Comprehensive transcriptome analysis and tissue-specific profiling of gene expression in jute (Corchorus olitorius L.)

Abstract

Transcriptome sequencing is a convenient and rapid technology for assessing gene expression and associated pathways in various tissues and stages of differentiation at the whole-genome level. Jute (Corchorus spp.) is a very important multi-purpose commercial crop. No study has addressed the transcriptional profiles of various tissues during the different growth stages of the jute species Corchorus olitorius L. In this study, the first comprehensive transcriptome analysis was performed for the leaves, flowers, stem bast, and fruit of Corchorus olitorius during different growth stages to identify differentially expressed genes (DEGs) and metabolic pathways among the tissues. More than 77 % of the known genes 28,540 in the reference genome and 4772 novel genes were detected in the tissues. We discovered consistently upregulated and downregulated genes in the stem bast, fruit, flower, and leaf at frequencies of 576/379, 291/227, 2367/255, and 1766/736, respectively, compared with all other tissues. The metabolic pathway ‘biosynthesis of secondary metabolites’ was significantly enriched in the stem bast and 26 genes in this pathway were consistently upregulated, including four enzyme-encoding genes involved in glucan metabolism, compared stem bast with other tissues at all stages. The ‘phenylpropanoid biosynthesis pathway’ was significantly enriched in flower compared with the other tissues. In total, 53 genes were discovered involved in flavonoid biosynthesis that were enriched, most of them upregulated compared with the other tissues. The results obtained in this study serve as a resource for unraveling the functions of many specific genes involved in the development and growth of various tissues in jute and other bast fiber crops.