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Liu Y, Zhang B, Wen X, Zhang S, Wei Y, Lu Q, Liu Z, Wang K, Liu F, Peng R. Construction and characterization of a bacterial artificial chromosome library for Gossypium mustelinum. PLoS One 2018; 13:e0196847. [PMID: 29771937 PMCID: PMC5957370 DOI: 10.1371/journal.pone.0196847] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 04/20/2018] [Indexed: 11/18/2022] Open
Abstract
A bacterial artificial chromosome (BAC) library for G. mustelinum Miers ex G. Watt (AD4) was constructed. Intact nuclei from G. mustelinum (AD4) were used to isolate high molecular weight DNA, which was partially cleaved with Hind III and cloned into pSMART BAC (Hind III) vectors. The BAC library consisted of 208,182 clones arrayed in 542 384-microtiter plates, with an average insert size of 121.72 kb ranging from 100 to 150 kb. About 2% of the clones did not contain inserts. Based on an estimated genome size of 2372 Mb for G. mustelinum, the BAC library was estimated to have a total coverage of 10.50 × genome equivalents. The high capacity library of G. mustelinum will serve as a giant gene resource for map-based cloning of quantitative trait loci or genes associated with important agronomic traits or resistance to Verticillium wilt, physical mapping and comparative genome analysis.
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Affiliation(s)
- Yuling Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, United States of America
| | - Xinpeng Wen
- Anyang Institute of Technology, Anyang, Henan, China
| | - Shulin Zhang
- Anyang Institute of Technology, Anyang, Henan, China
| | - Yangyang Wei
- Anyang Institute of Technology, Anyang, Henan, China
| | - Quanwei Lu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Zhen Liu
- Anyang Institute of Technology, Anyang, Henan, China
| | - Kunbo Wang
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (FL); (RP)
| | - Renhai Peng
- Anyang Institute of Technology, Anyang, Henan, China
- State Key Laboratory of Cotton Biology / Institute of Cotton Research of Chinese Academy of Agricultural Science, Anyang, Henan, China
- * E-mail: (FL); (RP)
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Saski CA, Scheffler BE, Hulse-Kemp AM, Liu B, Song Q, Ando A, Stelly DM, Scheffler JA, Grimwood J, Jones DC, Peterson DG, Schmutz J, Chen ZJ. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. Sci Rep 2017; 7:15274. [PMID: 29127298 PMCID: PMC5681701 DOI: 10.1038/s41598-017-14885-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 10/18/2017] [Indexed: 01/06/2023] Open
Abstract
Like those of many agricultural crops, the cultivated cotton is an allotetraploid and has a large genome (~2.5 gigabase pairs). The two sub genomes, A and D, are highly similar but unequally sized and repeat-rich, which pose significant challenges for accurate genome reconstruction using standard approaches. Here we report the development of BAC libraries, sub genome specific physical maps, and a new-generation sequencing approach that will lead to a reference-grade genome assembly for Upland cotton. Three BAC libraries were constructed, fingerprinted, and integrated with BAC-end sequences (BES) to produce a de novo whole-genome physical map. The BAC map was partitioned by sub genomes through alignment to the diploid progenitor D-genome reference sequence with densely spaced BES anchor points and computational filtering. The physical maps were validated with FISH and genetic mapping of SNP markers derived from BES. Two pairs of homeologous chromosomes, A11/D11 and A12/D12, were used to assess multiplex sequencing approaches for completeness and scalability. The results represent the first sub genome anchored physical maps of Upland cotton, and a new-generation approach to the whole-genome sequencing, which will lead to the reference-grade assembly of allopolyploid cotton and serve as a general strategy for sequencing other polyploid species.
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Affiliation(s)
| | - Brian E Scheffler
- USDA-ARS, Genomics and Bioinformatics Research Unit, Stoneville, MS, USA
| | - Amanda M Hulse-Kemp
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Bo Liu
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | - Qingxin Song
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
| | - Atsumi Ando
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
| | - David M Stelly
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
| | | | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Don C Jones
- Agriculture and Environmental Research, Cotton Incorporated, Cary, NC, USA
| | - Daniel G Peterson
- Institute for Genomics, Biocomputing & Biotechnology and Department of Plant & Soil Sciences, Mississippi State University, Mississippi State, MS, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Z Jeffery Chen
- Department of Molecular Biosciences, Center for Computational Biology and Bioinformatics, and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA.
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