Plant Molecular Biology

, 77:299

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

Article

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.

Keywords

De novo assembly Hevea brasiliensis RNA-Seq Transcriptome 

Supplementary material

11103_2011_9811_MOESM1_ESM.xls (8.9 mb)
Table S1. BLAST hits from NCBI Nr databases (XLS 9116 kb)
11103_2011_9811_MOESM2_ESM.xls (82 kb)
Table S2. Statistical analysis of GO classifications of H. brasiliensis unigenes. (XLS 81 kb)
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Table S3. Statistical analysis of COG classifications of H. brasiliensis unigenes. (XLS 310 kb)
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Table S4. Summary of annotated unigenes to the reference canonical pathways in the KEGG database. (XLS 30 kb)
11103_2011_9811_MOESM5_ESM.xls (222 kb)
Table S5. Statistical analysis of COG classifications of Hevea nucleotide sequences deposited in NCBI. (XLS 221 kb)
11103_2011_9811_MOESM6_ESM.doc (51 kb)
Supplementary material 6 (DOC 51 kb)
11103_2011_9811_MOESM7_ESM.xls (3.9 mb)
Table S7. BLASTX results of Hevea nucleotide sequences of NCBI against Nr databases. (XLS 3962 kb)
11103_2011_9811_MOESM8_ESM.xls (7 mb)
Table S8. BLASTX results of unigenes with a priority of matching with Nr proteins with known functions. Screening was performed for annotations containing the terms “hypothetical”, “predicted”, “putative” or “unknown”, which were shown only when a unigene could not be annotated to a known function. (XLS 7123 kb)
11103_2011_9811_MOESM9_ESM.doc (63 kb)
Supplementary material 9 (DOC 63 kb)
11103_2011_9811_MOESM10_ESM.doc (27 kb)
Supplementary material 10 (DOC 27 kb)

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Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  1. 1.Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresources/Institute of BioScience and Technology, College of AgricultureHainan UniversityHaikouPeople’s Republic of China
  2. 2.Key Laboratory of Rubber Biology, Ministry of Agriculture, Rubber Research InstituteChinese Academy of Tropical Agricultural SciencesDanzhouPeople’s Republic of China

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