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Transcriptome sequencing and characterization for Kappaphycus alvarezii
Zhang, Zhen1; Pang, Tong1; Li, Qianqian1,2; Zhang, Litao1; Li, Ling1; Liu, Jianguo1
2015
Source PublicationEUROPEAN JOURNAL OF PHYCOLOGY
Volume50Issue:4Pages:400-407
SubtypeArticle
AbstractThe transcriptome of Kappaphycus alvarezii was profiled using high-throughput Solexa paired-end sequencing technology. A total of 61 million sequencing reads was generated by filtering the low-quality reads, and 28 701 unigenes with a mean length of 901 bp were obtained based on de novo assembly. In similarity alignments against the NCBI non-redundant protein sequence (NR) database, Swissprot database, Cluster of Orthologous Groups (COG) database, Gene ontology (GO) database, and Kyoto Encyclopedia of Genes and Genomes (KEGG) database, 11 996 (41.79%) unigenes were identified with significant hits (E-value < 10(-5)) against existing genes. Functional annotation with the KEGG pathway database identified 8975 unigenes and mapped to 125 pathways. Through functional enrichment analysis of the genes with a higher expression value than the average RPKM (reads per kilobase per million reads), we found that some important pathways were highly expressed. The substantial number of transcript sequences of K. alvarezii provides a valuable resource for potential gene identification and comparative genomic studies.
KeywordFunctional Annotation Kappaphycus Alvarezii Kegg Pathway Rhodophyta Rpkm Transcriptome
DOI10.1080/09670262.2015.1069403
Indexed BySCI
Language英语
WOS IDWOS:000363951900004
Citation statistics
Document Type期刊论文
Identifierhttp://ir.qdio.ac.cn/handle/337002/82280
Collection海洋生物技术研发中心
Affiliation1.Chinese Acad Sci, Inst Oceanol, R&D Ctr Marine Biotechnol, Natl & Local Joint Engn Lab Ecol Mariculture, Qingdao 266071, Peoples R China
2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China
Recommended Citation
GB/T 7714
Zhang, Zhen,Pang, Tong,Li, Qianqian,et al. Transcriptome sequencing and characterization for Kappaphycus alvarezii[J]. EUROPEAN JOURNAL OF PHYCOLOGY,2015,50(4):400-407.
APA Zhang, Zhen,Pang, Tong,Li, Qianqian,Zhang, Litao,Li, Ling,&Liu, Jianguo.(2015).Transcriptome sequencing and characterization for Kappaphycus alvarezii.EUROPEAN JOURNAL OF PHYCOLOGY,50(4),400-407.
MLA Zhang, Zhen,et al."Transcriptome sequencing and characterization for Kappaphycus alvarezii".EUROPEAN JOURNAL OF PHYCOLOGY 50.4(2015):400-407.
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