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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
Corresponding AuthorLi, 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
Source PublicationMOLECULAR ECOLOGY RESOURCES
ISSN1755-098X
Volume13Issue:5Pages:938-945
AbstractPhylogenetic 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.
KeywordPhylogeny Polyploid Restriction Site-associated Dna Snp Markers Temperate Bamboos
Subject AreaBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
Indexed BySCI
Language英语
WOS Research AreaBiochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology
WOS SubjectBiochemistry & Molecular Biology ; Ecology ; Evolutionary Biology
WOS IDWOS:000322953400019
Citation statistics
Document Type期刊论文
Identifierhttp://ir.kib.ac.cn/handle/151853/16871
Collection中国西南野生生物种质资源库
Affiliation1.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
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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