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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.

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Acknowledgments

We thank Beijing Genomics Institute at Shenzhen for technical assistance with data analysis. This work was supported by grants from the Project for High-Level Returned Scholar of Ministry of Personnel of P.R. China, the National Natural Science Foundation of China (No. 31060107), and the Project of Doctoral Degree Program of Minister of Education (No. 20104601110003).

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Correspondence to Chaozu He or Xi Huang.

Additional information

Zhihui Xia, Huimin Xu and Jinling Zhai contributed equally to this work.

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Table S1. BLAST hits from NCBI Nr databases (XLS 9116 kb)

Table S2. Statistical analysis of GO classifications of H. brasiliensis unigenes. (XLS 81 kb)

Table S3. Statistical analysis of COG classifications of H. brasiliensis unigenes. (XLS 310 kb)

Table S4. Summary of annotated unigenes to the reference canonical pathways in the KEGG database. (XLS 30 kb)

Table S5. Statistical analysis of COG classifications of Hevea nucleotide sequences deposited in NCBI. (XLS 221 kb)

Supplementary material 6 (DOC 51 kb)

Table S7. BLASTX results of Hevea nucleotide sequences of NCBI against Nr databases. (XLS 3962 kb)

11103_2011_9811_MOESM8_ESM.xls

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)

Supplementary material 9 (DOC 63 kb)

Supplementary material 10 (DOC 27 kb)

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Xia, Z., Xu, H., Zhai, J. et al. RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis . Plant Mol Biol 77, 299 (2011). https://doi.org/10.1007/s11103-011-9811-z

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  • DOI: https://doi.org/10.1007/s11103-011-9811-z

Keywords

  • De novo assembly
  • Hevea brasiliensis
  • RNA-Seq
  • Transcriptome