De novo assembly of kenaf (Hibiscus cannabinus) transcriptome using Illumina sequencing for gene discovery and marker identification

Kenaf (Hibiscus cannabinus) is one of important nature fiber crops in the world. However, the EST sequence resources available for kenaf are still very limited. In this study, 131,262,686 clean reads (13.12 Gb) using Illumina paired-end sequencing were assembled. De novo assembly yielded 90,175 unigenes with an average length of 700 bp. By sequence similarity searching for known proteins, 46,165 (51.19 %) unigenes were annotated for their function. Out of these annotated unigenes, 37,080 (41.12 %) unigenes showed significant similarity to genes of a diploid cotton (Gossypium raimondii). Searching against the Kyoto encyclopedia of genes and genomes (KEGG) indicated that 23,051 unigenes were mapped to 254 KEGG pathways, and 317 genes were assigned to starch and sucrose metabolic pathway which was related with cellulose biosynthesis. Furthermore, a total of 52,521 putative gene associated SNPs and 11,083 SSRs (designated as HcEMS) were identified from these assembled unigenes. Among these HcEMS markers, mono-, di-, and trinucleotide repeat types were the most abundant types (40.3, 22.3, and 34.7 %, respectively). The AG-rich nucleotide repeats, including (AG) n, (AAG) n, and (AAAG) n types, were the most abundant and could be considered as the dominant types in kenaf. A sample of 835 HcEMSs were used to survey polymorphisms with eight kenaf accessions. Of them, 753 (90.1 %) successfully amplified at least one fragment and 450 (53.9 %) detected polymorphism. All these results will accelerate the understanding of genetic basis of the fiber development and marker-assisted breeding in kenaf.