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Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo YN, Huynh BL, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ. Genome resources for climate-resilient cowpea, an essential crop for food security. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 89:1042-1054. [PMID: 27775877 DOI: 10.1111/tpj.13404] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 05/20/2023]
Abstract
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Hamid Mirebrahim
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou, 310021, China
| | - Steve I Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Hind Alhakami
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Matthew Alpert
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Ibrahim Atokple
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana
| | - Benoit J Batieno
- Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropical Agriculture, Kano, Nigeria
| | - Serdar Bozdag
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA
| | - Ndiaga Cisse
- Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Issa Drabo
- Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso
| | - Jeffrey D Ehlers
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- The Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Yong Q Gu
- USDA-ARS Western Regional Research Center, Albany, CA, USA
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Bao-Lam Huynh
- Department of Nematology, University of California, Riverside, CA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Francis Kusi
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana
| | | | - Mitchell R Lucas
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Jiajie Wu
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Frank You
- Department of Plant Sciences, University of California, Davis, CA, USA
- Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Noelle A Barkley
- USDA-ARS Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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3
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Lonardi S, Mirebrahim H, Wanamaker S, Alpert M, Ciardo G, Duma D, Close TJ. When less is more: 'slicing' sequencing data improves read decoding accuracy and de novo assembly quality. Bioinformatics 2015; 31:2972-80. [PMID: 25995232 DOI: 10.1093/bioinformatics/btv311] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 05/13/2015] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION As the invention of DNA sequencing in the 70s, computational biologists have had to deal with the problem of de novo genome assembly with limited (or insufficient) depth of sequencing. In this work, we investigate the opposite problem, that is, the challenge of dealing with excessive depth of sequencing. RESULTS We explore the effect of ultra-deep sequencing data in two domains: (i) the problem of decoding reads to bacterial artificial chromosome (BAC) clones (in the context of the combinatorial pooling design we have recently proposed), and (ii) the problem of de novo assembly of BAC clones. Using real ultra-deep sequencing data, we show that when the depth of sequencing increases over a certain threshold, sequencing errors make these two problems harder and harder (instead of easier, as one would expect with error-free data), and as a consequence the quality of the solution degrades with more and more data. For the first problem, we propose an effective solution based on 'divide and conquer': we 'slice' a large dataset into smaller samples of optimal size, decode each slice independently, and then merge the results. Experimental results on over 15 000 barley BACs and over 4000 cowpea BACs demonstrate a significant improvement in the quality of the decoding and the final assembly. For the second problem, we show for the first time that modern de novo assemblers cannot take advantage of ultra-deep sequencing data. AVAILABILITY AND IMPLEMENTATION Python scripts to process slices and resolve decoding conflicts are available from http://goo.gl/YXgdHT; software Hashfilter can be downloaded from http://goo.gl/MIyZHs CONTACT stelo@cs.ucr.edu or timothy.close@ucr.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Stefano Lonardi
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Hamid Mirebrahim
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Steve Wanamaker
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew Alpert
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Gianfranco Ciardo
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Denisa Duma
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
| | - Timothy J Close
- Department of Computer Science and Engineering, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, Department of Computer Science, Iowa State University, Ames, IA 50011 and Baylor College of Medicine, Houston, TX 77030, USA
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