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RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis

文献类型： 外文期刊

作者： Xia, Zhihui 1 ; Xu, Huimin 1 ; Zhai, Jinling 1 ; Li, Dejun 2 ; Luo, Hongli 1 ; He, Chaozu 1 ; Huang, Xi 1 ;

作者机构： 1.Hainan Univ, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Inst BioSci & Technol, Coll Agr, Haikou 570228, Peoples R China

2.Chinese Acad Trop Agr Sci, Key Lab Rubber Biol, Minist Agr, Rubber Res Inst, Danzhou 571737, Hainan, Peoples R China

关键词： De novo assembly;Hevea brasiliensis;RNA-Seq;Transcriptome

期刊名称：PLANT MOLECULAR BIOLOGY （ 影响因子：4.076； 五年影响因子：4.89 ）

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收录情况： SCI

摘要： Hevea brasiliensis, being the only source of commercial natural rubber, is an extremely economically important crop. In an effort to facilitate biological, biochemical and molecular research in rubber biosynthesis, here we report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain a comprehensive overview of the H. brasiliensis transcriptome. The sequencing output generated more than 12 million reads with an average length of 90 nt. In total 48,768 unigenes (mean size = 436 bp, median size = 328 bp) were assembled through de novo transcriptome assembly. Out of 13,807 H. brasiliensis cDNA sequences deposited in Genbank of the National Center for Biotechnology Information (NCBI) (as of Feb 2011), 11,746 sequences (84. 5%) could be matched with the assembled unigenes through nucleotide BLAST. The assembled sequences were annotated with gene descriptions, Gene Ontology (GO) and Clusters of Orthologous Group (COG) terms. In all, 37,432 unigenes were successfully annotated, of which 24,545 (65. 5%) aligned to Ricinus communis proteins. Furthermore, the annotated uingenes were functionally classified according to the GO, COG and Kyoto Encyclopedia of Genes and Genomes databases. Our data provides the most comprehensive sequence resource available for the study of rubber trees as well as demonstrates effective use of Illumina sequencing and de novo transcriptome assembly in a species lacking genomic information.

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