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Chu L, Yang K, Chen C, Zhao B, Hou Y, Wang W, Zhao P, Wang K, Wang B, Xiao Y, Li Y, Li Y, Song Q, Liu B, Fan R, Bohra A, Yu J, Sonnenschein EC, Varshney RK, Tian Z, Jian J, Wan P. Chromosome-level reference genome and resequencing of 322 accessions reveal evolution, genomic imprint and key agronomic traits in adzuki bean. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38497586 DOI: 10.1111/pbi.14337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/22/2024] [Accepted: 03/02/2024] [Indexed: 03/19/2024]
Abstract
Adzuki bean (Vigna angularis) is an important legume crop cultivated in over 30 countries worldwide. We developed a high-quality chromosome-level reference genome of adzuki bean cultivar Jingnong6 by combining PacBio Sequel long-read sequencing with short-read and Hi-C technologies. The assembled genome covers 97.8% of the adzuki bean genome with a contig N50 of approximately 16 Mb and a total of 32 738 protein-coding genes. We also generated a comprehensive genome variation map of adzuki bean by whole-genome resequencing (WGRS) of 322 diverse adzuki beans accessions including both wild and cultivated. Furthermore, we have conducted comparative genomics and a genome-wide association study (GWAS) on key agricultural traits to investigate the evolution and domestication. GWAS identified several candidate genes, including VaCycA3;1, VaHB15, VaANR1 and VaBm, that exhibited significant associations with domestication traits. Furthermore, we conducted functional analyses on the roles of VaANR1 and VaBm in regulating seed coat colour. We provided evidence for the highest genetic diversity of wild adzuki (Vigna angularis var. nipponensis) in China with the presence of the most original wild adzuki bean, and the occurrence of domestication process facilitating transition from wild to cultigen. The present study elucidates the genetic basis of adzuki bean domestication traits and provides crucial genomic resources to support future breeding efforts in adzuki bean.
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Affiliation(s)
- Liwei Chu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
- College of Life and Health, Dalian University, Dalian, Liaoning, China
| | - Kai Yang
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | | | - Bo Zhao
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Yanan Hou
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | | | - Pu Zhao
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Kaili Wang
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Binhu Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Ying Xiao
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Yongqiang Li
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Yisong Li
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, Maryland, USA
| | - Biao Liu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Ruoxi Fan
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | - Abhishek Bohra
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Jianping Yu
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
| | | | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Ping Wan
- College of Plant Science and Technology, Key Laboratory of New Technology in Agricultural Application, Beijing University of Agriculture, Beijing, China
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2
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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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3
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Dias S, de Oliveira Bustamante F, do Vale Martins L, da Costa VA, Montenegro C, Oliveira ARDS, de Lima GS, Braz GT, Jiang J, da Costa AF, Benko-Iseppon AM, Brasileiro-Vidal AC. Translocations and inversions: major chromosomal rearrangements during Vigna (Leguminosae) evolution. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:29. [PMID: 38261028 DOI: 10.1007/s00122-024-04546-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
KEY MESSAGE Inversions and translocations are the major chromosomal rearrangements involved in Vigna subgenera evolution, being Vigna vexillata the most divergent species. Centromeric repositioning seems to be frequent within the genus. Oligonucleotide-based fluorescence in situ hybridization (Oligo-FISH) provides a powerful chromosome identification system for inferring plant chromosomal evolution. Aiming to understand macrosynteny, chromosomal diversity, and the evolution of bean species from five Vigna subgenera, we constructed cytogenetic maps for eight taxa using oligo-FISH-based chromosome identification. We used oligopainting probes from chromosomes 2 and 3 of Phaseolus vulgaris L. and two barcode probes designed from V. unguiculata (L.) Walp. genome. Additionally, we analyzed genomic blocks among the Ancestral Phaseoleae Karyotype (APK), two V. unguiculata subspecies (V. subg. Vigna), and V. angularis (Willd.) Ohwi & Ohashi (V. subg. Ceratotropis). We observed macrosynteny for chromosomes 2, 3, 4, 6, 7, 8, 9, and 10 in all investigated taxa except for V. vexillata (L.) A. Rich (V. subg. Plectrotropis), in which only chromosomes 4, 7, and 9 were unambiguously identified. Collinearity breaks involved with chromosomes 2 and 3 were revealed. We identified minor differences in the painting pattern among the subgenera, in addition to multiple intra- and interblock inversions and intrachromosomal translocations. Other rearrangements included a pericentric inversion in chromosome 4 (V. subg. Vigna), a reciprocal translocation between chromosomes 1 and 5 (V. subg. Ceratotropis), a potential deletion in chromosome 11 of V. radiata (L.) Wilczek, as well as multiple intrablock inversions and centromere repositioning via genomic blocks. Our study allowed the visualization of karyotypic patterns in each subgenus, revealing important information for understanding intrageneric karyotypic evolution, and suggesting V. vexillata as the most karyotypically divergent species.
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Affiliation(s)
- Sibelle Dias
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Fernanda de Oliveira Bustamante
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade do Estado de Minas Gerais, Unidade Divinópolis, Divinópolis, MG, Brazil
| | - Lívia do Vale Martins
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
- Universidade Federal do Piauí, Floriano, PI, Brazil
| | | | - Claudio Montenegro
- Departamento de Botânica, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Geyse Santos de Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Guilherme Tomaz Braz
- Departamento de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
| | - Jiming Jiang
- Department of Plant Biology, Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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Ogiso-Tanaka E, Chankaew S, Yoshida Y, Isemura T, Marubodee R, Kongjaimun A, Baba-Kasai A, Okuno K, Ehara H, Tomooka N. Unique Salt-Tolerance-Related QTLs, Evolved in Vigna riukiuensis (Na + Includer) and V. nakashimae (Na + Excluder), Shed Light on the Development of Super-Salt-Tolerant Azuki Bean ( V. angularis) Cultivars. PLANTS (BASEL, SWITZERLAND) 2023; 12:1680. [PMID: 37111908 PMCID: PMC10146836 DOI: 10.3390/plants12081680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
Wild relatives of crops have the potential to improve food crops, especially in terms of improving abiotic stress tolerance. Two closely related wild species of the traditional East Asian legume crops, Azuki bean (Vigna angularis), V. riukiuensis "Tojinbaka" and V. nakashimae "Ukushima" were shown to have much higher levels of salt tolerance than azuki beans. To identify the genomic regions responsible for salt tolerance in "Tojinbaka" and "Ukushima", three interspecific hybrids were developed: (A) azuki bean cultivar "Kyoto Dainagon" × "Tojinbaka", (B) "Kyoto Dainagon" × "Ukushima" and (C) "Ukushima" × "Tojinbaka". Linkage maps were developed using SSR or restriction-site-associated DNA markers. There were three QTLs for "percentage of wilt leaves" in populations A, B and C, while populations A and B had three QTLs and population C had two QTLs for "days to wilt". In population C, four QTLs were detected for Na+ concentration in the primary leaf. Among the F2 individuals in population C, 24% showed higher salt tolerance than both wild parents, suggesting that the salt tolerance of azuki beans can be further improved by combining the QTL alleles of the two wild relatives. The marker information would facilitate the transfer of salt tolerance alleles from "Tojinbaka" and "Ukushima" to azuki beans.
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Affiliation(s)
- Eri Ogiso-Tanaka
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Sompong Chankaew
- Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Yutaro Yoshida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennohdai 1-1-1, Tsukuba 305-8571, Ibaraki, Japan
| | - Takehisa Isemura
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Rusama Marubodee
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu 514-0102, Mie, Japan
| | - Alisa Kongjaimun
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Akiko Baba-Kasai
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
| | - Kazutoshi Okuno
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennohdai 1-1-1, Tsukuba 305-8571, Ibaraki, Japan
| | - Hiroshi Ehara
- Graduate School of Bioresources, Mie University, 1577 Kurimamachiya-cho, Tsu 514-0102, Mie, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba 305-8602, Ibaraki, Japan
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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
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Somta P, Laosatit K, Yuan X, Chen X. Thirty Years of Mungbean Genome Research: Where Do We Stand and What Have We Learned? FRONTIERS IN PLANT SCIENCE 2022; 13:944721. [PMID: 35909762 PMCID: PMC9335052 DOI: 10.3389/fpls.2022.944721] [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: 05/15/2022] [Accepted: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Mungbean is a socioeconomically important legume crop in Asia that is currently in high demand by consumers and industries both as dried beans and in plant-based protein foods. Marker-assisted and genomics-assisted breeding are promising approaches to efficiently and rapidly develop new cultivars with improved yield, quality, and resistance to biotic and abiotic stresses. Although mungbean was at the forefront of research at the dawn of the plant genomics era 30 years ago, the crop is a "slow runner" in genome research due to limited genomic resources, especially DNA markers. Significant progress in mungbean genome research was achieved only within the last 10 years, notably after the release of the VC1973A draft reference genome constructed using next-generation sequencing technology, which enabled fast and efficient DNA marker development, gene mapping, and identification of candidate genes for complex traits. Resistance to biotic stresses has dominated mungbean genome research to date; however, research is on the rise. In this study, we provide an overview of the past progress and current status of mungbean genomics research. We also discuss and evaluate some research results to provide a better understanding of mungbean genomics.
