Assembly and comparative analysis of the complete mitochondrial genome of Holmskioldia sanguinea

Holmskioldia sanguinea, a distinctive ornamental plant native to the subtropical Himalayas, is valued for its unique hat-shaped calyces, strong adaptability, and ecological significance in slope restoration and nectar provision. Its phylogenetic position within Lamiales has remained controversial due to limited molecular evidence. Although earlier studies have successfully elucidated its chloroplast (cp) genome, the complete mitochondrial (mt) genome remains uncovered.

This study undertook the sequencing, assembly, and comprehensive analysis of the complete mt genome of H. sanguinea.

The mt genome of H. sanguinea is a circular DNA molecule measuring 405,461 bp in length with a GC content of 46.00%. It contains 36 protein-coding genes (PCGs), three ribosomal RNAs (rrn5, rrn18, rrn26) and 33 transfer RNAs. The mt genome is rich in repetitive sequences; a total of 550 interspersed repeats were identified, including 300 palindromic repeats (54.55%) and 250 forward repeats (45.45%), without inverted or complementary repeats. Additionally, 79 simple sequence repeats (SSRs) were detected, with tetranucleotide repeats (AAAG/CTTT) being the most abundant. Codon usage analysis revealed a preference for A/U-ending codons, and the codon GCU (Ala) exhibited the highest relative synonymous codon usage (RSCU) value of 1.57. A total of 565 RNA editing sites (all C-to-U conversions) were predicted, with the majority (80.71%) potentially leading to increased protein hydrophobicity. Six cp plastid DNAs were identified in the mt genome, indicating intracellular gene transfer events. Most mt genes are under strong purifying selection (Ka/Ks < 1), while nucleotide diversity analysis showed that atp9 had the highest diversity (Pi = 0.06444) and nad4L the lowest (Pi = 0.00305). Phylogenetic analysis based on 14 shared mt PCGs placed H. sanguinea within Lamiaceae, forming a well-supported clade with Lavandula angustifolia, Salvia officinalis, Elsholtzia blanda, Callicarpa nudiflora and Vitex trifolia (bootstrap = 100%). Collinearity analysis revealed extensive genome rearrangements among related species, and gene content analysis indicated the loss of rps7, rpl2 and sdh3 as well as duplications of atp1, cox1 and nad4.

Understanding the mt genome characteristics of H. sanguinea is critical for elucidating its phylogenetic placement and genetic background. The results of this study serve as a foundation for future genetic, evolutionary, and breeding studies of this ornamental and potentially medicinal species.