Cargando…
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...
Autores principales: | , , , , , , , |
---|---|
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 |
_version_ | 1782155630126039040 |
---|---|
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. |
format | Text |
id | pubmed-2397501 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT zouxinhui analysisof142genesresolvestherapiddiversificationofthericegenus AT zhangfumin analysisof142genesresolvestherapiddiversificationofthericegenus AT zhangjianguo analysisof142genesresolvestherapiddiversificationofthericegenus AT zanglili analysisof142genesresolvestherapiddiversificationofthericegenus AT tangliang analysisof142genesresolvestherapiddiversificationofthericegenus AT wangjun analysisof142genesresolvestherapiddiversificationofthericegenus AT sangtao analysisof142genesresolvestherapiddiversificationofthericegenus AT gesong analysisof142genesresolvestherapiddiversificationofthericegenus |