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Affiliation(s)
- 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
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Pichot C, Djari A, Tran J, Verdenaud M, Marande W, Huneau C, Gautier V, Latrasse D, Arribat S, Sommard V, Troadec C, Poncet C, Bendahmane M, Szecsi J, Dogimont C, Salse J, Benhamed M, Zouine M, Boualem A, Bendahmane A. Cantaloupe melon genome reveals 3D chromatin features and structural relationship with the ancestral cucurbitaceae karyotype. iScience 2022; 25:103696. [PMID: 35059606 PMCID: PMC8760558 DOI: 10.1016/j.isci.2021.103696] [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: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/20/2021] [Indexed: 11/21/2022] Open
Abstract
Cucumis melo displays a large diversity of horticultural groups with cantaloupe melon the most cultivated type. Using a combination of single-molecule sequencing, 10X Genomics link-reads, high-density optical and genetic maps, and chromosome conformation capture (Hi-C), we assembled a chromosome scale C. melo var. cantalupensis Charentais mono genome. Integration of RNA-seq, MeDip-seq, ChIP-seq, and Hi-C data revealed a widespread compartmentalization of the melon genome, segregating constitutive heterochromatin and euchromatin. Genome-wide comparative and evolutionary analysis between melon botanical groups identified Charentais mono genome increasingly more divergent from Harukei-3 (reticulatus), Payzawat (inodorus), and HS (ssp. agrestis) genomes. To assess the paleohistory of the Cucurbitaceae, we reconstructed the ancestral Cucurbitaceae karyotype and compared it to sequenced cucurbit genomes. In contrast to other species that experienced massive chromosome shuffling, melon has retained the ancestral genome structure. We provide comprehensive genomic resources and new insights in the diversity of melon horticultural groups and evolution of cucurbits. We provide a chromosome scale C. melo var. cantalupensis Charentais mono genome Epigenomic analysis revealed a widespread compartmentalization of the melon genome We reconstructed the ancestral Cucurbitaceae karyotype Melon has retained the ancestral Cucurbitaceae genome structure
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Affiliation(s)
- Clement Pichot
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Anis Djari
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Joseph Tran
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Marion Verdenaud
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - William Marande
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Cecile Huneau
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Veronique Gautier
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - David Latrasse
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Sandrine Arribat
- INRAE, Centre National de Ressources Génomiques Végétales, 31326 Castanet-Tolosan, France
| | - Vivien Sommard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Charles Poncet
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRAE, CNRS, Université Lyon 1-ENSL, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Judit Szecsi
- Laboratoire Reproduction et Développement des Plantes, INRAE, CNRS, Université Lyon 1-ENSL, Ecole Normale Supérieure de Lyon, 69364 Lyon Cedex 07, France
| | - Catherine Dogimont
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Jerome Salse
- INRAE-UCA UMR 1095 GDEC, 5 chemin de Beaulieu, 63000 Clermont-Ferrand, France
| | - Moussa Benhamed
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Mohamed Zouine
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, 31320 Auzeville-Tolosane, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Université de Paris, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
- Corresponding author
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9
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do Vale Martins L, de Oliveira Bustamante F, da Silva Oliveira AR, da Costa AF, de Lima Feitoza L, Liang Q, Zhao H, Benko-Iseppon AM, Muñoz-Amatriaín M, Pedrosa-Harand A, Jiang J, Brasileiro-Vidal AC. BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris. Chromosoma 2021; 130:133-147. [PMID: 33909141 DOI: 10.1007/s00412-021-00758-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/17/2021] [Accepted: 04/05/2021] [Indexed: 01/29/2023]
Abstract
Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.
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Affiliation(s)
| | | | | | | | | | - Qihua Liang
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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10
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Unequal contribution of two paralogous CENH3 variants in cowpea centromere function. Commun Biol 2020; 3:775. [PMID: 33319863 PMCID: PMC7738545 DOI: 10.1038/s42003-020-01507-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
In most diploids the centromere-specific histone H3 (CENH3), the assembly site of active centromeres, is encoded by a single copy gene. Persistance of two CENH3 paralogs in diploids species raises the possibility of subfunctionalization. Here we analysed both CENH3 genes of the diploid dryland crop cowpea. Phylogenetic analysis suggests that gene duplication of CENH3 occurred independently during the speciation of Vigna unguiculata. Both functional CENH3 variants are transcribed, and the corresponding proteins are intermingled in subdomains of different types of centromere sequences in a tissue-specific manner together with the kinetochore protein CENPC. CENH3.2 is removed from the generative cell of mature pollen, while CENH3.1 persists. CRISPR/Cas9-based inactivation of CENH3.1 resulted in delayed vegetative growth and sterility, indicating that this variant is needed for plant development and reproduction. By contrast, CENH3.2 knockout individuals did not show obvious defects during vegetative and reproductive development. Hence, CENH3.2 of cowpea is likely at an early stage of pseudogenization and less likely undergoing subfunctionalization.
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11
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Boonjing P, Masuta Y, Nozawa K, Kato A, Ito H. The effect of zebularine on the heat-activated retrotransposon ONSEN in Arabidopsis thaliana and Vigna angularis. Genes Genet Syst 2020; 95:165-172. [PMID: 32741853 DOI: 10.1266/ggs.19-00046] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The Ty1/copia-like retrotransposon ONSEN is conserved among Brassica species, as well as in beans, including adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi), which is one of the economically important crops in Japan. ONSEN has acquired a heat-responsive element that is recognized by plant heat stress defense factors, resulting in its transcription and the production of full-length extrachromosomal DNA under conditions with elevated temperatures. DNA methylation plays an important role in regulating the activation of this transposon in plants. Therefore, chemical inhibition of DNA methyltransferases has been utilized to study the effect of DNA methylation on transposon activation. To understand the effect of DNA methylation on ONSEN activation, Arabidopsis thaliana and adzuki bean seedlings were treated with zebularine, which is known to be an effective chemical demethylation agent. The results showed that ONSEN transcription levels were upregulated in zebularine-treated plants. Extrachromosomal DNA of ONSEN also accumulated in the treated plants.
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Affiliation(s)
| | | | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University
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12
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Comparative genomics of muskmelon reveals a potential role for retrotransposons in the modification of gene expression. Commun Biol 2020; 3:432. [PMID: 32792560 PMCID: PMC7426833 DOI: 10.1038/s42003-020-01172-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/24/2020] [Indexed: 11/08/2022] Open
Abstract
Melon exhibits substantial natural variation especially in fruit ripening physiology, including both climacteric (ethylene-producing) and non-climacteric types. However, genomic mechanisms underlying such variation are not yet fully understood. Here, we report an Oxford Nanopore-based high-grade genome reference in the semi-climacteric cultivar Harukei-3 (378 Mb + 33,829 protein-coding genes), with an update of tissue-wide RNA-seq atlas in the Melonet-DB database. Comparison between Harukei-3 and DHL92, the first published melon genome, enabled identification of 24,758 one-to-one orthologue gene pairs, whereas others were candidates of copy number variation or presence/absence polymorphisms (PAPs). Further comparison based on 10 melon genome assemblies identified genome-wide PAPs of 415 retrotransposon Gag-like sequences. Of these, 160 showed fruit ripening-inducible expression, with 59.4% of the neighboring genes showing similar expression patterns (r > 0.8). Our results suggest that retrotransposons contributed to the modification of gene expression during diversification of melon genomes, and may affect fruit ripening-inducible gene expression.
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13
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Takahashi Y, Kongjaimun A, Muto C, Kobayashi Y, Kumagai M, Sakai H, Satou K, Teruya K, Shiroma A, Shimoji M, Hirano T, Isemura T, Saito H, Baba-Kasai A, Kaga A, Somta P, Tomooka N, Naito K. Same Locus for Non-shattering Seed Pod in Two Independently Domesticated Legumes, Vigna angularis and Vigna unguiculata. Front Genet 2020; 11:748. [PMID: 32793284 PMCID: PMC7391060 DOI: 10.3389/fgene.2020.00748] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
Loss of pod shattering is one of the most important domestication-related traits in legume crops. The non-shattering phenotypes have been achieved either by disturbed formation of abscission layer between the valves, or by loss of helical tension in sclerenchyma of endocarp, that split open the pods to disperse the seeds. During domestication, azuki bean (Vigna angularis) and yard-long bean (Vigna unguiculata cv-gr. Sesquipedalis) have reduced or lost the sclerenchyma and thus the shattering behavior of seed pods. Here we performed fine-mapping with backcrossed populations and narrowed the candidate genomic region down to 4 kbp in azuki bean and 13 kbp in yard-long bean. Among the genes located in these regions, we found MYB26 genes encoded truncated proteins in azuki bean, yard-long bean, and even cowpea. As such, our findings indicate that independent domestication on the two legumes has selected the same locus for the same traits. We also argue that MYB26 could be a target gene for improving shattering phenotype in other legumes, such as soybean.
