Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae
文献类型：期刊论文
| 作者 | Zhao, Lei1,2; Zhang, Ning3; Ma, Peng-Fei1,2; Liu, Qi4; Li, De-Zhu1,2 ; Guo, Zhen-Hua1,2
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| 刊名 | PLOS ONE
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| 出版日期 | 2013-05-29 |
| 卷号 | 8期号:5页码:e64642 |
| 关键词 | RNA-RECOGNITION MOTIF TRANSLATION INITIATION-FACTOR MULTIPLE SEQUENCE ALIGNMENT PROTEIN-CODING SEQUENCES LIKELIHOOD RATIO TESTS GRASS FAMILY POACEAE ARABIDOPSIS-THALIANA ADAPTIVE EVOLUTION MOLECULAR EVOLUTION PLANT PHYLOGENETICS |
| ISSN号 | 1932-6203 |
| 通讯作者 | Li, DZ (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming, Yunnan, Peoples R China. ; dzl@mail.kib.ac.cn ; guozhenhua@mail.kib.ac.cn |
| 英文摘要 | BEP clade of the grass family (Poaceae) is composed of three subfamilies, i.e. Bambusoideae, Ehrhartoideae, and Pooideae. Controversies on the phylogenetic relationships among three subfamilies still persist in spite of great efforts. However, previous evidence was mainly provided from plastid genes with only a few nuclear genes utilized. Given different evolutionary histories recorded by plastid and nuclear genes, it is indispensable to uncover their relationships based on nuclear genes. Here, eleven species with whole-sequenced genome and six species with transcriptomic data were included in this study. A total of 121 one-to-one orthologous groups (OGs) were identified and phylogenetic trees were reconstructed by different tree-building methods. Genes which might have undergone positive selection and played important roles in adaptive evolution were also investigated from 314 and 173 one-to-one OGs in two bamboo species and 14 grass species, respectively. Our results support the ((B, P) E) topology with high supporting values. Besides, our findings also indicate that 24 and nine orthologs with statistically significant evidence of positive selection are mainly involved in abiotic and biotic stress response, reproduction and development, plant metabolism and enzyme etc. from two bamboo species and 14 grass species, respectively. In summary, this study demonstrates the power of phylogenomic approach to shed lights on the evolutionary relationships within the BEP clade, and offers valuable insights into adaptive evolution of the grass family. |
| WOS标题词 | Science & Technology |
| 学科主题 | Multidisciplinary Sciences |
| 类目[WOS] | Multidisciplinary Sciences |
| 研究领域[WOS] | Science & Technology - Other Topics |
| 关键词[WOS] | RNA-RECOGNITION MOTIF ; TRANSLATION INITIATION-FACTOR ; MULTIPLE SEQUENCE ALIGNMENT ; PROTEIN-CODING SEQUENCES ; LIKELIHOOD RATIO TESTS ; GRASS FAMILY POACEAE ; ARABIDOPSIS-THALIANA ; ADAPTIVE EVOLUTION ; MOLECULAR EVOLUTION ; PLANT PHYLOGENETICS |
| 收录类别 | SCI |
| 资助信息 | Knowledge Innovation Project of the Chinese Academy of Sciences [KSCX2-YW-N-067]; National Natural Science Foundation of China [30990244]; NSFC-Yunnan province joint foundation [U1136603]; Scientific Research Foundation for the Returned Overseas Chinese Scholars; State Education Ministry and the Young Academic and Technical Leader Raising Foundation of Yunnan Province [2008PY065] |
| 语种 | 英语 |
| WOS记录号 | WOS:000319725500056 |
| 公开日期 | 2013-07-24 |
| 源URL | [http://ir.kib.ac.cn/handle/151853/16627]  |
| 专题 | 昆明植物研究所_中国西南野生生物种质资源库 |
| 作者单位 | 1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming, Yunnan, Peoples R China 2.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species, Kunming, Yunnan, Peoples R China 3.Penn State Univ, Dept Biol, University Pk, PA 16802 USA 4.Wenzhou Med Coll, Inst Genom Med, Wenzhou, Zhejiang, Peoples R China |
| 推荐引用方式 GB/T 7714 | Zhao, Lei,Zhang, Ning,Ma, Peng-Fei,et al. Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae[J]. PLOS ONE,2013,8(5):e64642. |
| APA | Zhao, Lei,Zhang, Ning,Ma, Peng-Fei,Liu, Qi,Li, De-Zhu,&Guo, Zhen-Hua.(2013).Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae.PLOS ONE,8(5),e64642. |
| MLA | Zhao, Lei,et al."Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae".PLOS ONE 8.5(2013):e64642. |
入库方式： OAI收割
来源：昆明植物研究所
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