Identification of Novel Transcripts and Exons by RNA-Seq of Transcriptome in Durio zibethinus Murr.

Durio zibethinus is a popular seasonal fruit among the Asian population and is frequently associated with economic losses due to a rapid post-harvest process. To identify novel transcripts and characterize D. zibethinus transcriptome, we employed high throughput RNA-Seq analysis. In this study, we characterized the growth and development of D. zibethinus at different growth stages, including the young, mature, and ripening stages of growth. After mapping, 110 million high-quality reads were analysed for each of the nine samples, revealing that each contains in range of 76,700 to 89,117 transcripts and 561,211 to 646,291 exons. With Cuffcompare to obtain the unannotated transcript, the novel exons, introns and loci were identified in the developmental stage with value of 3,438/313,476 (1.1%), 1,657/245,129 (0.7%) and 1,197/44,509 (2.7%), respectively. The differential expression genes (DEGs) in up-regulation were compared under the three growth stages: 1,496 (YS/MS), 2,154 (YS/RS), and 2,153 (MS/RS). These genes were then subjected to clustering analysis. A comprehensive study from the heatmap indicates that response to stress, hormone signalling, cuticle formation, general transporter, receptor and protein kinase and transcription factors are highly regulated gene functions for all growth stages. In the present analysis, we emphasized identifying and classifying unknown important transcripts, disregarding transcripts with accurate annotations. Differential expression analysis identified 280 unknown significant transcripts, presumably involved in various biological functions in durian growth. Top blastn results for 183 unknown transcripts revealed homology (80%-100%) to Bombax ceiba, Gossypium hirsutum, Gossypium raimondii, Herrania umbratica, Juglans regia, and Theobroma cacao. Under the category of unknown transcripts without a Blastn match, two unknown transcripts match GO terms. TCONS 00034019 and TCONS 00058246 match the InterPro GO Names for Biological Process (P) P:GO:0046622; P: positive regulation of organ growth. In the category of sequences with no BLASTx hit and no IPS match, three ORF sequences longer than 300 nt were identified. Our results significantly improved D. zibethinus transcript annotation and provide valuable resources for functional genomics and studies in durian.