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Affiliation(s)
- Yu Takahashi
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Alisa Kongjaimun
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Cha-Am, Thailand
| | - Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yuki Kobayashi
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | | | | | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences, Uruma, Japan
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences, Uruma, Japan
| | - Akino Shiroma
- Okinawa Institute of Advanced Sciences, Uruma, Japan
| | | | | | - Takehisa Isemura
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, Japan
| | - Akiko Baba-Kasai
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Akito Kaga
- Institute of Crop Science, NARO, Tsukuba, Japan
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/PERDO-CHE), Bangkok, Thailand
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Ken Naito
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
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14
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Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). Chromosome Res 2020; 28:293-306. [PMID: 32654079 DOI: 10.1007/s10577-020-09635-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/29/2020] [Accepted: 07/01/2020] [Indexed: 10/23/2022]
Abstract
Comparative cytogenetic mapping is a powerful approach to gain insights into genome organization of orphan crops, lacking a whole sequenced genome. To investigate the cytogenomic evolution of important Vigna and Phaseolus beans, we built a BAC-FISH (fluorescent in situ hybridization of bacterial artificial chromosome) map of Vigna aconitifolia (Vac, subgenus Ceratotropis), species with no sequenced genome, and compared with V. unguiculata (Vu, subgenus Vigna) and Phaseolus vulgaris (Pv) maps. Seventeen Pv BACs, eight Vu BACs, and 5S and 35S rDNA probes were hybridized in situ on the 11 Vac chromosome pairs. Five Vac chromosomes (Vac6, Vac7, Vac9, Vac10, and Vac11) showed conserved macrosynteny and collinearity between V. unguiculata and P. vulgaris. On the other hand, we observed collinearity breaks, identified by pericentric inversions involving Vac2 (Vu2), Vac4 (Vu4), and Vac3 (Pv3). We also detected macrosynteny breaks of translocation type involving chromosomes 1 and 8 of V. aconitifolia and P. vulgaris; 2 and 3 of V. aconitifolia and P. vulgaris; and 1 and 5 of V. aconitifolia and V. unguiculata. Considering our data and previous BAC-FISH studies, six chromosomes (1, 2, 3, 4, 5, and 8) are involved in major karyotype divergences between genera and five (1, 2, 3, 4, and 5) between Vigna subgenera, including mechanisms such as duplications, inversions, and translocations. Macrosynteny breaks between Vigna and Phaseolus suggest that the major chromosomal rearrangements have occurred within the Vigna clade. Our cytogenomic comparisons bring new light on the degree of shared macrosynteny and mechanisms of karyotype diversification during Vigna and Phaseolus evolution.
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15
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Tripathi P, Singh J, Lal JA, Tripathi V. Next-Generation Sequencing: An Emerging Tool for Drug Designing. Curr Pharm Des 2020; 25:3350-3357. [PMID: 31544713 DOI: 10.2174/1381612825666190911155508] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND With the outbreak of high throughput next-generation sequencing (NGS), the biological research of drug discovery has been directed towards the oncology and infectious disease therapeutic areas, with extensive use in biopharmaceutical development and vaccine production. METHOD In this review, an effort was made to address the basic background of NGS technologies, potential applications of NGS in drug designing. Our purpose is also to provide a brief introduction of various Nextgeneration sequencing techniques. DISCUSSIONS The high-throughput methods execute Large-scale Unbiased Sequencing (LUS) which comprises of Massively Parallel Sequencing (MPS) or NGS technologies. The Next geneinvolved necessarily executes Largescale Unbiased Sequencing (LUS) which comprises of MPS or NGS technologies. These are related terms that describe a DNA sequencing technology which has revolutionized genomic research. Using NGS, an entire human genome can be sequenced within a single day. CONCLUSION Analysis of NGS data unravels important clues in the quest for the treatment of various lifethreatening diseases and other related scientific problems related to human welfare.
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Affiliation(s)
- Pooja Tripathi
- Department of Computational Biology and Bioinformatics, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Jyotsna Singh
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
| | - Jonathan A Lal
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India.,Institute for Public Health Genomics, Maastricht University, Maastricht, Netherlands
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture Technology and Sciences, Prayagraj, India
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16
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Jayakumar V, Sakakibara Y. Comprehensive evaluation of non-hybrid genome assembly tools for third-generation PacBio long-read sequence data. Brief Bioinform 2020; 20:866-876. [PMID: 29112696 PMCID: PMC6585154 DOI: 10.1093/bib/bbx147] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/22/2017] [Indexed: 12/20/2022] Open
Abstract
Long reads obtained from third-generation sequencing platforms can help overcome the long-standing challenge of the de novo assembly of sequences for the genomic analysis of non-model eukaryotic organisms. Numerous long-read-aided de novo assemblies have been published recently, which exhibited superior quality of the assembled genomes in comparison with those achieved using earlier second-generation sequencing technologies. Evaluating assemblies is important in guiding the appropriate choice for specific research needs. In this study, we evaluated 10 long-read assemblers using a variety of metrics on Pacific Biosciences (PacBio) data sets from different taxonomic categories with considerable differences in genome size. The results allowed us to narrow down the list to a few assemblers that can be effectively applied to eukaryotic assembly projects. Moreover, we highlight how best to use limited genomic resources for effectively evaluating the genome assemblies of non-model organisms.
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17
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Ogiso-Tanaka E, Chankaew S, Isemura T, Kongjaimun A, Baba A, Naito K, Kaga A, Tomooka N. Whole genome sequencing data of Vigna nakashimae var. Ukushima and G418. Data Brief 2020; 29:105131. [PMID: 32021887 PMCID: PMC6994819 DOI: 10.1016/j.dib.2020.105131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/17/2019] [Accepted: 01/07/2020] [Indexed: 11/22/2022] Open
Abstract
Vigna nakashimae is one of the closely related species of Vigna angularis (Adzuki bean). Two strain of ‘Ukushima’ and ‘G418’ were identified as salt tolerance strains in Vigna nakashimae from gene bank collection. F2 populations from an inter- or intra-specific cross between the sensitive and tolerant strains are useful for the detection of salt tolerance QTL in Vigna nakashimae. Although Vigna angularis reference genome is available and useful for genetic analysis by genotyping-by-sequencing/RADseq in closely related species, it is not enough for isolation of responsible genes. To reveal sequence variation in Vigna nakashimae “Ukushima” and “G418”, the whole genome sequencing was performed using Illumina HiSeq X Ten system (411,174,986 and 478,116,282 read). NGS data was deposited in the DNA Data Bank of Japan (DDBJ) under accession number DRA009307.
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Affiliation(s)
- Eri Ogiso-Tanaka
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
- Corresponding author.
| | - Sompong Chankaew
- Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen, Nakhon Pathom 73140, Thailand
| | - Takehisa Isemura
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Alisa Kongjaimun
- Research Fellow of the Japan Society for the Promotion of Science, Japan
| | - Akiko Baba
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Ken Naito
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Akito Kaga
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
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18
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Affiliation(s)
- Malgorzata A. Witek
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66044, United States
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66044, United States
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ian M. Freed
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66044, United States
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66044, United States
| | - Steven A. Soper
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66044, United States
- Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66044, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66044, United States
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66044, United States
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19
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Abstract
Legumes (Fabaceae) are agronomically and economically one of the most important crops. Because legumes serve as a source of food, feed, and industrial materials, many studies in the field of legume genomics, including genome sequencing, have been conducted over the last decade. Here, we update the progress in genome sequencing of legume crops, including soybean (Glycine max [L.] Merr.), mung bean (V. radiata var. radiata), adzuki bean (V. angularis var. angularis), common bean (Phaseolus vulgaris L.), pigeon pea (Cajanus cajan), chickpea (Cicer arietinum), and peanut (Arachis hypogaea). Since the publication of the first reference genome sequence of each species, many accessions have been resequenced to study genetic diversity, speciation, and polyploidization in the legume lineage.
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Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
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20
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Whole genome sequencing of Entamoeba nuttalli reveals mammalian host-related molecular signatures and a novel octapeptide-repeat surface protein. PLoS Negl Trop Dis 2019; 13:e0007923. [PMID: 31805050 PMCID: PMC6917348 DOI: 10.1371/journal.pntd.0007923] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 12/17/2019] [Accepted: 11/12/2019] [Indexed: 11/19/2022] Open
Abstract
The enteric protozoa Entamoeba histolytica is the causative agent of amebiasis, which is one of the most common parasitic diseases in developed and developing countries. Entamoeba nuttalli is the genetically closest species to E. histolytica in current phylogenetic analyses of Entamoeba species, and is prevalent in wild macaques. Therefore, E. nuttalli may be a key organism in which to investigate molecules required for infection of human or non-human primates. To explore the molecular signatures of host-parasite interactions, we conducted de novo assembly of the E. nuttalli genome, utilizing self-correction of PacBio long reads and polishing corrected reads using Illumina short reads, followed by comparative genomic analysis with two other mammalian and a reptilian Entamoeba species. The final draft assembly of E. nuttalli included 395 contigs with a total length of approximately 23 Mb, and 9,647 predicted genes, of which 6,940 were conserved with E. histolytica. In addition, we found an E. histolytica-specific repeat known as ERE2 in the E. nuttalli genome. GO-term enrichment analysis of mammalian host-related molecules indicated diversification of transmembrane proteins, including AIG1 family and BspA-like proteins that may be involved in the host-parasite interaction. Furthermore, we identified an E. nuttalli-specific protein that contained 42 repeats of an octapeptide ([G,E]KPTDTPS). This protein was shown to be localized on the cell surface using immunofluorescence. Since many repeat-containing proteins in parasites play important roles in interactions with host cells, this unique octapeptide repeat-containing protein may be involved in colonization of E. nuttalli in the intestine of macaques. Overall, our draft assembly provides a valuable resource for studying Entamoeba evolution and host-parasite selection.
