Two Species of Wild Long-Fruited Jute (Corchorus olitorius) Characterization and Phylogenetic Analysis of the Complete Chloroplast Genomes

Jute (Corchorus spp.) is the most important bast fiber crop, providing raw materials for textiles, bio-composites, and papermaking. This study analyzed the chloroplast genomes of two wild long-fruited jute species: Qiaojianyehuangma (QJYHM) and Maliyehuangma (MLYHM). The chloroplast genomes exhibited typical circular quadripartite structures (LSC, SSC, IRa/IRb), containing 129 genes (37 tRNA, 8 rRNA, 84 mRNA). Overall GC content was 36.76%, indicating high genetic conservation. Compared with cultivated varieties, wild varieties exhibit differences in LSC region length, IR boundary positions, and repetitive sequences, reflecting minor sequence variations in the chloroplast genome that occurred during domestication. Codon preference analysis showed both wild species favor A/U-ending synonymous codons, with a strong preference for methionine’s AUG codon. Repetitive sequence analysis revealed 280 and 252 dispersed repeats in Qiaojianyehuangma and Maliyehuangma, respectively, primarily mononucleotide SSRs. Based on Ka/Ks analysis, it was discovered that most chloroplast genes were under purifying selection. In contrast, positive selection signals were detected in rpl23, ycf1, and ycf2, implying their involvement in adaptive evolution. We identified 161 polymorphic sites (97 SNPs, 64 InDels), with ycf1 as a mutation hotspot. Phylogenetic analysis clustered both wild species with Corchorus capsularis with a 100% bootstrap value, forming a well-supported sister group. This study provides basic chloroplast genome data for two wild Corchorus olitorius accessions, revealing their conserved genomic features and minor sequence variations.