De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways

• Published in: PloS one 2014-07, Vol.9 (7), p.e102665-e102665
• Main Authors: Mantello, Camila Campos, Cardoso-Silva, Claudio Benicio, da Silva, Carla Cristina, de Souza, Livia Moura, Scaloppi Junior, Erivaldo José, de Souza Gonçalves, Paulo, Vicentini, Renato, de Souza, Anete Pereira
• Format: Article
• Language: English
• Subjects: Analysis; Artificial rubber; Bark; Biology and Life Sciences; Biosynthesis; Biosynthetic Pathways; Chromosomes; Cluster Analysis; Encyclopedias; Erythritol; Euphorbiaceae; Gene expression; Gene Expression Profiling; Gene mapping; Gene Ontology; Gene sequencing; Genes; Genes, Plant; Genetic analysis; Genomes; Genomics; Genotypes; Hevea; Hevea - genetics; Hevea - metabolism; Hevea brasiliensis; Linkage disequilibrium; Marker-assisted selection; Markers; Mevalonic acid; Microsatellites; Natural rubber; Parthenium argentatum; Pathways; Plant Bark - genetics; Plant Bark - metabolism; Plant Proteins - genetics; Plant Proteins - metabolism; Polymorphism, Single Nucleotide; Quantitative genetics; Quantitative trait loci; Rainforests; Ribonucleic acid; RNA; Rubber; Rubber - metabolism; Rubber trees; Simple sequence repeats; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Synthetic rubber
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0102665

Hevea brasiliensis (Willd. Ex Adr. Juss.) Muell.-Arg. is the primary source of natural rubber that is native to the Amazon rainforest. The singular properties of natural rubber make it superior to and competitive with synthetic rubber for use in several applications. Here, we performed RNA sequencing (RNA-seq) of H. brasiliensis bark on the Illumina GAIIx platform, which generated 179,326,804 raw reads on the Illumina GAIIx platform. A total of 50,384 contigs that were over 400 bp in size were obtained and subjected to further analyses. A similarity search against the non-redundant (nr) protein database returned 32,018 (63%) positive BLASTx hits. The transcriptome analysis was annotated using the clusters of orthologous groups (COG), gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Pfam databases. A search for putative molecular marker was performed to identify simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs). In total, 17,927 SSRs and 404,114 SNPs were detected. Finally, we selected sequences that were identified as belonging to the mevalonate (MVA) and 2-C-methyl-D-erythritol 4-phosphate (MEP) pathways, which are involved in rubber biosynthesis, to validate the SNP markers. A total of 78 SNPs were validated in 36 genotypes of H. brasiliensis. This new dataset represents a powerful information source for rubber tree bark genes and will be an important tool for the development of microsatellites and SNP markers for use in future genetic analyses such as genetic linkage mapping, quantitative trait loci identification, investigations of linkage disequilibrium and marker-assisted selection.