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21
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Lonardi S, Muñoz‐Amatriaín M, Liang Q, Shu S, Wanamaker SI, Lo S, Tanskanen J, Schulman AH, Zhu T, Luo M, Alhakami H, Ounit R, Hasan AM, Verdier J, Roberts PA, Santos JR, Ndeve A, Doležel J, Vrána J, Hokin SA, Farmer AD, Cannon SB, Close TJ. The genome of cowpea (Vigna unguiculata [L.] Walp.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:767-782. [PMID: 31017340 PMCID: PMC6852540 DOI: 10.1111/tpj.14349] [Citation(s) in RCA: 153] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 05/19/2023]
Abstract
Cowpea (Vigna unguiculata [L.] Walp.) is a major crop for worldwide food and nutritional security, especially in sub-Saharan Africa, that is resilient to hot and drought-prone environments. An assembly of the single-haplotype inbred genome of cowpea IT97K-499-35 was developed by exploiting the synergies between single-molecule real-time sequencing, optical and genetic mapping, and an assembly reconciliation algorithm. A total of 519 Mb is included in the assembled sequences. Nearly half of the assembled sequence is composed of repetitive elements, which are enriched within recombination-poor pericentromeric regions. A comparative analysis of these elements suggests that genome size differences between Vigna species are mainly attributable to changes in the amount of Gypsy retrotransposons. Conversely, genes are more abundant in more distal, high-recombination regions of the chromosomes; there appears to be more duplication of genes within the NBS-LRR and the SAUR-like auxin superfamilies compared with other warm-season legumes that have been sequenced. A surprising outcome is the identification of an inversion of 4.2 Mb among landraces and cultivars, which includes a gene that has been associated in other plants with interactions with the parasitic weed Striga gesnerioides. The genome sequence facilitated the identification of a putative syntelog for multiple organ gigantism in legumes. A revised numbering system has been adopted for cowpea chromosomes based on synteny with common bean (Phaseolus vulgaris). An estimate of nuclear genome size of 640.6 Mbp based on cytometry is presented.
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Affiliation(s)
- Stefano Lonardi
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCA92521USA
| | - María Muñoz‐Amatriaín
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCA92521USA
- Present address:
Department of Soil and Crop SciencesColorado State UniversityFort CollinsCO80523USA
| | - Qihua Liang
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCA92521USA
| | - Shengqiang Shu
- US Department of Energy Joint Genome InstituteWalnut CreekCA94598USA
| | - Steve I. Wanamaker
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCA92521USA
| | - Sassoum Lo
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCA92521USA
| | - Jaakko Tanskanen
- Natural Resources Institute Finland (Luke)HelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Viikki Plant Science CentreUniversity of HelsinkiHelsinkiFinland
| | - Alan H. Schulman
- Natural Resources Institute Finland (Luke)HelsinkiFinland
- Institute of BiotechnologyUniversity of HelsinkiHelsinkiFinland
- Viikki Plant Science CentreUniversity of HelsinkiHelsinkiFinland
| | - Tingting Zhu
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Ming‐Cheng Luo
- Department of Plant SciencesUniversity of CaliforniaDavisCA95616USA
| | - Hind Alhakami
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCA92521USA
| | - Rachid Ounit
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCA92521USA
| | - Abid Md. Hasan
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCA92521USA
| | - Jerome Verdier
- Institut de Recherche en Horticulture et SemencesINRAUniversité d'Angers49071BeaucouzéFrance
| | | | - Jansen R.P. Santos
- Department of NematologyUniversity of CaliforniaRiversideCA92521USA
- Departamento de FitopatologiaInstituto de Ciências BiológicasUniversidade de BrasíliaBrasíliaDFBrazil
| | - Arsenio Ndeve
- Department of NematologyUniversity of CaliforniaRiversideCA92521USA
| | - Jaroslav Doležel
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | - Jan Vrána
- Centre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental BotanyOlomoucCzech Republic
| | | | | | - Steven B. Cannon
- US Department of Agriculture–Agricultural Research ServiceAmesIAUSA
| | - Timothy J. Close
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCA92521USA
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22
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Qiao X, Li Q, Yin H, Qi K, Li L, Wang R, Zhang S, Paterson AH. Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants. Genome Biol 2019; 20:38. [PMID: 30791939 PMCID: PMC6383267 DOI: 10.1186/s13059-019-1650-2] [Citation(s) in RCA: 442] [Impact Index Per Article: 88.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 02/08/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. RESULTS We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events-transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. CONCLUSIONS We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.
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Affiliation(s)
- Xin Qiao
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Qionghou Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Leiting Li
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095 China
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30605 USA
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23
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Yundaeng C, Somta P, Amkul K, Kongjaimun A, Kaga A, Tomooka N. Construction of genetic linkage map and genome dissection of domestication-related traits of moth bean (Vigna aconitifolia), a legume crop of arid areas. Mol Genet Genomics 2019; 294:621-635. [PMID: 30739203 DOI: 10.1007/s00438-019-01536-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 01/31/2019] [Indexed: 10/27/2022]
Abstract
The moth bean (Vigna aconitifolia), possibly the most primitive crop of the genus Vigna, is a highly drought- and heat-resistant legume grown in arid areas. Moth bean domestication involved phenotypic changes, including reduction of seed dormancy and pod shattering, increased organ size, and earlier flowering and maturity. However, the genetics of the domestication process in moth bean is not known. In this study, we constructed a genetic linkage map for moth bean and used the map to identify quantitative trait loci (QTL) for domestication-related traits of an F2 population of 188 individuals produced from a cross of wild moth bean (TN67) and cultivated moth bean (ICPMO056). The genetic linkage map comprised 11 linkage groups (LG) of 172 simple sequence repeat markers and spanned a total length of 1016.8 centiMorgan (cM), with an average marker distance of 7.34 cM. A comparative genome analysis showed high genome synteny between moth bean and mungbean (Vigna radiata), adzuki bean (Vigna angularis), rice bean (Vigna umbellata), and yardlong bean (Vigna unguiculata). In total, 50 QTLs and 3 genes associated with 20 domestication-related traits were identified. Most of the QTLs belonged to five LGs (1, 2, 4, 7, and 10). Key traits related to domestication such as seed dormancy and pod shattering were controlled by large-effect QTLs (PVE > 20%) with one or two minor QTLs, whereas all other traits were controlled by one-seven minor QTLs, apart from seed weight, which was controlled by one major and seven minor QTLs. These results suggest that a small number of mutations with large phenotypic effects have contributed to the domestication of the moth bean. Comparative analysis of QTLs with related Vigna crops revealed that there are several domestication-related large-effect QTLs that had not been used in moth bean domestication. This study provides a basic genetic map and identified genome regions associated with domestication-related traits, which will be useful for the genetic improvement of the moth bean and related Vigna species.
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Affiliation(s)
- Chutintorn Yundaeng
- Department of Agronomy, Faculty of Agriculture at Kampaheng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kampaheng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand. .,Center for Agricultural Biotechnology (AG-BIO/PEDRO-CHE), Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand. .,Center of Advanced Studies for Agriculture and Food (CASAF), Kasetsart University Institute for Advanced Studies, Kasetsart University (NRU-KU), Bangkok, 10900, Thailand.
| | - Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kampaheng Saen, Kasetsart University, Kamphaeng Saen Campus, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand.,Center of Advanced Studies for Agriculture and Food (CASAF), Kasetsart University Institute for Advanced Studies, Kasetsart University (NRU-KU), Bangkok, 10900, Thailand
| | - Alisa Kongjaimun
- Faculty of Animal Sciences and Agricultural Technology, Silpakorn University, Cha-Am, Phetchaburi, 76120, Thailand
| | - Akito Kaga
- Soybean and Field Crop Applied Genomics Research Unit, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.
