Reference genomes of the two cultivated jute species

Abstract

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.

Multi‐omics provides new insights into the domestication and improvement of dark jute (Corchorus olitorius)

“…15) via a combination of techniques that produced paired‐end (PE) sequences (43.24 Gb), Nanopore long reads (111.02 Gb), 10X Genomics (10XG) sequencing data (94.72 Gb) and chromatin conformation capture (Hi‐C) data (48.24 Gb; Tables S1 and S2). A total of 411.26 Mb of the TC assembly was anchored onto seven pseudochromosomes, with a contig N50 size of 4.13 Mb, which was an improvement of 2.75‐fold compared with the best value of contig N50 in the three published genomes of C. olitorius (Figure 1a; Table 1; Islam et al., 2017; Sarkar et al., 2017; Zhang et al., 2021). Multiple evaluation indicators demonstrated the superior completeness and accuracy of our TC genome (Table S3).…”

“…Despite the great agronomic importance of this species, research on jute at the molecular level is scarce, and little progress has been made in its genetic improvement (Kundu et al., 2015; Tao et al., 2017). The two published C. olitorius genomes have 51.05 Mb of differences in their genome sizes (Islam et al., 2017; Zhang et al., 2021), and there is still much room for improvement in the completeness of their assembly. It is thus necessary to construct a higher‐quality dark jute reference genome to characterize these genomic variant resources.…”

“…It is thus necessary to construct a higher‐quality dark jute reference genome to characterize these genomic variant resources. There have been a few studies on whole genomic variation and expression in C. olitorius (Kundu et al., 2015; Sarkar et al., 2019; Zhang et al., 2021). However, the number of molecular markers of these studies was not adequate to cover the whole genome of jute, the accession type was single, the number of samples was small, or the studies were independent and did not involve the integration of multiple methods.…”

Caffeoyl-CoA 3-O-methyltransferase gene family in jute: Genome-wide identification, evolutionary progression and transcript profiling under different quandaries

“…According to Zhang et al. (2021) the sequences and all the required files of identified CCoAOMT genes in two species of jute ( C. capsularis var.…”

Intelligent Identification of Jute Pests Based on Transfer Learning and Deep Convolutional Neural Networks

“…More than 33% of the overall worldwide jute is produced in Bangladesh [ 1 ]. Likewise, in China, jute is considered one of its valuable plants, which makes a significant account of jute after Bangladesh and occupies the third rank in the world [ 2 ]. An extensive study on jute is sorely needed since people are nowadays more concerned about the environment.…”