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Analysis of 142 genes resolves the rapid diversification of the rice genus

BACKGROUND: The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genom...

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Autores principales: Zou, Xin-Hui, Zhang, Fu-Min, Zhang, Jian-Guo, Zang, Li-Li, Tang, Liang, Wang, Jun, Sang, Tao, Ge, Song
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397501/
https://www.ncbi.nlm.nih.gov/pubmed/18315873
http://dx.doi.org/10.1186/gb-2008-9-3-r49
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author Zou, Xin-Hui
Zhang, Fu-Min
Zhang, Jian-Guo
Zang, Li-Li
Tang, Liang
Wang, Jun
Sang, Tao
Ge, Song
author_facet Zou, Xin-Hui
Zhang, Fu-Min
Zhang, Jian-Guo
Zang, Li-Li
Tang, Liang
Wang, Jun
Sang, Tao
Ge, Song
author_sort Zou, Xin-Hui
collection PubMed
description BACKGROUND: The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genome resources for biological research and rice breeding, we will benefit from the availability of a robust phylogeny of the rice genus. RESULTS: Through screening rice genome sequences, we sampled and sequenced 142 single-copy genes to clarify the relationships among all diploid genome types of the rice genus. The analysis identified two short internal branches around which most previous phylogenetic inconsistency emerged. These represent two episodes of rapid speciation that occurred approximately 5 and 10 million years ago (Mya) and gave rise to almost the entire diversity of the genus. The known chromosomal distribution of the sampled genes allowed the documentation of whole-genome sorting of ancestral alleles during the rapid speciation, which was responsible primarily for extensive incongruence between gene phylogenies and persisting phylogenetic ambiguity in the genus. Random sample analysis showed that 120 genes with an average length of 874 bp were needed to resolve both short branches with 95% confidence. CONCLUSION: Our phylogenomic analysis successfully resolved the phylogeny of rice genome types, which lays a solid foundation for comparative and functional genomic studies of rice and its relatives. This study also highlights that organismal genomes might be mosaics of conflicting genealogies because of rapid speciation and demonstrates the power of phylogenomics in the reconstruction of rapid diversification.
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spelling pubmed-23975012008-05-30 Analysis of 142 genes resolves the rapid diversification of the rice genus Zou, Xin-Hui Zhang, Fu-Min Zhang, Jian-Guo Zang, Li-Li Tang, Liang Wang, Jun Sang, Tao Ge, Song Genome Biol Research BACKGROUND: The completion of rice genome sequencing has made rice and its wild relatives an attractive system for biological studies. Despite great efforts, phylogenetic relationships among genome types and species in the rice genus have not been fully resolved. To take full advantage of rice genome resources for biological research and rice breeding, we will benefit from the availability of a robust phylogeny of the rice genus. RESULTS: Through screening rice genome sequences, we sampled and sequenced 142 single-copy genes to clarify the relationships among all diploid genome types of the rice genus. The analysis identified two short internal branches around which most previous phylogenetic inconsistency emerged. These represent two episodes of rapid speciation that occurred approximately 5 and 10 million years ago (Mya) and gave rise to almost the entire diversity of the genus. The known chromosomal distribution of the sampled genes allowed the documentation of whole-genome sorting of ancestral alleles during the rapid speciation, which was responsible primarily for extensive incongruence between gene phylogenies and persisting phylogenetic ambiguity in the genus. Random sample analysis showed that 120 genes with an average length of 874 bp were needed to resolve both short branches with 95% confidence. CONCLUSION: Our phylogenomic analysis successfully resolved the phylogeny of rice genome types, which lays a solid foundation for comparative and functional genomic studies of rice and its relatives. This study also highlights that organismal genomes might be mosaics of conflicting genealogies because of rapid speciation and demonstrates the power of phylogenomics in the reconstruction of rapid diversification. BioMed Central 2008-03-03 /pmc/articles/PMC2397501/ /pubmed/18315873 http://dx.doi.org/10.1186/gb-2008-9-3-r49 Text en Copyright © 2008 Zou et al.; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Zou, Xin-Hui
Zhang, Fu-Min
Zhang, Jian-Guo
Zang, Li-Li
Tang, Liang
Wang, Jun
Sang, Tao
Ge, Song
Analysis of 142 genes resolves the rapid diversification of the rice genus
title Analysis of 142 genes resolves the rapid diversification of the rice genus
title_full Analysis of 142 genes resolves the rapid diversification of the rice genus
title_fullStr Analysis of 142 genes resolves the rapid diversification of the rice genus
title_full_unstemmed Analysis of 142 genes resolves the rapid diversification of the rice genus
title_short Analysis of 142 genes resolves the rapid diversification of the rice genus
title_sort analysis of 142 genes resolves the rapid diversification of the rice genus
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2397501/
https://www.ncbi.nlm.nih.gov/pubmed/18315873
http://dx.doi.org/10.1186/gb-2008-9-3-r49
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