Therefore, it is necessary to carried out high-throughput transcriptome sequencing of rubber tree bark to generate enormous transcript sequences for the functional characterization and molecular marker development.
(XLS 37 kb) Additional file 5: Alignment of predicted amino acid sequences of rubber tree aquaporins with structure determined Spinach SoPIP2 1.
An analysis of the structure of JAZs genes based on the genomic sequences of rubber clone CATAS 7-33-97 (BIG-CATAS Project, unpublished data), and an analysis of the corresponding transcripts revealed the existence of a mechanism of alternative splicing of JAZ gene transcripts.
We assembled the mitochondrial sequence of the rubber tree variety BPM 24 from 454 sequence data into 37 contigs ranging from 101 bp to 147 kb in length with an N50 size of 51 kb (DDBJ: AP014526).
Read alignments against RNA sequencing data of rubber tree shoot apex, leaf, laticifer, bark, root and somatic embryogenesis [ 30– 35] indicated that the expression of 44 HbAQP genes was observed in at least one of the examined tissues (Table 1).
We used TBLASTN against assembled DNA sequences of the rubber genome to manually identify proteins missed by automatic annotation by orthologs identified with best reciprocal hit method from BLASTP results.
To dissect the molecular mechanism for the regulation of latex regeneration and duration of latex flow, we sequenced and comparatively analyzed latex of rubber tree clone CATAS8-79 and PR107 at transriptome level.
This research generated a substantial fraction of rubber tree transcriptome sequences, which were very useful resources for gene annotation and discovery, molecular markers development, genome assembly and annotation, and microarrays development in rubber tree.
In total, BLAST searches identified 13,115 unique protein accessions from the nr and Swissprot protein databases, suggesting that this Illumina paried-end sequencing project generated a substantial fraction of rubber tree genes in this study.
By assembling and analyzing de novo transcriptome sequencing data, we reported the comprehensive functional characterization of rubber tree bark.
