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

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

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

Journal Article · 10 November 2017 · Scientific Reports

DOI: https://doi.org/10.1038/s41598-017-14885-w · OSTI ID:1543775

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)

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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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC)

Sponsoring Organization:: USDOE Office of Science (SC); National Science Foundation (NSF)

OSTI ID:: 1543775

Journal Information:: Scientific Reports, Vol. 7, Issue 1; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 18 works

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Cotton CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING genes functionally diverged to differentially impact plant architecture Prewitt, Sarah F.; Ayre, Brian G.; McGarry, Roisin C. Journal of Experimental Botany https://doi.org/10.1093/jxb/ery324	journal	September 2018
Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution Susek, Karolina; Bielski, Wojciech; Czyż, Katarzyna B. Genes, Vol. 10, Issue 4 https://doi.org/10.3390/genes10040259	journal	April 2019
Unraveling cis and trans regulatory evolution during cotton domestication Bao, Ying; Hu, Guanjing; Grover, Corrinne E. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13386-w	journal	November 2019
Functional divergence of cellulose synthase orthologs in between wild Gossypium raimondii and domesticated G. arboreum diploid cotton species Kim, Hee Jin; Thyssen, Gregory N.; Song, Xianliang Cellulose, Vol. 26, Issue 18 https://doi.org/10.1007/s10570-019-02744-y	journal	September 2019
Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.) Grover, Corrinne E.; Yoo, Mi-Jeong; Lin, Meng G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 2 https://doi.org/10.1534/g3.119.400909	journal	February 2020
Genetic analysis of the transition from wild to domesticated cotton (G. hirsutum L.) Grover, Corrinne E.; Yoo, Mi-Jeong; Lin, Meng https://doi.org/10.1101/616763	posted_content	November 2019
Unraveling cis and trans regulatory evolution during cotton domestication Bao, Ying; Hu, Guanjing; Grover, Corrinne E. Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-13386-w	journal	November 2019
Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution Susek, Karolina; Bielski, Wojciech; Czyż, Katarzyna B. Genes, Vol. 10, Issue 4 https://doi.org/10.3390/genes10040259	journal	April 2019
Genetic Analysis of the Transition from Wild to Domesticated Cotton ( Gossypium hirsutum L.) Grover, Corrinne E.; Yoo, Mi-Jeong; Lin, Meng G3 Genes\|Genomes\|Genetics, Vol. 10, Issue 2 https://doi.org/10.1534/g3.119.400909	journal	February 2020
Identification of cotton MOTHER OF FT AND TFL1 homologs, GhMFT1 and GhMFT2, involved in seed germination Yu, Xiuli; Liu, Hui; Sang, Na PLOS ONE, Vol. 14, Issue 4 https://doi.org/10.1371/journal.pone.0215771	journal	April 2019

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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

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