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Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons....

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Autores principales: Chen, Z. Jeffrey, Sreedasyam, Avinash, Ando, Atsumi, Song, Qingxin, De Santiago, Luis M., Hulse-Kemp, Amanda M., Ding, Mingquan, Ye, Wenxue, Kirkbride, Ryan C., Jenkins, Jerry, Plott, Christopher, Lovell, John, Lin, Yu-Ming, Vaughn, Robert, Liu, Bo, Simpson, Sheron, Scheffler, Brian E., Wen, Li, Saski, Christopher A., Grover, Corrinne E., Hu, Guanjing, Conover, Justin L., Carlson, Joseph W., Shu, Shengqiang, Boston, Lori B., Williams, Melissa, Peterson, Daniel G., McGee, Keith, Jones, Don C., Wendel, Jonathan F., Stelly, David M., Grimwood, Jane, Schmutz, Jeremy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203012/
https://www.ncbi.nlm.nih.gov/pubmed/32313247
http://dx.doi.org/10.1038/s41588-020-0614-5
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author Chen, Z. Jeffrey
Sreedasyam, Avinash
Ando, Atsumi
Song, Qingxin
De Santiago, Luis M.
Hulse-Kemp, Amanda M.
Ding, Mingquan
Ye, Wenxue
Kirkbride, Ryan C.
Jenkins, Jerry
Plott, Christopher
Lovell, John
Lin, Yu-Ming
Vaughn, Robert
Liu, Bo
Simpson, Sheron
Scheffler, Brian E.
Wen, Li
Saski, Christopher A.
Grover, Corrinne E.
Hu, Guanjing
Conover, Justin L.
Carlson, Joseph W.
Shu, Shengqiang
Boston, Lori B.
Williams, Melissa
Peterson, Daniel G.
McGee, Keith
Jones, Don C.
Wendel, Jonathan F.
Stelly, David M.
Grimwood, Jane
Schmutz, Jeremy
author_facet Chen, Z. Jeffrey
Sreedasyam, Avinash
Ando, Atsumi
Song, Qingxin
De Santiago, Luis M.
Hulse-Kemp, Amanda M.
Ding, Mingquan
Ye, Wenxue
Kirkbride, Ryan C.
Jenkins, Jerry
Plott, Christopher
Lovell, John
Lin, Yu-Ming
Vaughn, Robert
Liu, Bo
Simpson, Sheron
Scheffler, Brian E.
Wen, Li
Saski, Christopher A.
Grover, Corrinne E.
Hu, Guanjing
Conover, Justin L.
Carlson, Joseph W.
Shu, Shengqiang
Boston, Lori B.
Williams, Melissa
Peterson, Daniel G.
McGee, Keith
Jones, Don C.
Wendel, Jonathan F.
Stelly, David M.
Grimwood, Jane
Schmutz, Jeremy
author_sort Chen, Z. Jeffrey
collection PubMed
description Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N(6)-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement.
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spelling pubmed-72030122020-05-13 Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement Chen, Z. Jeffrey Sreedasyam, Avinash Ando, Atsumi Song, Qingxin De Santiago, Luis M. Hulse-Kemp, Amanda M. Ding, Mingquan Ye, Wenxue Kirkbride, Ryan C. Jenkins, Jerry Plott, Christopher Lovell, John Lin, Yu-Ming Vaughn, Robert Liu, Bo Simpson, Sheron Scheffler, Brian E. Wen, Li Saski, Christopher A. Grover, Corrinne E. Hu, Guanjing Conover, Justin L. Carlson, Joseph W. Shu, Shengqiang Boston, Lori B. Williams, Melissa Peterson, Daniel G. McGee, Keith Jones, Don C. Wendel, Jonathan F. Stelly, David M. Grimwood, Jane Schmutz, Jeremy Nat Genet Article Polyploidy is an evolutionary innovation for many animals and all flowering plants, but its impact on selection and domestication remains elusive. Here we analyze genome evolution and diversification for all five allopolyploid cotton species, including economically important Upland and Pima cottons. Although these polyploid genomes are conserved in gene content and synteny, they have diversified by subgenomic transposon exchanges that equilibrate genome size, evolutionary rate heterogeneities and positive selection between homoeologs within and among lineages. These differential evolutionary trajectories are accompanied by gene-family diversification and homoeolog expression divergence among polyploid lineages. Selection and domestication drive parallel gene expression similarities in fibers of two cultivated cottons, involving coexpression networks and N(6)-methyladenosine RNA modifications. Furthermore, polyploidy induces recombination suppression, which correlates with altered epigenetic landscapes and can be overcome by wild introgression. These genomic insights will empower efforts to manipulate genetic recombination and modify epigenetic landscapes and target genes for crop improvement. Nature Publishing Group US 2020-04-20 2020 /pmc/articles/PMC7203012/ /pubmed/32313247 http://dx.doi.org/10.1038/s41588-020-0614-5 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Chen, Z. Jeffrey
Sreedasyam, Avinash
Ando, Atsumi
Song, Qingxin
De Santiago, Luis M.
Hulse-Kemp, Amanda M.
Ding, Mingquan
Ye, Wenxue
Kirkbride, Ryan C.
Jenkins, Jerry
Plott, Christopher
Lovell, John
Lin, Yu-Ming
Vaughn, Robert
Liu, Bo
Simpson, Sheron
Scheffler, Brian E.
Wen, Li
Saski, Christopher A.
Grover, Corrinne E.
Hu, Guanjing
Conover, Justin L.
Carlson, Joseph W.
Shu, Shengqiang
Boston, Lori B.
Williams, Melissa
Peterson, Daniel G.
McGee, Keith
Jones, Don C.
Wendel, Jonathan F.
Stelly, David M.
Grimwood, Jane
Schmutz, Jeremy
Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
title Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
title_full Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
title_fullStr Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
title_full_unstemmed Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
title_short Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement
title_sort genomic diversifications of five gossypium allopolyploid species and their impact on cotton improvement
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7203012/
https://www.ncbi.nlm.nih.gov/pubmed/32313247
http://dx.doi.org/10.1038/s41588-020-0614-5
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