Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing

	Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing
	Wang, X. Q.1,2; Zhao, L.1; Eaton, D. A. R.3; Li, D. Z.4 ; Guo, Z. H.1
通讯作者	Li, DZ (reprint author), Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming 650201, Peoples R China. ; dzl@mail.kib.ac.cn ; guozhenhua@mail.kib.ac.cn
	2013-09-01
发表期刊	MOLECULAR ECOLOGY RESOURCES
ISSN	1755-098X
卷号	13 期号:5 页码:938-945
摘要	Phylogenetic relationships among temperate species of bamboo are difficult to resolve, owing to both the challenge of detecting sufficiently variable markers and their polyploid history. Here, we use restriction site-associated DNA sequencing to identify candidate loci with fixed allelic differences segregating between and within two temperate species of bamboos: Arundinaria faberi and Yushania brevipaniculata. Approximately 27 million paired-end sequencing reads were generated across four samples. From pooled data, we assembled 67685 and 70668 de novo contigs from partial overlap among paired-end reads, with an average length of 240 and 241bp for the two species, respectively, which were used to investigate functional classification of RAD tags in a blastx search. Analysed separately by population, we recovered 29443 putatively orthologous RAD tags shared across the four sampled populations, containing 28023 sequence variants, of which c. 13000 are segregating between species, and c. 3000 segregating between populations within each species. Analyses based on these RAD tags yielded robust phylogenetic inferences, even with data set constructed from surprisingly few loci. This study illustrates the potential for reduced-representation genome data to resolve difficult phylogenetic relationships in temperate bamboos.
关键词	Phylogeny Polyploid Restriction Site-associated Dna Snp Markers Temperate Bamboos
学科领域	Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
收录类别	SCI
语种	英语
WOS记录号	WOS:000322953400019
引用统计	被引频次：43[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://ir.kib.ac.cn/handle/151853/16871
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, Germplasm Bank Wild Species, Plant Germplasm & Genom Ctr, Kunming 650201, Peoples R China 2.Univ Chinese Acad Sci, Coll Life Sci, Beijing 100049, Peoples R China 3.Univ Chicago, Comm Evolutionary Biol, Chicago, IL 60637 USA 4.Chinese Acad Sci, Kunming Inst Bot, Key Lab Biodivers & Biogeog, Kunming 650201, Peoples R China
推荐引用方式 GB/T 7714	Wang, X. Q.,Zhao, L.,Eaton, D. A. R.,et al. Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing[J]. MOLECULAR ECOLOGY RESOURCES,2013,13(5):938-945.
APA	Wang, X. Q.,Zhao, L.,Eaton, D. A. R.,Li, D. Z.,&Guo, Z. H..(2013).Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing.MOLECULAR ECOLOGY RESOURCES,13(5),938-945.
MLA	Wang, X. Q.,et al."Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing".MOLECULAR ECOLOGY RESOURCES 13.5(2013):938-945.

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