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

Abstract

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.

An RNA-Seq Transcriptome Analysis of Orthophosphate-Deficient White Lupin Reveals Novel Insights into Phosphorus Acclimation in Plants

“…For many species, nextgeneration sequencing technology has allowed the development of a transcriptome sequence prior to the sequencing of the genome, as in alfalfa (Medicago sativa; Yang et al, 2011), lentil (Lens culinaris; Kaur et al, 2011), pea (Pisum sativum; Franssen et al, 2011), pigeon pea (Cajanus cajan; Dubey et al, 2011), sweet potato (Ipomoea batatas; Wang et al, 2010b), eucalyptus (Eucalyptus spp. ; Mizrachi et al, 2010), carrot (Daucus carota; Iorizzo et al, 2011), watermelon (Citrullis vulgaris; Guo et al, 2011), rubber tree (Hevea brasiliensis; Xia et al, 2011), pitcher plant (Sarracenia spp. ; Srivastava et al, 2011), and cucurbits (Cucurbitaceae spp.…”

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…This can be investigated with either in silico or in vitro approaches. One in silico approach is to match the contigs to known cDNA or EST sequences to confirm the accuracy of the de novo assembly [8,46]. However, due to the scarcity of cDNA or EST sequences for menhaden, another alignment technique was performed for the validation.…”

Transcriptome Analyses to Reveal Genes Involved in Terpene Biosynthesis in Resin Producing Pine Tree Pinus kesiya var. langbianensis

“…The COG database was an attempt to classify proteins from completely sequenced genomes on the basis of the orthology concept (Tatusov et al 2000). The aim of GO analysis was to standardize the representation of genes and their derivatives by insisting on a controlled vocabulary and a strictly defined concept (Wand et al 2010;Xia et al 2011). The annotations acquired from NR and Swiss-Prot were processed through the Blast2 GO program (v2.5.0) (Conesa et al 2005) to obtain the relevant GO terms, and these were then analyzed using the WEGO software (v2.0) (Ye et al 2006) to assign a GO functional classification and to illustrate the distribution of gene functions.…”