The complete mitochondrial genome of Sinojackia microcarpa: evolutionary insights and gene transfer

Abstract

Background: As a dicotyledonous plant within the Styracaceae family, Sinojackia microcarpa (S. microcarpa) is notable for its library-shaped fruit and sparse distribution, serving as a model system for studying the entire tree family. However, the scarcity of genomic data, particularly concerning the mitochondrial and nuclear sequences of S. microcarpa, has substantially impeded our understanding of its evolutionary traits and fundamental biological mechanisms.

Results: This study presents the first complete mitochondrial genome sequence of S. microcarpa and conducts a comparative analysis of its protein-encoding genes across eight plant species. Our analysis revealed that the mitochondrial genome of S. microcarpa spans 687,378 base pairs and contains a total of 59 genes, which include 37 protein-coding genes (PCGs), 20 transfer RNA (tRNA) genes, and 2 ribosomal RNA (rRNA) genes. Sixteen plastid-derived fragments strongly linked with mitochondrial genes, including one intact plastid-related gene (rps7), were identified. Additionally, Ka/Ks ratio analysis revealed that most mitochondrial genes are under purifying selection, with a few genes, such as nad9 and ccmB, showing signs of relaxed or adaptive evolution. An analysis of twenty-nine protein-coding genes from twenty-four plant species reveals that S. microcarpa exhibits a closer evolutionary relationship with species belonging to the genus Camellia. The findings of this study provide new genomic data that enhance our understanding of S. microcarpa, and reveal its mitochondrial genome's evolutionary proximity to other dicotyledonous species.

Conclusions: Overall, this research enhances our understanding of the evolutionary and comparative genomics of S. microcarpa and other plants in the Styracaceae family and lays the foundation for future genetic studies and evolutionary analyses in the Styracaceae family.

Keywords: Sinojackia microcarpa; Gene transfer; Mitochondria genome; Phylogenetic analysis.

Fig. 1

Circular mitochondrial genome of S. microcarpa. Genes belonging to different functional groups are color-coded. The GC content is represented on the inner circle by the dark gray plot

Fig. 2

Relative synonymous codon usage. Different proportions correspond to different RSCUs

Fig. 3

The Non-synonymous (Ka)/synonymous (Ks) ratio values for 23 mitochondrial protein-coding genes of Sinojackia microcarpa compared with the mitochondrial genome of Stewartia sinensis Ka represents the non-synonymous substitution rate, Ks represents the synonymous substitution rate, and Ka/Ks indicates the selective pressure acting on each gene

Fig. 4

Analysis of conservative gene clusters between the S. microcarpa mt genome and other plant mt genomes

Fig. 5

Distribution of transfer RNA (tRNA) genes in plant mitochondrial genomes. The white boxes indicate that the gene is absent or lost in the mitochondrial genome. Yellow and green boxes indicate mitochondrial tRNA genes and plastid-derived tRNA genes, respectively, with one copy existing in each mitochondrial genome. The numbers represent the copy numbers in the mitochondrial genome

Fig. 6

Phylogenetic tree based on 29 homologous protein-coding genes in the mitochondrial genomes of 24 plants via maximum likelihood (ML) analysis. The numbers below the nodes are support values with ML bootstrap values. Amborella trichopoda was designated as the outgroup. Scale bar represents nucleotide substitutions per site