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 st...

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Autores principales:	Christopher A. Saski, Brian E. Scheffler, Amanda M. Hulse-Kemp, Bo Liu, Qingxin Song, Atsumi Ando, David M. Stelly, Jodi A. Scheffler, Jane Grimwood, Don C. Jones, Daniel G. Peterson, Jeremy Schmutz, Z. Jeffery Chen
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/1126e48bb6884a9eb68ca368d7dca33a
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spelling	oai:doaj.org-article:1126e48bb6884a9eb68ca368d7dca33a2021-12-02T15:05:46ZSub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids10.1038/s41598-017-14885-w2045-2322https://doaj.org/article/1126e48bb6884a9eb68ca368d7dca33a2017-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-14885-whttps://doaj.org/toc/2045-2322Abstract 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.Christopher A. SaskiBrian E. SchefflerAmanda M. Hulse-KempBo LiuQingxin SongAtsumi AndoDavid M. StellyJodi A. SchefflerJane GrimwoodDon C. JonesDaniel G. PetersonJeremy SchmutzZ. Jeffery ChenNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-14 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Christopher A. Saski Brian E. Scheffler Amanda M. Hulse-Kemp Bo Liu Qingxin Song Atsumi Ando David M. Stelly Jodi A. Scheffler Jane Grimwood Don C. Jones Daniel G. Peterson Jeremy Schmutz Z. Jeffery Chen Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
description	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.
format	article
author	Christopher A. Saski Brian E. Scheffler Amanda M. Hulse-Kemp Bo Liu Qingxin Song Atsumi Ando David M. Stelly Jodi A. Scheffler Jane Grimwood Don C. Jones Daniel G. Peterson Jeremy Schmutz Z. Jeffery Chen
author_facet	Christopher A. Saski Brian E. Scheffler Amanda M. Hulse-Kemp Bo Liu Qingxin Song Atsumi Ando David M. Stelly Jodi A. Scheffler Jane Grimwood Don C. Jones Daniel G. Peterson Jeremy Schmutz Z. Jeffery Chen
author_sort	Christopher A. Saski
title	Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
title_short	Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
title_full	Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
title_fullStr	Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
title_full_unstemmed	Sub genome anchored physical frameworks of the allotetraploid Upland cotton (Gossypium hirsutum L.) genome, and an approach toward reference-grade assemblies of polyploids
title_sort	sub genome anchored physical frameworks of the allotetraploid upland cotton (gossypium hirsutum l.) genome, and an approach toward reference-grade assemblies of polyploids
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/1126e48bb6884a9eb68ca368d7dca33a
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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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