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Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae
Zhao, Lei1,2; Zhang, Ning3; Ma, Peng-Fei1,2; Liu, Qi4; Li, De-Zhu1,2; Guo, Zhen-Hua1,2
Corresponding AuthorLi, 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
Source PublicationPLOS ONE
ISSN1932-6203
Volume8Issue:5Pages:e64642
AbstractBEP 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.
KeywordRna-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
Subject AreaMultidisciplinary Sciences
DOI10.1371/journal.pone.0064642
Indexed BySCI
Language英语
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000319725500056
Citation statistics
Cited Times:16[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/16627
Collection中国西南野生生物种质资源库
Affiliation1.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
Recommended Citation
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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