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Title: Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids

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.

Authors:
 [1]; ORCiD logo [2];  [3];  [3];  [4];  [4]; ORCiD logo [3];  [5];  [6];  [7];  [8];  [6]; ORCiD logo [4]
  1. Clemson Univ., SC (United States)
  2. US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS (United States). Genomics and Bioinformatics Research Unit
  3. Texas A & M Univ., College Station, TX (United States)
  4. Univ. of Texas, Austin, TX (United States)
  5. US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS (United States). Crop Genetics Research Unit
  6. HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  7. Cotton Inc., Cary, NC (United States). Agriculture and Environmental Research
  8. Mississippi State Univ., Mississippi State, MS (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)
Sponsoring Org.:
USDOE Office of Science (SC); National Science Foundation (NSF)
OSTI Identifier:
1543775
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Saski, Christopher A., Scheffler, Brian E., Hulse-Kemp, Amanda M., Liu, Bo, Song, Qingxin, Ando, Atsumi, Stelly, David M., Scheffler, Jodi A., Grimwood, Jane, Jones, Don C., Peterson, Daniel G., Schmutz, Jeremy, and Chen, Z. Jeffery. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. United States: N. p., 2017. Web. doi:10.1038/s41598-017-14885-w.
Saski, Christopher A., Scheffler, Brian E., Hulse-Kemp, Amanda M., Liu, Bo, Song, Qingxin, Ando, Atsumi, Stelly, David M., Scheffler, Jodi A., Grimwood, Jane, Jones, Don C., Peterson, Daniel G., Schmutz, Jeremy, & Chen, Z. Jeffery. Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids. United States. doi:10.1038/s41598-017-14885-w.
Saski, Christopher A., Scheffler, Brian E., Hulse-Kemp, Amanda M., Liu, Bo, Song, Qingxin, Ando, Atsumi, Stelly, David M., Scheffler, Jodi A., Grimwood, Jane, Jones, Don C., Peterson, Daniel G., Schmutz, Jeremy, and Chen, Z. Jeffery. Fri . "Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids". United States. doi:10.1038/s41598-017-14885-w. https://www.osti.gov/servlets/purl/1543775.
@article{osti_1543775,
title = {Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids},
author = {Saski, Christopher A. and Scheffler, Brian E. and Hulse-Kemp, Amanda M. and Liu, Bo and Song, Qingxin and Ando, Atsumi and Stelly, David M. and Scheffler, Jodi A. and Grimwood, Jane and Jones, Don C. and Peterson, Daniel G. and Schmutz, Jeremy and Chen, Z. Jeffery},
abstractNote = {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.},
doi = {10.1038/s41598-017-14885-w},
journal = {Scientific Reports},
number = 1,
volume = 7,
place = {United States},
year = {2017},
month = {11}
}

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