What question did this study set out to answer?

The research aims to analyze the chloroplast genome of Crotalaria juncea for insights into its evolutionary biology and phylogenetic relationships within the Fabaceae family.

April 11, 2026Open Access

Complete chloroplast genome of Crotalaria juncea, a bast fibre crop with late-acting self-incompatibility, reveals evolutionary insights and phylogenetic relationships within Fabaceae

DSDipnarayan SahaCentral Research Institute for Jute and Allied Fibres SDSubhojit DattaCentral Research Institute for Jute and Allied Fibres

Key Points

The research aims to analyze the chloroplast genome of Crotalaria juncea for insights into its evolutionary biology and phylogenetic relationships within the Fabaceae family.
Whole-genome skimming data was used to identify the chloroplast genome of C. juncea.
The genome analysis included gene count and GC content evaluation.
Comparative analysis against other Crotalaria species was conducted for collinearity and synteny comparison.
Phylogenetic analysis of shared chloroplast genes was performed to assess clade resolution.
The chloroplast genome was found to be 152,635 base pairs long with 36.62% GC content.
A total of 127 genes were identified, including protein-coding, tRNA, and rRNA genes.
Higher Ka/Ks values suggest positive selection on most protein-coding genes.
Identification of highly diverse genes indicates their potential for species-level identification.

Abstract

Crotalaria juncea, a member of Fabaceae family, offers significant agricultural, commercial, and environmental benefits. The bast fibres from C. juncea stems are utilised across diverse industries for the production of ropes, threads, twines, fishing nets, and paper. This fast-growing legume enhances soil fertility through nitrogen fixation when applied as green manure. It exhibits a late-acting self-incompatibility trait, promoting outcrossing and resulting in a heterogeneous plant population. The maternally inherited chloroplast sequence is ideal for species identification, understanding the evolution of self-incompatible species, and analysing population dynamics. The chloroplast genome of C. juncea was identified using whole-genome skimming data. The chloroplast genome was 152,635 base pairs in length and contained 36.62% GC content. It comprises 127 genes, including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Comparative analysis revealed significant collinearity and synteny between the chloroplast genomes of C. juncea and other Crotalaria spp. Despite conserved codon usage and repetitive sequences distributions across Crotalaria spp., most protein-coding genes exhibited higher Ka/Ks values, suggesting positive evolutionary selection with adaptive significance. Phylogenetic analysis of shared chloroplast genes, compared to the whole chloroplast genome, yielded superior clade resolution within the Fabaceae family. The analysis also identified highly diverse genes—clpP, matK, ndhF, and rpoC2—based on nucleotide diversity estimation, underscoring their potential utility for species identification within the Crotalaria genus and broader Fabaceae family members. This study presents a comprehensive analysis of the C. juncea chloroplast genome. The variable sequence and gene features offer substantial potential for applications in species- and population-level identification, phylogenetic studies, and the exploration of adaptive evolution in C. juncea and other Fabaceae species.

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