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
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
Volume7Issue:1Pages:11546
Abstract

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.

KeywordArundinarieae Poaceae Population Genomics Inferring Phylogeny Thamnocalamus Group Allies Gramineae Rpl16 Intron Gbssi Gene Evolution Identification Framework
Subject AreaMultidisciplinary Sciences
DOI10.1038/s41598-017-11367-x
Indexed BySCI
Language英语
WOS IDWOS:000410739000044
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/54884
Collection植物化学与西部植物资源持续利用国家重点实验室
Affiliation1.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
Recommended Citation
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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