GSE136290
Discovery of Novel Genes and Pathways through Comparative Transcriptomics Approach to Elucidate Genes Expressed in Durian (Durio zibethinus Murr) D24 Varieties Fruit Pulp Development and Ripening.
In this study, RNA Seq analysis was performed for the comprehensive understanding of the transcriptome of the durian, Durio zibethinus Murr. using Illumina HiSeq Platform. In comparison with the durian reference genome, the studies identified 3,438 novel exons and 1,197 novel loci. The total number of novel transcripts were 280. Ninety-seven novel transcripts did not show any similarity with any sequences available in the Genebank's nucleotide database. Comparison of the top five ranked gene abundances between three differential groups YS/MS, YS/RS and MS/RS showed a difference in their genes and the function. Several key genes involved in sugar metabolism, sulfur production, and ripening process were further studied and visualised using IGV to view changes in their expression profile. 1,4-alpha-glucan-branching enzyme 2-1, chloroplastic/amyloplastic-like, hexokinase-3-like, UDP-sugar pyrophosphorylase-like were detected among the genes responsible for sugar and starch metabolism in durian fruit. The highest expression of genes involved in sugar and starch metabolism pathway was in the mature stage. There is almost similar level of gene expression involved in sugar metabolism in young and ripening stage. Methionine gamma-lyase-like (MGL) and PAP-specific phosphatase HAL2-like genes responsible for sulphur production and the metabolism in durian showed a rapid change in expression (about two times) from the young stage to mature and ripening stage. Interestingly, 1-aminocyclopropane-1-carboxylate oxidase (ACO) genes responsible for ethylene biosynthesis for fruit ripening were showed a significant increase in young stage compared to other stages. Glucose and ribitol dehydrogenase-like were among the top gene abundance identified in the ripening stage, and responsible in carbohydrate metabolism and acquisition of desiccation tolerance. Endochitinase 1-like was the gene in all three stages and responsible in carbohydrate binding site. The categorization of differently expressed transcripts among the three groups to Gene Ontology (GO) and KEGG pathway indicates the highest number of assigned genes to cellular process, metabolic process, cellular metabolic process, cellular nitrogen compound metabolic process; (biological_process), binding, catalytic activity, ion binding (molecular_function) and intracellular, cell part, cell (cellular_component). KEGG pathway mapping was finally carried out to classify the genes into different metabolic pathway. The percentage of the mapped reads to the KEGG pathway was 96.50% (YS/MS), 60.20% (YS/RS) and 35.30% (MS/RS). KEGG pathway distributions of highly expressed genes were mapped to the pathway in a group of nucleotide metabolism, carbohydrate metabolism, lipid metabolism, amino acid metabolism, metabolism of other amino acids, metabolism of cofactors and vitamins, biosynthesis of other secondary metabolites, glycan biosynthesis and metabolism, metabolism of terpenoids and polyketides, and energy metabolism. Comparison of the output of the top 10 highly significant genes between four statistical methods; CLC, CuffDiff, DESeq2, and EdgeR showed the similarity and dissimilarity between the pipelines. The highest similarity of the significant genes was observed when compared using DESeq2 and EdgeR methods.  As a whole, the studies conducted successfully revealed several genetic attributes of durian (D24) cultivar. The information also serves as a preliminary genomics expression data which could serve as the foundation in creating a new durian variety that is drought-resistance, and has longer shelf-like and has low-sugar fruits suitable for diabetics and glucose intolerant patients. Overall design: Total of 9 samples; 3 biological replicates collected from three different stages of growth; young, mature and ripening,