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24
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Takahashi Y, Sakai H, Yoshitsu Y, Muto C, Anai T, Pandiyan M, Senthil N, Tomooka N, Naito K. Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses. FRONTIERS IN PLANT SCIENCE 2019; 10:1607. [PMID: 31867036 PMCID: PMC6909428 DOI: 10.3389/fpls.2019.01607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/15/2019] [Indexed: 05/03/2023]
Abstract
Though crossing wild relatives to modern cultivars is a usual means to introduce alleles of stress tolerance, an alternative is de novo domesticating wild species that are already tolerant to various kinds of stresses. As a test case, we chose Vigna stipulacea Kuntze, which has fast growth, short vegetative stage, and broad resistance to pests and diseases. We developed an ethyl methanesulfonate-mutagenized population and obtained three mutants with reduced seed dormancy and one with reduced pod shattering. We crossed one of the mutants of less seed dormancy to the wild type and confirmed that the phenotype was inherited in a Mendelian manner. De novo assembly of V. stipulacea genome, and the following resequencing of the F2 progenies successfully identified a Single Nucleotide Polymorphism (SNP) associated with seed dormancy. By crossing and pyramiding the mutant phenotypes, we will be able to turn V. stipulacea into a crop which is yet primitive but can be cultivated without pesticides.
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Affiliation(s)
| | | | - Yuki Yoshitsu
- Kenpoku Agricultural Institute, Iwate Agricultural Research Center, Iwate, Japan
| | - Chiaki Muto
- Genetic Resources Center, NARO, Tsukuba, Japan
| | - Toyoaki Anai
- Department of Agriculture, Saga University, Saga, Japan
| | - Muthaiyan Pandiyan
- Agricultural College and Research Institute, Tamil Nadu Agricultural University, Thanjavur, India
| | - Natesan Senthil
- Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India
| | | | - Ken Naito
- Genetic Resources Center, NARO, Tsukuba, Japan
- *Correspondence: Ken Naito,
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25
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Somta P, Jomsangawong A, Yundaeng C, Yuan X, Chen J, Tomooka N, Chen X. Genetic Dissection of Azuki Bean Weevil (Callosobruchus chinensis L.) Resistance in Moth Bean (Vigna aconitifolia [Jaqc.] Maréchal). Genes (Basel) 2018; 9:E555. [PMID: 30445788 PMCID: PMC6267224 DOI: 10.3390/genes9110555] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/09/2018] [Accepted: 11/12/2018] [Indexed: 11/16/2022] Open
Abstract
The azuki bean weevil (Callosobruchus chinensis L.) is an insect pest responsible for serious postharvest seed loss in leguminous crops. In this study, we performed quantitative trait locus (QTL) mapping of seed resistance to C. chinensis in moth bean (Vigna aconitifolia [Jaqc.] Maréchal). An F₂ population of 188 plants developed by crossing resistant accession 'TN67' (wild type from India; male parent) and susceptible accession 'IPCMO056' (cultivated type from India; female parent) was used for mapping. Seeds of the F₂ population from 2014 and F2:₃ populations from 2016 and 2017 were bioassayed with C. chinensis, and the percentage of damaged seeds and progress of infestation severity were measured. Segregation analysis suggested that C. chinensis resistance in TN176 is controlled by a single dominant gene, designated as Rcc. QTL analysis revealed one principal and one modifying QTL for the resistance, named qVacBrc2.1 and qVacBrc5.1, respectively. qVacBrc2.1 was located on linkage group 2 between simple sequence repeat markers CEDG261 and DMB-SSR160 and accounted for 50.41% to 64.23% of resistance-related traits, depending on the trait and population. Comparative genomic analysis suggested that qVacBrc2.1 is the same as QTL Brc2.1 conferring C. chinensis resistance in wild azuki bean (V. nepalensis Tateishi and Maxted). Markers CEDG261 and DMB-SSR160 should be useful for marker-assisted selection for C. chinensis resistance in moth bean.
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Affiliation(s)
- Prakit Somta
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.
- Center for Agricultural Biotechnology (AG-BIO/PEDRO-CHE), Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.
| | - Achara Jomsangawong
- Program in Plant Breeding, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand.
| | - Chutintorn Yundaeng
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
| | - Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
| | - Norihiko Tomooka
- Genetic Resources Center, Gene Bank, National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing 210014, China.
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26
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Belser C, Istace B, Denis E, Dubarry M, Baurens FC, Falentin C, Genete M, Berrabah W, Chèvre AM, Delourme R, Deniot G, Denoeud F, Duffé P, Engelen S, Lemainque A, Manzanares-Dauleux M, Martin G, Morice J, Noel B, Vekemans X, D'Hont A, Rousseau-Gueutin M, Barbe V, Cruaud C, Wincker P, Aury JM. Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. NATURE PLANTS 2018; 4:879-887. [PMID: 30390080 DOI: 10.1038/s41477-018-0289-4] [Citation(s) in RCA: 215] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 09/24/2018] [Indexed: 05/19/2023]
Abstract
Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions1-4. However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms.
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Affiliation(s)
- Caroline Belser
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Benjamin Istace
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Erwan Denis
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Marion Dubarry
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Franc-Christophe Baurens
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Cyril Falentin
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Mathieu Genete
- Université Lille, CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
| | - Wahiba Berrabah
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Anne-Marie Chèvre
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Régine Delourme
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Gwenaëlle Deniot
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - France Denoeud
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Philippe Duffé
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Stefan Engelen
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Arnaud Lemainque
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | | | - Guillaume Martin
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Jérôme Morice
- IGEPP, INRA, Agrocampus Ouest, Université Rennes 1, BP35327, Le Rheu, France
| | - Benjamin Noel
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Xavier Vekemans
- Université Lille, CNRS, UMR 8198-Evo-Eco-Paleo, Lille, France
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Université Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Valérie Barbe
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut de biologie François Jacob, CEA, CNRS, Université d'Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France.
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27
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Assembling the genome of the African wild rice Oryza longistaminata by exploiting synteny in closely related Oryza species. Commun Biol 2018; 1:162. [PMID: 30320230 PMCID: PMC6173730 DOI: 10.1038/s42003-018-0171-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 09/13/2018] [Indexed: 01/30/2023] Open
Abstract
The African wild rice species Oryza longistaminata has several beneficial traits compared to cultivated rice species, such as resistance to biotic stresses, clonal propagation via rhizomes, and increased biomass production. To facilitate breeding efforts and functional genomics studies, we de-novo assembled a high-quality, haploid-phased genome. Here, we present our assembly, with a total length of 351 Mb, of which 92.2% was anchored onto 12 chromosomes. We detected 34,389 genes and 38.1% of the genome consisted of repetitive content. We validated our assembly by a comparative linkage analysis and by examining well-characterized gene families. This genome assembly will be a useful resource to exploit beneficial alleles found in O. longistaminata. Our results also show that it is possible to generate a high-quality, functionally complete rice genome assembly from moderate SMRT read coverage by exploiting synteny in a closely related Oryza species. Stefan Reuscher et al. assembled the genome of an African wild rice species to facilitate breeding efforts and functional genomic studies. They used SMRT sequencing, chromosomal synteny between rice species, and a linkage map to assemble the 351 Mb genome into 12 chromosomes.
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28
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Iseki K, Takahashi Y, Muto C, Naito K, Tomooka N. Diversity of Drought Tolerance in the Genus Vigna. FRONTIERS IN PLANT SCIENCE 2018; 9:729. [PMID: 29963062 PMCID: PMC6014140 DOI: 10.3389/fpls.2018.00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 05/14/2018] [Indexed: 05/22/2023]
Abstract
Wild relatives of crop plants are thought as reservoir of prominent genetic resources for abiotic stress tolerance. However, insufficient information on genetic variation and phenotypic traits restricts their use for crop breeding. This study focused on wild species of genus Vigna (family Fabaceae) originated from highly humid to arid regions. To clarify the diversity of drought tolerance during the vegetative stage, 69 accessions, including 15 domesticated, and 54 wild accessions, were evaluated under two drought conditions of non-terminal and terminal stresses. In the non-terminal drought condition, the plants were grown in pipes of different heights where surface soil water content decreased faster in pipes with greater height. Relative shoot biomass was used for tolerance evaluation and we identified 19 drought tolerant accessions. Almost of them were wild accessions showing higher relative shoot biomass than that in the domesticated accessions. Domesticated species were mostly classified as drought susceptible but could be improved using tolerant conspecific wild ancestors with cross-compatibility. The tolerance was related with higher plant water status presumably due to small water consumption. However, the variation of drought tolerance could not be explained by simple tolerance factor alone, and other tolerance mechanisms such as deep rooting and increasing in root biomass were found in the tolerant accessions. In the terminal drought condition, the plants were grown in small pots, and the watering was stopped to expose them extreme and rapid soil water scarcity. The tolerance was evaluated as the number of days until wilting. However, the accessions found to be tolerant in the pot experiment were not the same as those in the pipe experiment. In this condition, plant water status was not related with the length of days to wilting. This indicates that different mechanisms are necessary for adaptation to each of the non-terminal and terminal drought conditions. Many accessions were tolerant to one of the conditions, although we identified that some accessions showed tolerance in both experiments. The great diversity in drought tolerance in the genus Vigna might serve to both improve crop drought tolerance and understand the mechanisms of adaptation in drought-prone environments.
