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Genomic insights into the evolution of Echinochloa species as weed and orphan crop
As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving th...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8814039/ https://www.ncbi.nlm.nih.gov/pubmed/35115514 http://dx.doi.org/10.1038/s41467-022-28359-9 |
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author | Wu, Dongya Shen, Enhui Jiang, Bowen Feng, Yu Tang, Wei Lao, Sangting Jia, Lei Lin, Han-Yang Xie, Lingjuan Weng, Xifang Dong, Chenfeng Qian, Qinghong Lin, Feng Xu, Haiming Lu, Huabing Cutti, Luan Chen, Huajun Deng, Shuiguang Guo, Longbiao Chuah, Tse-Seng Song, Beng-Kah Scarabel, Laura Qiu, Jie Zhu, Qian-Hao Yu, Qin Timko, Michael P. Yamaguchi, Hirofumi Merotto, Aldo Qiu, Yingxiong Olsen, Kenneth M. Fan, Longjiang Ye, Chu-Yu |
author_facet | Wu, Dongya Shen, Enhui Jiang, Bowen Feng, Yu Tang, Wei Lao, Sangting Jia, Lei Lin, Han-Yang Xie, Lingjuan Weng, Xifang Dong, Chenfeng Qian, Qinghong Lin, Feng Xu, Haiming Lu, Huabing Cutti, Luan Chen, Huajun Deng, Shuiguang Guo, Longbiao Chuah, Tse-Seng Song, Beng-Kah Scarabel, Laura Qiu, Jie Zhu, Qian-Hao Yu, Qin Timko, Michael P. Yamaguchi, Hirofumi Merotto, Aldo Qiu, Yingxiong Olsen, Kenneth M. Fan, Longjiang Ye, Chu-Yu |
author_sort | Wu, Dongya |
collection | PubMed |
description | As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements. |
format | Online Article Text |
id | pubmed-8814039 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-88140392022-02-16 Genomic insights into the evolution of Echinochloa species as weed and orphan crop Wu, Dongya Shen, Enhui Jiang, Bowen Feng, Yu Tang, Wei Lao, Sangting Jia, Lei Lin, Han-Yang Xie, Lingjuan Weng, Xifang Dong, Chenfeng Qian, Qinghong Lin, Feng Xu, Haiming Lu, Huabing Cutti, Luan Chen, Huajun Deng, Shuiguang Guo, Longbiao Chuah, Tse-Seng Song, Beng-Kah Scarabel, Laura Qiu, Jie Zhu, Qian-Hao Yu, Qin Timko, Michael P. Yamaguchi, Hirofumi Merotto, Aldo Qiu, Yingxiong Olsen, Kenneth M. Fan, Longjiang Ye, Chu-Yu Nat Commun Article As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements. Nature Publishing Group UK 2022-02-03 /pmc/articles/PMC8814039/ /pubmed/35115514 http://dx.doi.org/10.1038/s41467-022-28359-9 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/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/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Wu, Dongya Shen, Enhui Jiang, Bowen Feng, Yu Tang, Wei Lao, Sangting Jia, Lei Lin, Han-Yang Xie, Lingjuan Weng, Xifang Dong, Chenfeng Qian, Qinghong Lin, Feng Xu, Haiming Lu, Huabing Cutti, Luan Chen, Huajun Deng, Shuiguang Guo, Longbiao Chuah, Tse-Seng Song, Beng-Kah Scarabel, Laura Qiu, Jie Zhu, Qian-Hao Yu, Qin Timko, Michael P. Yamaguchi, Hirofumi Merotto, Aldo Qiu, Yingxiong Olsen, Kenneth M. Fan, Longjiang Ye, Chu-Yu Genomic insights into the evolution of Echinochloa species as weed and orphan crop |
title | Genomic insights into the evolution of Echinochloa species as weed and orphan crop |
title_full | Genomic insights into the evolution of Echinochloa species as weed and orphan crop |
title_fullStr | Genomic insights into the evolution of Echinochloa species as weed and orphan crop |
title_full_unstemmed | Genomic insights into the evolution of Echinochloa species as weed and orphan crop |
title_short | Genomic insights into the evolution of Echinochloa species as weed and orphan crop |
title_sort | genomic insights into the evolution of echinochloa species as weed and orphan crop |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8814039/ https://www.ncbi.nlm.nih.gov/pubmed/35115514 http://dx.doi.org/10.1038/s41467-022-28359-9 |
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