Chloroplast Genome Insights of Gleditsia japonica var. velutina and Evolutionary Implications for Variation and Phylogeny in Gleditsia

The genus Gleditsia possesses significant medicinal value, yet the Chinese endemic G. japonica var. velutina is threatened. Here, we integrated Nanopore long‐read and Illumina short‐read sequencing to assemble the complete chloroplast genome of G. japonica var. velutina , and perform a systematic analysis of its evolutionary characteristics. The results demonstrate that chloroplast genome size variation within the genus (162.4–170.8 kb) is primarily driven by expansions of repeat sequences in the large single‐copy (LSC) region. Genome‐wide comparisons revealed hypervariable intergenic regions and polymorphic genes as potential novel molecular markers for species delimitation within Gleditsia , particularly for the endangered G. japonica var. velutina . Comparative analysis further showed that codon usage bias is predominantly shaped by natural selection and remains highly conserved across the genus, with 30 optimal codons identified. Phylogenomic analyses support the close relationship of G. japonica var. velutina with G. japonica var. delavayi and G. japonica . This study presents the first comprehensive chloroplast genome analysis of the critically endangered G. japonica var. velutina , providing essential insights into its evolutionary divergence within the genus Gleditsia and offering a robust genomic foundation for its conservation.