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Affiliation(s)
| | | | | | | | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Japan
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29
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Masuta Y, Kawabe A, Nozawa K, Naito K, Kato A, Ito H. Characterization of a heat-activated retrotransposon in Vigna angularis. BREEDING SCIENCE 2018; 68:168-176. [PMID: 29875600 PMCID: PMC5982181 DOI: 10.1270/jsbbs.17085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 05/14/2023]
Abstract
In plants, several transposable elements are conserved across species. We found a homolog of ONSEN, which is a heat-activated retrotransposon originally isolated from Arabidopsis thaliana, in Vigna. The ONSEN-like elements (VaONS) were detected in all the analyzed Japanese accessions of Vigna angularis (adzuki bean) by Southern blot analysis. However, VaONS sequences were observed to be polymorphic in the different accessions. Interestingly, extrachromosomal DNA (ecDNA) was detected in some accessions of adzuki bean, indicating the conserved heat-activation of VaONS. Furthermore, we successfully induced retrotransposition of VaONS in adzuki plant regenerated through callus. Findings of our study should provide a new tool for molecular breeding of adzuki bean.
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Affiliation(s)
- Yukari Masuta
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Akira Kawabe
- Faculty of Life Sciences, Kyoto Sangyo University,
Kamigamo Motoyama, Kita-ku, Kyoto 603-8555,
Japan
| | - Kosuke Nozawa
- Graduate School of Life Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Ken Naito
- Genetic Resource Center, National Agriculture and Food Research Organization,
2-1-2, Kannondai, Tsukuba, Ibaraki 305-8602,
Japan
| | - Atsushi Kato
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
| | - Hidetaka Ito
- Faculty of Science, Hokkaido University,
Kita10 Nishi8, Kita-ku, Sapporo, Hokkaido 060-0810,
Japan
- Corresponding author (e-mail: )
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30
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Advances in Sequencing and Resequencing in Crop Plants. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018. [PMID: 29516115 DOI: 10.1007/10_2017_46] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequencing technologies have changed the face of biological research over the last 20 years. From reference genomes to population level resequencing studies, these technologies have made significant contributions to our understanding of plant biology and evolution. As the technologies have increased in power, the breadth and complexity of the questions that can be asked has increased. Along with this, the challenges of managing unprecedented quantities of sequence data are mounting. This chapter describes a few aspects of the journey so far and looks forward to what may lie ahead. Graphical Abstract.
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31
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She CW, Wei L, Jiang XH. Molecular cytogenetic characterization and comparison of the two cultivated Canavalia species (Fabaceae). COMPARATIVE CYTOGENETICS 2017; 11:579-600. [PMID: 29114355 PMCID: PMC5672272 DOI: 10.3897/compcytogen.v11i4.13604] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/07/2017] [Indexed: 05/25/2023]
Abstract
The two cultivated Canavalia (Adanson, 1763) species, Canavalia gladiata (N. J. von Jacquin, 1788) A. P. de Candolle, 1825 and Canavalia ensiformis (Linnaeus, 1753) A. P. de Candolle, 1825 are closely related based on morphological and molecular phylogenetic data. However, the similarities and differences in genome organization between them have not been evaluated at molecular cytogenetic level. Here, detailed karyotypes of both species were constructed using combined PI and DAPI (CPD) staining, rDNA-FISH and self-genomic in situ hybridization (sGISH). For further comparison, comparative genomic in situ hybridization (cGISH) and sequence analysis of 5S rDNA were applied. Their chromosomes were accurately identified by sGISH and rDNA-FISH signals. Both species had the karyotype formula 2n = 22 = 18m + 4m-SAT, but the karyotype of C. ensiformis was shorter and more asymmetric than that of C. gladiata. They displayed similar CPD bands at all 45S rDNA sites and centromeres. C. gladiata had ten centromeric 5S rDNA loci and two SC (secondary constriction)-associated 45S rDNA loci. C. ensiformis had nine centromeric and one interstitial 5S loci, two SC-associated and one proximal 45S loci. Their sGISH signal patterns displayed both basic similarities and distinct differences. Reciprocal cGISH generated prominent signals in all pericentromeric regions and 45S sites. There was lower level of sequence identity of the non-transcribed spacer between their 5S rDNA repeats. These data confirmed the evolutionary closeness between C. gladiata and C. ensiformis and demonstrated obvious differentiation between their genomes, and supported the opinion that C. ensiformis is more advanced in evolution than C. gladiata.
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Affiliation(s)
- Chao-Wen She
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan, 418008, China
- Key Laboratory of Xiangxi Medicinal Plant and Ethnobotany of Hunan Higher Education, Huaihua University, Huaihua, Hunan, 418008, China
- College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan, 418008, China
| | - Lin Wei
- Key Laboratory of Research and Utilization of Ethnomedicinal Plant Resources of Hunan Province, Huaihua University, Huaihua, Hunan, 418008, China
- Key Laboratory of Xiangxi Medicinal Plant and Ethnobotany of Hunan Higher Education, Huaihua University, Huaihua, Hunan, 418008, China
- College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan, 418008, China
| | - Xiang-Hui Jiang
- Key Laboratory of Xiangxi Medicinal Plant and Ethnobotany of Hunan Higher Education, Huaihua University, Huaihua, Hunan, 418008, China
- College of Biological and Food Engineering, Huaihua University, Huaihua, Hunan, 418008, China
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Dallery JF, Lapalu N, Zampounis A, Pigné S, Luyten I, Amselem J, Wittenberg AHJ, Zhou S, de Queiroz MV, Robin GP, Auger A, Hainaut M, Henrissat B, Kim KT, Lee YH, Lespinet O, Schwartz DC, Thon MR, O'Connell RJ. Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics 2017; 18:667. [PMID: 28851275 PMCID: PMC5576322 DOI: 10.1186/s12864-017-4083-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/21/2017] [Indexed: 11/11/2022] Open
Abstract
Background The ascomycete fungus Colletotrichum higginsianum causes anthracnose disease of brassica crops and the model plant Arabidopsis thaliana. Previous versions of the genome sequence were highly fragmented, causing errors in the prediction of protein-coding genes and preventing the analysis of repetitive sequences and genome architecture. Results Here, we re-sequenced the genome using single-molecule real-time (SMRT) sequencing technology and, in combination with optical map data, this provided a gapless assembly of all twelve chromosomes except for the ribosomal DNA repeat cluster on chromosome 7. The more accurate gene annotation made possible by this new assembly revealed a large repertoire of secondary metabolism (SM) key genes (89) and putative biosynthetic pathways (77 SM gene clusters). The two mini-chromosomes differed from the ten core chromosomes in being repeat- and AT-rich and gene-poor but were significantly enriched with genes encoding putative secreted effector proteins. Transposable elements (TEs) were found to occupy 7% of the genome by length. Certain TE families showed a statistically significant association with effector genes and SM cluster genes and were transcriptionally active at particular stages of fungal development. All 24 subtelomeres were found to contain one of three highly-conserved repeat elements which, by providing sites for homologous recombination, were probably instrumental in four segmental duplications. Conclusion The gapless genome of C. higginsianum provides access to repeat-rich regions that were previously poorly assembled, notably the mini-chromosomes and subtelomeres, and allowed prediction of the complete SM gene repertoire. It also provides insights into the potential role of TEs in gene and genome evolution and host adaptation in this asexual pathogen. Electronic supplementary material The online version of this article (10.1186/s12864-017-4083-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jean-Félix Dallery
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Nicolas Lapalu
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Antonios Zampounis
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.,Present Address: Department of Deciduous Fruit Trees, Institute of Plant Breeding and Plant Genetic Resources, Hellenic Agricultural Organization 'Demeter', Naoussa, Greece
| | - Sandrine Pigné
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | | | | | | | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Marisa V de Queiroz
- Laboratório de Genética Molecular de Fungos, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Guillaume P Robin
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Annie Auger
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France
| | - Matthieu Hainaut
- CNRS UMR 7257, Aix-Marseille University, Marseille, France.,INRA, USC 1408 AFMB, Marseille, France
| | - Bernard Henrissat
- CNRS UMR 7257, Aix-Marseille University, Marseille, France.,INRA, USC 1408 AFMB, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ki-Tae Kim
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Center for Fungal Genetic Resources, Seoul National University, Seoul, Korea
| | - Olivier Lespinet
- Laboratoire de Recherche en Informatique, CNRS, Université Paris-Sud, Orsay, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Orsay, France
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael R Thon
- Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Department of Microbiology and Genetics, University of Salamanca, Salamanca, Spain
| | - Richard J O'Connell
- UMR BIOGER, INRA, AgroParisTech, Université Paris-Saclay, Thiverval-Grignon, France.
