 10.1111/nph.15770] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 02/24/2019] [Indexed: 05/18/2023]
Abstract
Reconstruction of an ancestral genome for a set of plant species has been a challenging task because of complex histories that may include whole-genome duplications, segmental duplications, independent gene duplications or losses, diploidization and rearrangement events. Here, we describe the reconstruction a hypothetical ancestral genome for the papilionoid legumes (the largest subfamily within the third largest family in flowering plants), and evaluate the results relative to phylogenetic and chromosomal count data for this group of legumes, spanning 294 diverse papilionoid genera. To reconstruct the ancestral genomes for nine legume species with sequenced genomes, we used a maximum likelihood approach combined with a novel method for identifying informative markers for this purpose. Analyzing genomes from four species within the Phaseoleae, two in Dalbergieae, two in the 'inverted repeat loss' clade, and one in the Robinieae, we infer a common ancestral genome with nine chromosomes. The reconstructed genome structural histories are consistent with chromosomal and phylogenetic histories, but we also infer that a common ancestor with nine chromosomes was probably intermediate to an earlier state of 14 chromosomes following a whole-genome duplication that pre-dated the radiation of the papilionoid legumes, evidence for which is found in early-diverging papilionoid lineages.
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Affiliation(s)
- Longhui Ren
- Interdepartmental Genetics Graduate Program, 2014 Molecular Biology, Iowa State University, 2437 Pammel Drive, Ames, IA, 50011, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, 716 Farm House Ln, Ames, IA, 50011, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, 819 Wallace Rd, Ames, IA, 50011, USA
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