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Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)
Ma, Peng-Fei1,2,3; Zhang, Yu-Xiao1,2; Zeng, Chun-Xia2; Guo, Zhen-Hua2; Li, De-Zhu1,2; Li,DZ (reprint author),Chinese Acad Sci,Kunming Inst Bot,132 Lanhei Rd,Kunming 650201,Yunnan,Peoples R China.; dzl@mail.kib.ac.cn
2014-11-01
发表期刊SYSTEMATIC BIOLOGY
ISSN1063-5157
卷号63期号:6页码:933-950
产权排序第一
摘要The temperate woody bamboos constitute a distinct tribe Arundinarieae (Poaceae: Bambusoideae) with high species diversity. Estimating phylogenetic relationships among the 11 major lineages of Arundinarieae has been particularly difficult, owing to a possible rapid radiation and the extremely low rate of sequence divergence. Here, we explore the use of chloroplast genome sequencing for phylogenetic inference. We sampled 25 species (22 temperate bamboos and 3 outgroups) for the complete genome representing eight major lineages of Arundinarieae in an attempt to resolve backbone relationships. Phylogenetic analyses of coding versus noncoding sequences, and of different regions of the genome (large single copy and small single copy, and inverted repeat regions) yielded no well-supported contradicting topologies but potential incongruence was found between the coding and noncoding sequences. The use of various data partitioning schemes in analysis of the complete sequences resulted in nearly identical topologies and node support values, although the partitioning schemes were decisively different from each other as to the fit to the data. Our full genomic data set substantially increased resolution along the backbone and provided strong support for most relationships despite the very short internodes and long branches in the tree. The inferred relationships were also robust to potential confounding factors (e. g., long-branch attraction) and received support from independent indels in the genome. We then added taxa from the three Arundinarieae lineages that were not included in the full-genome data set; each of these were sampled for more than 50% genome sequences. The resulting trees not only corroborated the reconstructed deep-level relationships but also largely resolved the phylogenetic placements of these three additional lineages. Furthermore, adding 129 additional taxa sampled for only eight chloroplast loci to the combined data set yielded almost identical relationships, albeit with low support values. We believe that the inferred phylogeny is robust to taxon sampling. Having resolved the deep-level relationships of Arundinarieae, we illuminate how chloroplast phylogenomics can be used for elucidating difficult phylogeny at low taxonomic levels in intractable plant groups.
关键词Branch Length Chloroplast Phylogenomics Data Partitioning Low Sequence Divergence Sampling Temperate Woody Bamboos
资助信息NSFC [81373288]; Natural Science Foundation of Yunnan Province [2008CD158]; Western Doctoral Foundation of Chinese Academy of Sciences; Foundation of State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences [P2008ZZ23, P2010ZZ14]; Cooperative Project of Guangdong Province; CAS [2009B091300135]; NSFC [81373288]; Natural Science Foundation of Yunnan Province [2008CD158]; Western Doctoral Foundation of Chinese Academy of Sciences; Foundation of State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences [P2008ZZ23, P2010ZZ14]; Cooperative Project of Guangdong Province; CAS [2009B091300135]
学科领域Evolutionary Biology
DOI10.1093/sysbio/syu054
收录类别SCI
语种英语
WOS研究方向Evolutionary Biology
WOS类目Evolutionary Biology
WOS记录号WOS:000344695900006
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文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/18515
专题中国西南野生生物种质资源库
通讯作者Li,DZ (reprint author),Chinese Acad Sci,Kunming Inst Bot,132 Lanhei Rd,Kunming 650201,Yunnan,Peoples R China.; dzl@mail.kib.ac.cn
作者单位1.Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Yunnan, Peoples R China
2.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming 650201, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
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Ma, Peng-Fei,Zhang, Yu-Xiao,Zeng, Chun-Xia,et al. Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)[J]. SYSTEMATIC BIOLOGY,2014,63(6):933-950.
APA Ma, Peng-Fei.,Zhang, Yu-Xiao.,Zeng, Chun-Xia.,Guo, Zhen-Hua.,Li, De-Zhu.,...&dzl@mail.kib.ac.cn.(2014).Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae).SYSTEMATIC BIOLOGY,63(6),933-950.
MLA Ma, Peng-Fei,et al."Chloroplast Phylogenomic Analyses Resolve Deep-Level Relationships of an Intractable Bamboo Tribe Arundinarieae (Poaceae)".SYSTEMATIC BIOLOGY 63.6(2014):933-950.
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