The complete mitochondrial genome of Hemiboea subcapitata (Gesneriaceae) and comparative analysis across Lamiales

The mitochondrial genomes of plants in extreme environments often harbor distinctive evolutionary signals. However, the differences between karstic and non-karstic species remain unclear.

In this study, the complete mitochondrial genome of karstic species Hemiboea subcapitata (Gesneriaceae) was assembled and annotated.The selective pressure, nucleotide diversity and nucleotide substitution spectrum within Lamiales were conducted to investigate the adaptation pattern of mitochondrial protein-coding genes (PCGs) between karstic and non-karstic species. Further, the phylogenetic conflicts of Lamiales based on mitochondrial and chloroplast PCGs were assessed.

The assembled mitochondrial genome of H. subcapitata is a circular molecule of 621,547 bp with 43.6% GC content, and 67 genes were annotated, including 37 PCGs, 27 tRNA genes, and 3 rRNA genes. Our analyses identified 121 SSRs and 450 RNA editing sites of H. subcapitata. Within Gesneriaceae, the mitochondrial showed the diverse genome structure and gene composition, and the conserved GC content. Strikingly, three genes (atp4, atp8, and ccmB) exhibited elevated nonsynonymous/synonymous ratios (Ka/Ks) both in karstic and non-karstic Lamiales species, while only rps10 with Ka/Ks >1 in karstic species. The mutational spectrum showed that transition was the predominant type in both karstic and non-karstic Lamiales species. Furthermore, five genes (atp1, atp9, rpl2, rpl5 and sdh3) with highest Pi values were the candidate hypervariable regions of Lamiales. Phylogenetic conflicts between mitochondrial and chloroplast PCGs was mainly related to incomplete lineage sorting.

This study revealed the differences of mitochondrial genomes in karstic and non-karstic species plants across Lamiales and highlighted the impact of habitat on organellar genome evolution.