Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)
Wang, Xueqin1,2; Ye, Xiaying1,3,4; Zhao, Lei1,3,4; Li, Dezhu1,5; Guo, Zhenhua1; Zhuang, Huifu6
2017-09-14
发表期刊SCIENTIFIC REPORTS
ISSN2045-2322
卷号7期号:1页码:11546
摘要

The temperate bamboos (tribe Arundinarieae, Poaceae) are strongly supported as monophyly in recent molecular studies, but taxonomic delineation and phylogenetic relationships within the tribe lack resolution. Here, we sampled 39 species (36 temperate bamboos and 3 outgroups) for restriction-site associated DNA sequencing (RAD-seq) with an emphasis on Phyllostachys clade and related clades. Using the largest data matrix for the bamboos to date, we were able to infer phylogenetic relationships with unparalleled resolution. The Phyllostachys, Shibataea, and Arundinaria clades defined from plastid phylogeny, were not supported as monophyletic group. However, the RAD-seq phylogeny largely agreed with the morphology-based taxonomy, with two clades having leptomorph rhizomes strongly supported as monophyletic group. We also explored two approaches, BWA-GATK (a mapping system) and Stacks (a grouping system), for differences in SNP calling and phylogeny inference. For the same level of missing data, the BWA-GATK pipeline produced much more SNPs in comparison with Stacks. Phylogenetic analyses of the largest data matrices from both pipelines, using concatenation and coalescent methods provided similar tree topologies, despite the presence of missing data. Our study demonstrates the utility of RAD-seq data for elucidating phylogenetic relationships between genera and higher taxonomic levels in this important but phylogenetically challenging group.

关键词Arundinarieae Poaceae Population Genomics Inferring Phylogeny Thamnocalamus Group Allies Gramineae Rpl16 Intron Gbssi Gene Evolution Identification Framework
收录类别SCI
语种英语
引用统计
文献类型期刊论文
条目标识符http://ir.kib.ac.cn/handle/151853/54884
专题植物化学与西部植物资源持续利用国家重点实验室
作者单位1.Chinese Acad Sci, Kunming Inst Bot, Plant Germplasm & Genom Ctr, Germplasm Bank Wild Species, Kunming 650201, Yunnan, Peoples R China
2.Zhoukou Normal Univ, Coll Life Sci & Agron, Zhoukou 466001, Peoples R China
3.Univ Chinese Acad Sci, Kunming Coll Life Sci, Kunming 650201, Yunnan, Peoples R China
4.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
5.Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming 650201, Yunnan, Peoples R China
6.Chinese Acad Sci, Kunming Inst Bot, Key Lab Econ Plants & Biotechnol, Yunnan Key Lab Wild Plant Resources, Kunming 650201, Yunnan, Peoples R China
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GB/T 7714
Wang, Xueqin,Ye, Xiaying,Zhao, Lei,et al. Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)[J]. SCIENTIFIC REPORTS,2017,7(1):11546.
APA Wang, Xueqin,Ye, Xiaying,Zhao, Lei,Li, Dezhu,Guo, Zhenhua,&Zhuang, Huifu.(2017).Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae).SCIENTIFIC REPORTS,7(1),11546.
MLA Wang, Xueqin,et al."Genome-wide RAD sequencing data provide unprecedented resolution of the phylogeny of temperate bamboos (Poaceae: Bambusoideae)".SCIENTIFIC REPORTS 7.1(2017):11546.
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