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

doi:10.1038/s41598-017-14885-w

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:

Saski, Christopher A. ^[1];

^[2]; Hulse-Kemp, Amanda M. ^[3]; Liu, Bo ^[3]; Song, Qingxin ^[4]; Ando, Atsumi ^[4];

^[3]; Scheffler, Jodi A. ^[5]; Grimwood, Jane ^[6]; Jones, Don C. ^[7]; Peterson, Daniel G. ^[8]; Schmutz, Jeremy ^[6];

^[4]

Clemson Univ., SC (United States)
US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS (United States). Genomics and Bioinformatics Research Unit
Texas A & M Univ., College Station, TX (United States)
Univ. of Texas, Austin, TX (United States)
US Dept. of Agriculture-Agricultural Research Service (USDA-ARS), Stoneville, MS (United States). Crop Genetics Research Unit
HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
Cotton Inc., Cary, NC (United States). Agriculture and Environmental Research
Mississippi State Univ., Mississippi State, MS (United States)

Publication Date:: 2017-11-10

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.

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                    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.

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                    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.

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@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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DOI: 10.1038/s41598-017-14885-w

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Works referenced in this record:

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

Altschul, Stephen F.; Madden, Thomas L.; Schäffer, Alejandro A.
Nucleic Acids Research, Vol. 25, Issue 17, p. 3389-3402
DOI: 10.1093/nar/25.17.3389

The B73 Maize Genome: Complexity, Diversity, and Dynamics
journal, November 2009

Schnable, P. S.; Ware, D.; Fulton, R. S.
Science, Vol. 326, Issue 5956, p. 1112-1115
DOI: 10.1126/science.1178534

Similar Records in DOE PAGES and OSTI.GOV collections:

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Journal Article Radin, J.W. ; Hartung, W. ; Mauney, J.R. ; ... - Plant Physiology; (USA)

Some evidence indicates that photosynthetic rate (A) and stomatal conductance (g) of leaves are correlated across diverse environments. The correlation between A and g has led to the postulation of a messenger from the mesophyll that directs stomatal behavior. Because A is a function of intercellular CO{sub 2} concentration (c{sub i}), which is in turn a function of g, such a correlation may be partially mediated by c{sub i} if g is to some degree an independent variable. Among individual sunlit leaves in a cotton (Gossypium hirsutum L.) canopy in the field, A was significantly correlated with g. The relativemore »« less
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Journal Article Dzhabarov, Kh. - Dokl. Akad. Nauk Tadzh. SSR 14: No. 10, 59-61(1971).
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DOI: 10.1104/pp.94.2.704

Similar Records

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

Citation Formats

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs journal, September 1997

The B73 Maize Genome: Complexity, Diversity, and Dynamics journal, November 2009

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
journal, September 1997

The B73 Maize Genome: Complexity, Diversity, and Dynamics
journal, November 2009