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题名: Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing
作者: Wang, X. Q.1, 2; Zhao, L.1; Eaton, D. A. R.3; null(李德铢)4; Guo, Z. H.1
刊名: MOLECULAR ECOLOGY RESOURCES
关键词: phylogeny ; polyploid ; restriction site-associated DNA ; SNP markers ; temperate bamboos
英文摘要: 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.
出版日期: 2013-09-01
卷号: 13, 期号:5, 页码:938-945
语种: 英语
收录类别: SCI
学科分类: Biochemistry & Molecular Biology; Ecology; Evolutionary Biology
ISSN号: 1755-098X
Citation statistics:
内容类型: 期刊论文
URI标识: http://ir.kib.ac.cn/handle/151853/16871
Appears in Collections:中国西南野生生物种质资源库_期刊论文

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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

Recommended Citation:
Wang, X. Q.; Zhao, L.; Eaton, D. A. R.; Li, D. Z.; Guo, Z. H..Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing,MOLECULAR ECOLOGY RESOURCES,2013,13(5):938-945
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