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Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau
Zhang, Faqi1,2; Gao, Qingbo1; Khan, Gulzar1; Luo, Keming1,2; Chen, Shilong1; Chen, SL (reprint author), Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810001, Peoples R China.
2014-12-15
发表期刊GENE
卷号553期号:2页码:90-97
文章类型Article
摘要Transcriptome sequencing is a powerful tool for the assessment of gene expression and the identification and characterization of molecular markers in non-model organisms. Rhodiola algida L. (Crassulaceae), endemic to the Qinghai-Tibetan Plateau, has long been used in traditional Chinese medicine to prevent altitude sickness and eliminate fatigue. Illumina-based high-throughput transcriptome sequencing of aboveground and underground tissues of R. algida respectively yielded 5.40 million and 5.18 million clean reads. A total of 82,664 unigenes averaging 577 bp in length were generated from the aboveground clean reads, with 86,237 unigenes of 502-bp mean length obtained from the underground tissues. Of 55,028 unigenes compared with sequences in UniProt databases, 20,413 unigenes had significant similarities with existing sequences in NR, NT, SwissProt, GO, KEGG, and COG databases. Single nucleotide polymorphism (SNP) analysis identified 237,294 SNPs from 154,636 contigs of aboveground tissues and 197,540 SNPs from 144,963 underground-derived contigs. The information uncovered in this study should serve as a valuable resource for the characterization of important traits related to secondary metabolite formation and for the identification of associated molecular mechanisms. (C) 2014 Elsevier B.V. All rights reserved.
关键词Rna-seq Transcriptome Rhodiola Algida Gene Expression
WOS标题词Science & Technology ; Life Sciences & Biomedicine
关键词[WOS]RNA-SEQ ; REFERENCE GENOME ; SNP DISCOVERY ; GENE ; ANNOTATION ; ALIGNMENT ; SEQUENCE ; PEPPER ; ATLAS ; PLANT
收录类别SCI
语种英语
WOS研究方向Genetics & Heredity
WOS类目Genetics & Heredity
WOS记录号WOS:000345488400004
引用统计
文献类型期刊论文
条目标识符http://210.75.249.4/handle/363003/6580
专题中国科学院西北高原生物研究所
通讯作者Chen, SL (reprint author), Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810001, Peoples R China.
作者单位1.Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810001, Peoples R China
2.Southwest Univ, Sch Life Sci, Chongqing 400715, Peoples R China
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Zhang, Faqi,Gao, Qingbo,Khan, Gulzar,et al. Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau[J]. GENE,2014,553(2):90-97.
APA Zhang, Faqi,Gao, Qingbo,Khan, Gulzar,Luo, Keming,Chen, Shilong,&Chen, SL .(2014).Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau.GENE,553(2),90-97.
MLA Zhang, Faqi,et al."Comparative transcriptome analysis of aboveground and underground tissues of Rhodiola algida, an important ethno-medicinal herb endemic to the Qinghai-Tibetan Plateau".GENE 553.2(2014):90-97.
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