Comparative analysis of mitochondrial genomes of Stemona tuberosa lour. reveals heterogeneity in structure, synteny, intercellular gene transfer, and RNA editing

Abstract

Background: Stemona tuberosa, a vital species in traditional Chinese medicine, has been extensively cultivated and utilized within its natural distribution over the past decades. While the chloroplast genome of S. tuberosa has been characterized, its mitochondrial genome (mitogenome) remains unexplored.

Results: This paper details the assembly of the complete S. tuberosa mitogenome, achieved through the integration of Illumina and Nanopore sequencing technologies. The assembled mitogenome is 605,873 bp in size with a GC content of 45.63%. It comprises 66 genes, including 38 protein-coding genes, 25 tRNA genes, and 3 rRNA genes. Our analysis delved into codon usage, sequence repeats, and RNA editing within the mitogenome. Additionally, we conducted a phylogenetic analysis involving S. tuberosa and 17 other taxa to clarify its evolutionary and taxonomic status. This study provides a crucial genetic resource for evolutionary research within the genus Stemona and other related genera in the Stemonaceae family.

Conclusion: Our study provides the inaugural comprehensive analysis of the mitochondrial genome of S. tuberosa, revealing its unique multi-branched structure. Through our investigation of codon usage, sequence repeats, and RNA editing within the mitogenome, coupled with a phylogenetic analysis involving S. tuberosa and 17 other taxa, we have elucidated its evolutionary and taxonomic status. These investigations provide a crucial genetic resource for evolutionary research within the genus Stemona and other related genera in the Stemonaceae family.

Keywords: Stemona tuberosa; Mitochondrial genome; Phylogenetic relationship; RNA editing; Repeated sequences.

Fig. 1

Circular representation of the mitochondrial genome assembly ofS. tuberosa. The figure shows the assembly result visualized in Bandage, displaying three circular chromosomes. Chromosome 1 (ctg1) has a length of 505,146 bp with 97x coverage, Chromosome 2 (ctg2) is 62,944 bp long with 93x coverage, and Chromosome 3 (ctg3) measures 37,783 bp with 90x coverage. Each circular chromosome is indicated by a closed loop, representing the structure of the S. tuberosa mitochondrial genome

Fig. 2

The map of the mitogenome of S. tuberosa. The arrows shown transcriptional direction of the mitogenome. Genes with different functions were depicted using different colors

Fig. 3

Relative synonymous codon usage (RSCU) in the mitochondrial protein-coding genes ofS. tuberosa. The figure displays the RSCU values for the 38 unique protein-coding genes in the S. tuberosa mitochondrial genome. The codon usage patterns are represented for 20 amino acids and stop codons (End), showing the preference for certain codons over others. Codons with higher RSCU values indicate a greater frequency of usage relative to other synonymous codons

Fig. 4

Analysis of repeat elements in the mitochondrial genome ofS. tuberosa.(A) Distribution of repeat motifs classified by repeat unit length (monomeric, dimeric, trimeric, tetrameric, pentameric, and hexameric) across the three mitochondrial chromosomes of S. tuberosa. (B) Classification of repeats based on structural types, including tandem, palindromic, forward, reverse, and complementary repeats

Fig. 5

Predicted RNA Editing Sites Based on Protein-Coding Genes. This bar chart displays the number of predicted RNA editing sites in various protein-coding genes. The x-axis represents different genes, while the y-axis indicates the number of RNA editing sites for each gene. Each bar corresponds to the number of editing sites in a gene, visually representing the distribution of editing sites across the genes

Fig. 6

Homologous analysis between two organelles. The blue arc represents mtDNA. The green arc represents chloroplast genome. The homologous fragments are indicated using the yellow lines between blue and green arcs

Fig. 7

Collinear analysis of sixspecies. The pink arcs indicated inverted regions. The gray arcs indicated better homologous regions. The regions with no colinear blocks are indicated as unique in the species

Fig. 8

Construction of the maximum likelihood tree based on the 18 species