Genome-wide analysis of the laccase gene family in tossa jute (Corchorus olitorius): insights into stem development, lignification, and responses to abiotic stress

Tossa jute (<i>Corchorus olitorius</i>) dominates global jute cultivation but has a high lignin content (13-14%) in its fibres, making them coarse and limiting their industrial applications. Reducing the lignin content requires a deeper understanding of the lignification process and the associated genes. Laccase (EC 1.10.3.2) is a key enzyme in the final step of lignin biosynthesis. A genome-wide analysis of the 361 Mb <i>C. olitorius</i> genome identified 46 laccase genes (<i>ColLAC</i>s) from a total of 28,479 genes. <i>In-silico</i> analysis revealed that <i>ColLAC</i> genes are distributed across seven chromosomes, encode proteins ranging from 7.98 to 173.99 kDa, with 74 to 1548 amino acids and 10 conserved motifs. Additionally, 48.83% of ColLACs are predicted to be transmembrane proteins. Phylogenetic analysis classified them into eight groups, with GO term assignments suggesting their involvement in lignification. Tissue-specific expression analysis showed that 43.47% of <i>ColLAC</i> genes are predominantly expressed in roots, aligning with RNA-seq data. <i>ColLAC</i> gene expression varied across the developmental stages, from seedling to fibre harvest, and was influenced by heavy metal copper and abscisic acid (ABA) treatments. This variation correlated with upstream cis-acting elements. <i>Ath-miR397</i> target sites were identified in 14 <i>ColLAC</i> genes, indicating potential post-transcriptional regulation. Further expression analysis in X-ray-induced <i>bfs</i> (bast fibre-shy) mutant tossa jute lines suggested that <i>ColLAC34</i> is involved in both lignification and structural development, while <i>ColLAC22, ColLAC40</i>, and <i>ColLAC46</i> play key roles in lignification. This study presents the first comprehensive genome-wide identification and characterization of the <i>LAC</i> gene family in jute. Understanding <i>ColLAC</i> functions could facilitate the development of low-lignin jute fibres, meeting the growing industrial demand for high-quality natural fibres of jute.