The evolutionary landscape of mitogenomes: Insights from Elsholtzia blanda and comparative analysis of ten related species

Abstract

We investigated the mitogenomes of 11 Lamiaceae species, including the newly sequenced Elsholtzia blanda mitogenome (304,466 bp), which identified 58 genes. The analysis revealed a negative correlation between genome size and GC content, as well as between gene length and GC content. A positive correlation was also observed between GC content, gene length, and the total number of amino acids. Gene lengths varied across species, with genes like cox2, nad6, ccmC, matR, nad1, and nad2 showing high standard deviations, suggesting selective pressures. Conversely, genes like atp1, atp4, atp6, atp8, and ccmB displayed conserved lengths, potentially indicating crucial roles in mitochondrial function. SSR analysis revealed moderate repeats in nad1 and nad2, suggesting hotspots for genomic variability. Nucleotide diversity and Ka/Ks ratios indicated high variability and adaptive evolution, with genes like atp9 and atp6 exhibiting higher Pi values, while nad1 and nad5 are under purifying selection. Codon usage analysis revealed non-random patterns, with optimal codons showing mean RSCU values between 1.146 and 1.726 and ΔRSCU values ranging from 0.146 to 0.726. The RSCU heatmap and dendrogram corroborated phylogenetic data, situating E. blanda within the Lamiaceae family and indicating close relationships with Pogostemon heyneanus and Salvia splendens. E. blanda possesses 6310 RNA editing sites, with 445 exhibiting scores >0.90, predominantly C-to-U conversions in genes like nad4 and ccmC, reflecting adaptive mechanisms. These findings provide insights into mitochondrial evolution and phylogeny, supporting functional genomics research and conservation strategies for E. blanda and other Lamiaceae species.