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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
Source PublicationGENE
Volume553Issue:2Pages:90-97
SubtypeArticle
AbstractTranscriptome 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.
KeywordRna-seq Transcriptome Rhodiola Algida Gene Expression
WOS HeadingsScience & Technology ; Life Sciences & Biomedicine
WOS KeywordRNA-SEQ ; REFERENCE GENOME ; SNP DISCOVERY ; GENE ; ANNOTATION ; ALIGNMENT ; SEQUENCE ; PEPPER ; ATLAS ; PLANT
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000345488400004
Citation statistics
Cited Times:9[WOS]   [WOS Record]     [Related Records in WOS]
Document Type期刊论文
Identifierhttp://210.75.249.4/handle/363003/6580
Collection中国科学院西北高原生物研究所
Corresponding AuthorChen, SL (reprint author), Chinese Acad Sci, Northwest Inst Plateau Biol, Key Lab Adaptat & Evolut Plateau Biota, Xining 810001, Peoples R China.
Affiliation1.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
Recommended Citation
GB/T 7714
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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