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Yuan Y, Bayer PE, Batley J, Edwards D. Improvements in Genomic Technologies: Application to Crop Genomics. Trends Biotechnol 2017; 35:547-558. [DOI: 10.1016/j.tibtech.2017.02.009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/13/2022]
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34
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Gilbert JR, Taylor GM, Losee JE, Mooney MP, Cooper GM. Resequencing of the Col1A1 gene of Oryctolagus cuniculus identifies splicing errors and single nucleotide polymorphisms. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0521-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Nakano K, Shiroma A, Shimoji M, Tamotsu H, Ashimine N, Ohki S, Shinzato M, Minami M, Nakanishi T, Teruya K, Satou K, Hirano T. Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area. Hum Cell 2017; 30:149-161. [PMID: 28364362 PMCID: PMC5486853 DOI: 10.1007/s13577-017-0168-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/22/2017] [Indexed: 12/30/2022]
Abstract
PacBio RS II is the first commercialized third-generation DNA sequencer able to sequence a single molecule DNA in real-time without amplification. PacBio RS II's sequencing technology is novel and unique, enabling the direct observation of DNA synthesis by DNA polymerase. PacBio RS II confers four major advantages compared to other sequencing technologies: long read lengths, high consensus accuracy, a low degree of bias, and simultaneous capability of epigenetic characterization. These advantages surmount the obstacle of sequencing genomic regions such as high/low G+C, tandem repeat, and interspersed repeat regions. Moreover, PacBio RS II is ideal for whole genome sequencing, targeted sequencing, complex population analysis, RNA sequencing, and epigenetics characterization. With PacBio RS II, we have sequenced and analyzed the genomes of many species, from viruses to humans. Herein, we summarize and review some of our key genome sequencing projects, including full-length viral sequencing, complete bacterial genome and almost-complete plant genome assemblies, and long amplicon sequencing of a disease-associated gene region. We believe that PacBio RS II is not only an effective tool for use in the basic biological sciences but also in the medical/clinical setting.
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Affiliation(s)
- Kazuma Nakano
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan.
| | - Akino Shiroma
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Hinako Tamotsu
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Noriko Ashimine
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Shun Ohki
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Misuzu Shinzato
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Maiko Minami
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | | | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences, Uruma, Okinawa, Japan
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36
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Soorni A, Haak D, Zaitlin D, Bombarely A. Organelle_PBA, a pipeline for assembling chloroplast and mitochondrial genomes from PacBio DNA sequencing data. BMC Genomics 2017; 18:49. [PMID: 28061749 PMCID: PMC5219736 DOI: 10.1186/s12864-016-3412-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 12/10/2016] [Indexed: 11/18/2022] Open
Abstract
Background The development of long-read sequencing technologies, such as single-molecule real-time (SMRT) sequencing by PacBio, has produced a revolution in the sequencing of small genomes. Sequencing organelle genomes using PacBio long-read data is a cost effective, straightforward approach. Nevertheless, the availability of simple-to-use software to perform the assembly from raw reads is limited at present. Results We present Organelle-PBA, a Perl program designed specifically for the assembly of chloroplast and mitochondrial genomes. For chloroplast genomes, the program selects the chloroplast reads from a whole genome sequencing pool, maps the reads to a reference sequence from a closely related species, and then performs read correction and de novo assembly using Sprai. Organelle-PBA completes the assembly process with the additional step of scaffolding by SSPACE-LongRead. The program then detects the chloroplast inverted repeats and reassembles and re-orients the assembly based on the organelle origin of the reference. We have evaluated the performance of the software using PacBio reads from different species, read coverage, and reference genomes. Finally, we present the assembly of two novel chloroplast genomes from the species Picea glauca (Pinaceae) and Sinningia speciosa (Gesneriaceae). Conclusion Organelle-PBA is an easy-to-use Perl-based software pipeline that was written specifically to assemble mitochondrial and chloroplast genomes from whole genome PacBio reads. The program is available at https://github.com/aubombarely/Organelle_PBA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3412-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aboozar Soorni
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.,Department of Horticulture, Faculty of Horticultural Sciences and Plant Protection, University of Tehran, Karaj, 31587, Iran
| | - David Haak
- Department of Plant Pathology, Physiology and Weed Science, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - David Zaitlin
- Kentucky Tobacco Research and Development Center (KTRDC), University of Kentucky, Lexington, KY, 40546, USA
| | - Aureliano Bombarely
- Department of Horticulture, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
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Minio A, Lin J, Gaut BS, Cantu D. How Single Molecule Real-Time Sequencing and Haplotype Phasing Have Enabled Reference-Grade Diploid Genome Assembly of Wine Grapes. FRONTIERS IN PLANT SCIENCE 2017; 8:826. [PMID: 28567052 PMCID: PMC5434136 DOI: 10.3389/fpls.2017.00826] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/02/2017] [Indexed: 05/23/2023]
Affiliation(s)
- Andrea Minio
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Jerry Lin
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
| | - Brandon S. Gaut
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, United States
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, DavisDavis, CA, United States
- *Correspondence: Dario Cantu
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38
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Hoshino A, Jayakumar V, Nitasaka E, Toyoda A, Noguchi H, Itoh T, Shin-I T, Minakuchi Y, Koda Y, Nagano AJ, Yasugi M, Honjo MN, Kudoh H, Seki M, Kamiya A, Shiraki T, Carninci P, Asamizu E, Nishide H, Tanaka S, Park KI, Morita Y, Yokoyama K, Uchiyama I, Tanaka Y, Tabata S, Shinozaki K, Hayashizaki Y, Kohara Y, Suzuki Y, Sugano S, Fujiyama A, Iida S, Sakakibara Y. Genome sequence and analysis of the Japanese morning glory Ipomoea nil. Nat Commun 2016; 7:13295. [PMID: 27824041 PMCID: PMC5105172 DOI: 10.1038/ncomms13295] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 09/21/2016] [Indexed: 12/18/2022] Open
Abstract
Ipomoea is the largest genus in the family Convolvulaceae. Ipomoea nil (Japanese morning glory) has been utilized as a model plant to study the genetic basis of floricultural traits, with over 1,500 mutant lines. In the present study, we have utilized second- and third-generation-sequencing platforms, and have reported a draft genome of I. nil with a scaffold N50 of 2.88 Mb (contig N50 of 1.87 Mb), covering 98% of the 750 Mb genome. Scaffolds covering 91.42% of the assembly are anchored to 15 pseudo-chromosomes. The draft genome has enabled the identification and cataloguing of the Tpn1 family transposons, known as the major mutagen of I. nil, and analysing the dwarf gene, CONTRACTED, located on the genetic map published in 1956. Comparative genomics has suggested that a whole genome duplication in Convolvulaceae, distinct from the recent Solanaceae event, has occurred after the divergence of the two sister families.
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Affiliation(s)
- Atsushi Hoshino
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Vasanthan Jayakumar
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Eiji Nitasaka
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Hideki Noguchi
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Takehiko Itoh
- Department of Biological Information, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan
| | - Tadasu Shin-I
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yohei Minakuchi
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yuki Koda
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
| | - Atsushi J Nagano
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan.,Faculty of Agriculture, Ryukoku University, Otsu, Shiga 520-2194, Japan
| | - Masaki Yasugi
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Mie N Honjo
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Motoaki Seki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Asako Kamiya
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | | | - Piero Carninci
- RIKEN Center for Life Science Technologies, Yokohama, Kanagawa 230-0045, Japan
| | - Erika Asamizu
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hiroyo Nishide
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Sachiko Tanaka
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kyeung-Il Park
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Horticulture &Life Science, Yeungnam University, Gyeongbuk 712-749, Korea
| | - Yasumasa Morita
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan
| | - Kohei Yokoyama
- Graduate School of Science, Kyushu University, Fukuoka, Fukuoka 819-0395, Japan
| | - Ikuo Uchiyama
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yoshikazu Tanaka
- Suntory Global Innovation Center Ltd, Seika, Kyoto 619-0284, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Kazuo Shinozaki
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Yuji Kohara
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yutaka Suzuki
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 108-8639, Japan
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.,Principles of Informatics Research Division, National Institute of Informatics, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Shigeru Iida
- National Institute for Basic Biology, Okazaki, Aichi 444-8585, Japan.,Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8585, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama, Kanagawa 223-8522, Japan
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Iseki K, Takahashi Y, Muto C, Naito K, Tomooka N. Diversity and Evolution of Salt Tolerance in the Genus Vigna. PLoS One 2016; 11:e0164711. [PMID: 27736995 PMCID: PMC5063378 DOI: 10.1371/journal.pone.0164711] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 09/27/2016] [Indexed: 11/19/2022] Open
Abstract
Breeding salt tolerant plants is difficult without utilizing a diversity of wild crop relatives. Since the genus Vigna (family Fabaceae) is comprised of many wild relatives adapted to various environmental conditions, we evaluated the salt tolerance of 69 accessions of this genus, including that of wild and domesticated accessions originating from Asia, Africa, Oceania, and South America. We grew plants under 50 mM and 200 mM NaCl for two weeks and then measured the biomass, relative quantum yield of photosystem II, leaf Na+ concentrations, and leaf K+ concentrations. The accessions were clustered into four groups: the most tolerant, tolerant, moderately susceptible, and susceptible. From the most tolerant group, we selected six accessions, all of which were wild accessions adapted to coastal environments, as promising sources of salt tolerance because of their consistently high relative shoot biomass and relative quantum yield. Interestingly, variations in leaf Na+ concentration were observed between the accessions in the most tolerant group, suggesting different mechanisms were responsible for their salt tolerance. Phylogenetic analysis with nuclear DNA sequences revealed that salt tolerance had evolved independently at least four times in the genus Vigna, within a relatively short period. The findings suggested that simple genetic changes in a few genes might have greatly affected salt tolerances. The elucidation of genetic mechanisms of salt tolerances in the selected accessions may contribute to improving the poor salt tolerance in legume crops.
