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Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution
Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable nu...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287411/ https://www.ncbi.nlm.nih.gov/pubmed/32537559 http://dx.doi.org/10.1002/pld3.232 |
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author | Li, Wei Zhang, Qun‐Jie Zhu, Ting Tong, Yan Li, Kui Shi, Cong Zhang, Yun Liu, Yun‐Long Jiang, Jian‐Jun Liu, Yuan Xia, En‐Hua Huang, Hui Zhang, Li‐Ping Zhang, Dan Shi, Chao Jiang, Wen‐Kai Zhao, You‐Jie Mao, Shu‐Yan Jiao, Jun‐ying Xu, Ping‐Zhen Yang, Li‐Li Gao, Li‐Zhi |
author_facet | Li, Wei Zhang, Qun‐Jie Zhu, Ting Tong, Yan Li, Kui Shi, Cong Zhang, Yun Liu, Yun‐Long Jiang, Jian‐Jun Liu, Yuan Xia, En‐Hua Huang, Hui Zhang, Li‐Ping Zhang, Dan Shi, Chao Jiang, Wen‐Kai Zhao, You‐Jie Mao, Shu‐Yan Jiao, Jun‐ying Xu, Ping‐Zhen Yang, Li‐Li Gao, Li‐Zhi |
author_sort | Li, Wei |
collection | PubMed |
description | Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage‐specific gene families associated with the self‐incompatibility (SI) and formation of reproductive separation. We show how lineage‐specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage‐specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome‐wide expansion of genes encoding NBS‐LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata. |
format | Online Article Text |
id | pubmed-7287411 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-72874112020-06-12 Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution Li, Wei Zhang, Qun‐Jie Zhu, Ting Tong, Yan Li, Kui Shi, Cong Zhang, Yun Liu, Yun‐Long Jiang, Jian‐Jun Liu, Yuan Xia, En‐Hua Huang, Hui Zhang, Li‐Ping Zhang, Dan Shi, Chao Jiang, Wen‐Kai Zhao, You‐Jie Mao, Shu‐Yan Jiao, Jun‐ying Xu, Ping‐Zhen Yang, Li‐Li Gao, Li‐Zhi Plant Direct Original Research Oryza rufipogon and O. longistaminata are important wild relatives of cultivated rice, harboring a promising source of novel genes for rice breeding programs. Here, we present de novo assembled draft genomes and annotation of O. rufipogon and O. longistaminata. Our analysis reveals a considerable number of lineage‐specific gene families associated with the self‐incompatibility (SI) and formation of reproductive separation. We show how lineage‐specific expansion or contraction of gene families with functional enrichment of the recognition of pollen, thus enlightening their reproductive diversification. We documented a large number of lineage‐specific gene families enriched in salt stress, antifungal response, and disease resistance. Our comparative analysis further shows a genome‐wide expansion of genes encoding NBS‐LRR proteins in these two outcrossing wild species in contrast to six other selfing rice species. Conserved noncoding sequences (CNSs) in the two wild rice genomes rapidly evolve relative to selfing rice species, resulting in the reduction of genomic variation owing to shifts of mating systems. We find that numerous genes related to these rapidly evolving CNSs are enriched in reproductive structure development, flower development, and postembryonic development, which may associate with SI in O. rufipogon and O. longistaminata. John Wiley and Sons Inc. 2020-06-11 /pmc/articles/PMC7287411/ /pubmed/32537559 http://dx.doi.org/10.1002/pld3.232 Text en © 2020 The Authors. Plant Direct published by American Society of Plant Biologists, Society for Experimental Biology and John Wiley & Sons Ltd This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Research Li, Wei Zhang, Qun‐Jie Zhu, Ting Tong, Yan Li, Kui Shi, Cong Zhang, Yun Liu, Yun‐Long Jiang, Jian‐Jun Liu, Yuan Xia, En‐Hua Huang, Hui Zhang, Li‐Ping Zhang, Dan Shi, Chao Jiang, Wen‐Kai Zhao, You‐Jie Mao, Shu‐Yan Jiao, Jun‐ying Xu, Ping‐Zhen Yang, Li‐Li Gao, Li‐Zhi Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution |
title | Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution |
title_full | Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution |
title_fullStr | Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution |
title_full_unstemmed | Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution |
title_short | Draft genomes of two outcrossing wild rice, Oryza rufipogon and O. longistaminata, reveal genomic features associated with mating‐system evolution |
title_sort | draft genomes of two outcrossing wild rice, oryza rufipogon and o. longistaminata, reveal genomic features associated with mating‐system evolution |
topic | Original Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7287411/ https://www.ncbi.nlm.nih.gov/pubmed/32537559 http://dx.doi.org/10.1002/pld3.232 |
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