Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

doi:10.1371/journal.pone.0064642

	Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae
	Zhao, Lei 1,2; Zhang, Ning 3; Ma, Peng-Fei 1,2; Liu, Qi 4; Li, De-Zhu1,2 ; Guo, Zhen-Hua1,2
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
	2013-05-29
发表期刊	PLOS ONE
ISSN	1932-6203
卷号	8 期号:5 页码:e64642
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.
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
学科领域	Multidisciplinary Sciences
DOI	10.1371/journal.pone.0064642
收录类别	SCI
语种	英语
WOS记录号	WOS:000319725500056
引用统计
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/16627
专题	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.

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