Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Diospyros oleifera, the first representative from the family Ebenaceae

Abstract

Plant mitochondrial genomes are a valuable source of genetic information for a better understanding of phylogenetic relationships. However, no mitochondrial genome of any species in Ebenaceae has been reported. In this study, we reported the first mitochondrial genome of an Ebenaceae model plant Diospyros oleifera. The mitogenome was 493,958 bp in length, contained 39 protein-coding genes, 27 transfer RNA genes, and 3 ribosomal RNA genes. The rps2 and rps11 genes were missing in the D. oleifera mt genome, while the rps10 gene was identified. The length of the repetitive sequence in the D. oleifera mt genome was 31 kb, accounting for 6.33%. A clear bias in RNA-editing sites were found in the D. oleifera mt genome. We also detected 28 chloroplast-derived fragments significantly associated with D. oleifera mt genes, indicating intracellular tRNA genes transferred frequently from chloroplasts to mitochondria in D. oleifera. Phylogenetic analysis based on the mt genomes of D. oleifera and 27 other taxa reflected the exact evolutionary and taxonomic status of D. oleifera. Ka/Ks analysis revealed that 95.16% of the protein-coding genes in the D. oleifera mt genome had undergone negative selections. But, the rearrangement of mitochondrial genes has been widely occur among D. oleifera and these observed species. These results will lay the foundation for identifying further evolutionary relationships within Ebenaceae.

Keywords: Diospyros oleifera; Mitochondrial genome; Phylogenetic analysis.

Figure 1

The circular map of D. oleifera mt genome. Gene map showing 69 annotated genes of different functional groups.

Figure 2

Secondary structures of tRNAs of D. oleifera. Each region of tRNA is named as follows [69, 70]: Amino acid accepting stem, AAS (upper arm); dihydrouridine stem and loop, DSL (left arm); anticodon stem and loop, ASL (lower arm); thymidine stem and loop, TSL (right arm); variable stem and loop, VSL (between ASL and TSL).

Figure 3

The repeats in the D. oleifera mt genome. A: The synteny between the mt genome and its copy showing the direct repeats. B: The length distribution of reverse and inverted repeats in the D. oleifera mt genome. The number on the histograms represents the repeat number of designated lengths shown on the horizontal axi.

Figure 4

The distribution of RNA-editing sites in the D. oleifera mt protein-coding genes. The blue bars represent the number of RNA-editing sites of each gene.

Figure 5

Relative synonymous codon usage in the D. oleifera mt genome.

Figure 6

DNA and gene transfer between Chloroplast and Mitochondrial genomes in D. oleifera. The track shows complete genomes of cp and mt in green and red respectively.

Figure 7

The phylogenetic relationships of D. oleifera with other 27 plant species using the maximum likelihood (ML) analysis. The bootstrapping values are listed in each node. The number after the species name is the GenBank accession number. Colors indicate the groups that the specific species belongs.

Figure 8

The Ka/Ks values of 28 protein-coding genes of D. oleifera versus 27 species.

Figure 9

Synteny analysis of D. oleifera and other five species mitogenomes as generated with Mauve. The sizes and relative positions of the homologous fragments varied across mitogenomes.