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Affiliation(s)
- Kohtaro Iseki
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki, Japan
| | - Yu Takahashi
- Genetic Resources Center, National Agriculture and Food Science Organization, Tsukuba, Ibaraki, Japan
| | - Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Science Organization, Tsukuba, Ibaraki, Japan
| | - Ken Naito
- Genetic Resources Center, National Agriculture and Food Science Organization, Tsukuba, Ibaraki, Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Agriculture and Food Science Organization, Tsukuba, Ibaraki, Japan
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40
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Ingvarsson PK, Hvidsten TR, Street NR. Towards integration of population and comparative genomics in forest trees. THE NEW PHYTOLOGIST 2016; 212:338-44. [PMID: 27575589 DOI: 10.1111/nph.14153] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/27/2016] [Indexed: 05/08/2023]
Abstract
Contents 338 I. 338 II. 339 III. 340 IV. 342 343 References 343 SUMMARY: The past decade saw the initiation of an ongoing revolution in sequencing technologies that is transforming all fields of biology. This has been driven by the advent and widespread availability of high-throughput, massively parallel short-read sequencing (MPS) platforms. These technologies have enabled previously unimaginable studies, including draft assemblies of the massive genomes of coniferous species and population-scale resequencing. Transcriptomics studies have likewise been transformed, with RNA-sequencing enabling studies in nonmodel organisms, the discovery of previously unannotated genes (novel transcripts), entirely new classes of RNAs and previously unknown regulatory mechanisms. Here we touch upon current developments in the areas of genome assembly, comparative regulomics and population genetics as they relate to studies of forest tree species.
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Affiliation(s)
- Pär K Ingvarsson
- Umeå Plant Science Centre, Department of Ecology and Environmental Science, Umeå University, 901 87, Umeå, Sweden
| | - Torgeir R Hvidsten
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden.
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41
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Monte E, Rosa-Garrido M, Vondriska TM, Wang J. Undiscovered Physiology of Transcript and Protein Networks. Compr Physiol 2016; 6:1851-1872. [PMID: 27783861 PMCID: PMC10751805 DOI: 10.1002/cphy.c160003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The past two decades have witnessed a rapid evolution in our ability to measure RNA and protein from biological systems. As a result, new principles have arisen regarding how information is processed in cells, how decisions are made, and the role of networks in biology. This essay examines this technological evolution, reviewing (and critiquing) the conceptual framework that has emerged to explain how RNA and protein networks control cellular function. We identify how future investigations into transcriptomes, proteomes, and other cellular networks will enable development of more robust, quantitative models of cellular behavior whilst also providing new avenues to use knowledge of biological networks to improve human health. © 2016 American Physiological Society. Compr Physiol 6:1851-1872, 2016.
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Affiliation(s)
- Emma Monte
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Manuel Rosa-Garrido
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Thomas M. Vondriska
- Department of Anesthesiology & Perioperative Medicine, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Jessica Wang
- Department of Medicine/Cardiology, David Geffen School of Medicine, University of California, Los Angeles, USA
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Yasui Y, Hirakawa H, Oikawa T, Toyoshima M, Matsuzaki C, Ueno M, Mizuno N, Nagatoshi Y, Imamura T, Miyago M, Tanaka K, Mise K, Tanaka T, Mizukoshi H, Mori M, Fujita Y. Draft genome sequence of an inbred line of Chenopodium quinoa, an allotetraploid crop with great environmental adaptability and outstanding nutritional properties. DNA Res 2016; 23:535-546. [PMID: 27458999 PMCID: PMC5144677 DOI: 10.1093/dnares/dsw037] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/22/2016] [Indexed: 11/21/2022] Open
Abstract
Chenopodium quinoa Willd. (quinoa) originated from the Andean region of South America, and is a pseudocereal crop of the Amaranthaceae family. Quinoa is emerging as an important crop with the potential to contribute to food security worldwide and is considered to be an optimal food source for astronauts, due to its outstanding nutritional profile and ability to tolerate stressful environments. Furthermore, plant pathologists use quinoa as a representative diagnostic host to identify virus species. However, molecular analysis of quinoa is limited by its genetic heterogeneity due to outcrossing and its genome complexity derived from allotetraploidy. To overcome these obstacles, we established the inbred and standard quinoa accession Kd that enables rigorous molecular analysis, and presented the draft genome sequence of Kd, using an optimized combination of high-throughput next generation sequencing on the Illumina Hiseq 2500 and PacBio RS II sequencers. The de novo genome assembly contained 25 k scaffolds consisting of 1 Gbp with N50 length of 86 kbp. Based on these data, we constructed the free-access Quinoa Genome DataBase (QGDB). Thus, these findings provide insights into the mechanisms underlying agronomically important traits of quinoa and the effect of allotetraploidy on genome evolution.
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Affiliation(s)
- Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tetsuo Oikawa
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Masami Toyoshima
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Chiaki Matsuzaki
- Laboratory of Plant Gene Function, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Mariko Ueno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Nobuyuki Mizuno
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Yukari Nagatoshi
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
| | - Tomohiro Imamura
- Laboratory of Plant Gene Function, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Manami Miyago
- Technology Development Group, Actree Co., Hakusan, Ishikawa 924-0053, Japan
| | - Kojiro Tanaka
- Technology Development Group, Actree Co., Hakusan, Ishikawa 924-0053, Japan
| | - Kazuyuki Mise
- Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
| | - Tsutomu Tanaka
- Technology Development Group, Actree Co., Hakusan, Ishikawa 924-0053, Japan
| | - Hiroharu Mizukoshi
- Technology Development Group, Actree Co., Hakusan, Ishikawa 924-0053, Japan
| | - Masashi Mori
- Laboratory of Plant Gene Function, Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan
| | - Yasunari Fujita
- Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki 305-8686, Japan
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Bellasio M, Peymann A, Steiger MG, Valli M, Sipiczki M, Sauer M, Graf AB, Marx H, Mattanovich D. Complete genome sequence and transcriptome regulation of the pentose utilizing yeastSugiyamaella lignohabitans. FEMS Yeast Res 2016; 16:fow037. [DOI: 10.1093/femsyr/fow037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2016] [Indexed: 01/17/2023] Open
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Sakai H, Naito K, Takahashi Y, Sato T, Yamamoto T, Muto I, Itoh T, Tomooka N. The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna Based on High-Quality, Annotated Genome Sequence of the Azuki Bean, Vigna angularis (Willd.) Ohwi & Ohashi. PLANT & CELL PHYSIOLOGY 2016; 57:e2. [PMID: 26644460 DOI: 10.1093/pcp/pcv189] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/20/2015] [Indexed: 05/19/2023]
Abstract
The genus Vigna includes legume crops such as cowpea, mungbean and azuki bean, as well as >100 wild species. A number of the wild species are highly tolerant to severe environmental conditions including high-salinity, acid or alkaline soil; drought; flooding; and pests and diseases. These features of the genus Vigna make it a good target for investigation of genetic diversity in adaptation to stressful environments; however, a lack of genomic information has hindered such research in this genus. Here, we present a genome database of the genus Vigna, Vigna Genome Server ('VigGS', http://viggs.dna.affrc.go.jp), based on the recently sequenced azuki bean genome, which incorporates annotated exon-intron structures, along with evidence for transcripts and proteins, visualized in GBrowse. VigGS also facilitates user construction of multiple alignments between azuki bean genes and those of six related dicot species. In addition, the database displays sequence polymorphisms between azuki bean and its wild relatives and enables users to design primer sequences targeting any variant site. VigGS offers a simple keyword search in addition to sequence similarity searches using BLAST and BLAT. To incorporate up to date genomic information, VigGS automatically receives newly deposited mRNA sequences of pre-set species from the public database once a week. Users can refer to not only gene structures mapped on the azuki bean genome on GBrowse but also relevant literature of the genes. VigGS will contribute to genomic research into plant biotic and abiotic stresses and to the future development of new stress-tolerant crops.
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Affiliation(s)
- Hiroaki Sakai
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Ken Naito
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Yu Takahashi
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Toshiyuki Sato
- Mizuho Information & Research Institute, Inc., 2-3 Kanda-Nishikicho, Chiyoda-ku, Tokyo, 101-8443 Japan
| | - Toshiya Yamamoto
- BITS Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan
| | - Isamu Muto
- BITS Co., Ltd., 5-201 Kandamatsunaga-cho, Chiyoda-ku, Tokyo, 101-0023 Japan
| | - Takeshi Itoh
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
| | - Norihiko Tomooka
- Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602 Japan
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