Characterization and comparative analysis of the complete mitochondrial genome of Phlomoides rotata, a traditional Tibetan medicinal plant

Abstract

Background: Phlomoides rotata, an endemic Tibetan medicinal plant adapted to extreme alpine environments, faces conservation challenges due to habitat degradation and overharvesting. Despite its ecological and medicinal importance, its mitochondrial genome remains uncharacterized, limiting insights into its evolutionary adaptations and genomic architecture.

Results: We present the initial de novo assembly and annotation of the P. rotata mitochondrial genome, a circular molecule with a GC content of 45.06% and a length of 377,312 bp. A total of 32 protein-coding genes (PCGs), three ribosomal RNA (rRNA) genes, and 12 transfer RNA (tRNA) genes were identified through genome annotation. These genes include multicopy genes (trnM-CAU, matR). Analysis of codon usage bias indicated a preference for A/U ending synonymous codons, aligning with trends observed in other angiosperms. RNA editing research revealed 445 C-to-U transitions, predominantly at the second codon position, with nonsynonymous alterations (71%) surpassing synonymous changes, indicating potential functional adaptive roles. Repetitive sequence analysis uncovered 81 simple sequence repeats (SSRs) and a large palindromic repeat (13,075 bp), linked to genomic rearrangements. Homologous alignments identified 12 chloroplast-derived fragments in the mitogenome, including intact tRNA and rpl23 genes, evidencing interorganellar gene transfer. Phylogenetic analysis using 27 conserved PCGs positioned P. rotata within a well-supported Lamiales clade, closely related to Leonurus japonicus, corroborating its taxonomic placement and providing a framework for evolutionary studies.

Conclusions: The P. rotata mitogenome exhibits structural complexity and adaptive features, including codon bias, RNA editing, and repetitive sequences, underscoring its role in high-altitude adaptation. These findings provide critical genomic resources for conservation, breeding, and understanding the molecular mechanisms of organellar evolution in extreme environments.

Keywords: Phlomoides rotata; Adaptation evolution; Mitochondrial genome; Phylogenetics; Qinghai-Tibet plateau.

Fig. 1

Structural characteristics of the mitochondrial and chloroplast genomes of P. rotata. A/B Draft mitogenome sequence and structural organization of P. rotata. C Mitogenomic schematic of P. rotata. D chloroplast genomic schematic of P. rotata. Genes from distinct functional categories are color-coded for visual differentiation

Fig. 2

Characterization of Simple Sequence Repeats (SSRs) and Repeat Elements in Mitochondrial Genomes of P. rotata. A Types and frequencies of SSRs in the P. rotata mitogenome. The legend, dark blue, gray, orange, light green, purple, and red, denotes monomeric, dimeric, trimeric, tetrameric, pentameric, and hexameric SSRs, respectively. B Classification and counts of repeat elements in the P. rotata mitogenome. The red, blue, and green legend indicates tandem repeats, palindromic repeats, and forward repeats, respectively

Fig. 3

Relative Synonymous Codon Usage (RSCU) Analysis of PCGs in the Mitochondrial Genome of P. rotata. The x-axis denotes codon families, and the y-axis represents codon usage frequency. Codons encoding the same amino acid are color-coded by distinct hues to differentiate their corresponding amino acids

Fig. 4

A Distribution of RNA editing sites in mitochondrial PCGs of P. rotata. B Incidence of amino acid changes induced by RNA editing in the P. rotata mitogenome

Fig. 5

Comparative analysis of organelle genome sequences. The mitochondrial and chloroplast genomes are represented by green and blue arcs, respectively, while the yellow lines connecting the arcs represent homologous genomic fragments

Fig. 6

Best maximum likelihood phylogenetic tree based on mitogenomes of 39 species. The red font indicates the species of this study

Fig. 7

Mitochondrial genome collinear analysis of eight selected Lamiaceae species. Red arc-shaped regions denote inversion-prone areas, while gray sections indicate regions with high homology