Summary Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo‐chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole‐genome resequencing resulted in post‐domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker‐trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome‐wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops.

Background: The jute plant is of great significance and economic relevance to humanity, but its production has been hindered due to abiotic influences, especially salt stress. Hitherto, the molecular bases for this vital feature await future exploration. The abscisic acid (ABA) signaling pathway comprises many regulated genes and plays a role in plant response to stress, however, a balance between the multiple pathways is always needed for any plant developmental process. In this study, we used a transcriptomic approach to unveil the molecular bases behind this trait. Salt tolerant (J194) and sensitive (J7) germplasms were subjected to sodium chloride (NaCl) stress at a different time point, from which leaf and roots samples were taken for transcriptome analyses. Result: The plant hormone signal transduction pathway was the most abundant observed in the study; the Pyrrolysine (PYL) gene (Cc.03G0016680) was up-regulated, which supports the basic model of abscisic acid (ABA). The quantitative reverse transcription-PCR (qRT –PCR) and the correlation analysis validated the Ribonucleic acid sequence (RNA-seq) results. The candidate genes’ relative expression level was higher in J194, especially in protein phosphate 2C (PP2C). Corchorus capsularis PP2C gene family revealed 38 members, phylogenetic analysis categorized PP2C into 15 based upon conserved domains. Eleven conserved motifs were identified, and most of the genes had the same number of conserved motifs. The exon-intron ranges of (3-21) and (2-20), respectively. Moreover, among the plant hormone signal transduction pathway PP2C genes, Cc.03G0016550 and Cc.07G0028160 were up-regulated in J194 root tissues at 6-hour exposure NaCl, as such recommended to be salt-tolerant candidature genes. It was noted that most of the Corchorus capsularis PP2C genes were involved from segmental duplication, and analysis of the key stress marker salt-tolerant PP2C genes validated the salt tolerance individuals. Conclusion: These results provided valuable insight into salt tolerance transcriptome and indicated that PP2C had provided a stepping-stone to the molecular mechanism in Corchorus capsularis. Furthermore, differentially expressed genes, motifs, gene structure, and the chromosomal location of salt tolerance candidate genes might have experienced functional divergence. As such, their further study will enhance salt tolerance in Corchorus capsularis.

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