Identification of SNP markers for inferring phylogeny in temperate bamboos (Poaceae: Bambusoideae) using RAD sequencing
文献类型：期刊论文
| 作者 | Wang, X. Q.1,2; Zhao, L.1; Eaton, D. A. R.3; Li, D. Z.4 ; Guo, Z. H.1
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| 刊名 | MOLECULAR ECOLOGY RESOURCES
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| 出版日期 | 2013-09-01 |
| 卷号 | 13期号:5页码:938-945 |
| 关键词 | phylogeny polyploid restriction site-associated DNA SNP markers temperate bamboos |
| ISSN号 | 1755-098X |
| 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 |
| 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. |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine |
| 学科主题 | Biochemistry & Molecular Biology; Ecology; Evolutionary Biology |
| 类目[WOS] | Biochemistry & Molecular Biology ; Ecology ; Evolutionary Biology |
| 研究领域[WOS] | Biochemistry & Molecular Biology ; Environmental Sciences & Ecology ; Evolutionary Biology |
| 关键词[WOS] | GRASS FAMILY POACEAE ; ARUNDINARIEAE POACEAE ; GENE ONTOLOGY ; MIXED MODELS ; RPL16 INTRON ; SSR MARKERS ; DE-NOVO ; TOOL ; BAMBUSEAE ; DNA |
| 收录类别 | SCI |
| 资助信息 | Knowledge Innovation Project of the Chinese Academy of Sciences [KSCX2-YW-N-067]; National Natural Science Foundation of China [30990244]; NSFC-Yunnan province joint foundation [U1136603]; Scientific Research Foundation for the Returned Overseas Chinese Scholars, State Education Ministry; Young Academic and Technical Leader Raising Foundation of Yunnan Province [2008PY065]; Yunnan Provincial Government through an innovation team programme |
| 语种 | 英语 |
| WOS记录号 | WOS:000322953400019 |
| 公开日期 | 2013-10-16 |
| 源URL | [http://ir.kib.ac.cn/handle/151853/16871]  |
| 专题 | 昆明植物研究所_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. |
入库方式： OAI收割
来源：昆明植物研究所
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