Inverted repeats dynamics shape Asclepiadoideae (Apocynaceae) Chloroplast genomes: effects on genome size, gene content, structural arrangement, and mutation rate.

Unlabelled: Comparative analyses of chloroplast (cp.) genomes in Asclepiadoideae (Apocynaceae) have previously revealed genome size and gene content variation, primarily linked to inverted repeats (IRs) expansion or contraction and pseudogene formations. In the current study, the cp. genome of was sequenced, assembled, and compared with those of 25 other Asclepiadoideae species. The 160,494 base pairs (bp) long genome of exhibited a typical quadripartite structure, comprising a large single-copy (LSC) region of 91,508 bp and a small single-copy (SSC) region of 19,384 bp, separated by two IRs of 24,801 bp each. Across species, genome sizes varied substantially (157,158–178,400 bp), mainly due to IR dynamics. The LSC, SSC, and IR regions ranged from 85,024 to 94,367 bp, 2,294–20,026 bp, and 24,057–42,233 bp, respectively. Each cp. genome comprised 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes. Total annotated genes ranged from 129 to 142, including 84–96 protein-coding, 8 rRNA genes, and 37–38 tRNA genes. IR contraction and expansion produced six distinct genome types, accompanied by gene rearrangements resembling inversion events. The IRs expansion reduced the rate of mutations in the part of the genome and genes that transfer from single-copy regions to IRs. Phylogenetic analysis placed Marsdenieae and Ceropegieae as sister clades, followed by Asclepiadeae and Fockeeae. A strong correlation was observed between IR contraction/expansion and phylogenetic placement, with one exception. These findings suggest that IR variations provide valuable phylogenetic signals within the subfamily Asclepiadoideae.

Supplementary Information: The online version contains supplementary material available at 10.1186/s12864-025-11839-9.