The first mitochondrial genome of Calophyllum soulattri Burm.f

Abstract

Calophyllum soulattri Burm.f. is traditionally used to treat skin infections and reduce rheumatic pain, yet genetic and genomic studies are still limited. Here, we present the first complete mitochondrial genome of C. soulattri. It is 378,262 bp long with 43.97% GC content, containing 55 genes (30 protein-coding, 5 rRNA, and 20 tRNA). Repeat analysis of the mitochondrial genome revealed 194 SSRs, mostly mononucleotides, and 266 pairs of dispersed repeats ( $\ge$ 30 bp) that were predominantly palindromic. There were 23 homologous fragments found between the mitochondrial and plastome genomes. We also predicted 345 C-to-U RNA editing sites from 30 protein-coding genes (PCGs) of the C. soulatrii mitochondrial genome. These RNA editing events created the start codon of nad1 and the stop codon of ccmFc. Most PCGs of the C. soulattri mitochondrial genome underwent negative selection, but atp4 and ccmB experienced positive selection. Phylogenetic analyses showed C. soulattri is a sister taxon of Garcinia mangostana. This study has shed light on C. soulattri's evolution and Malpighiales' phylogeny. As the first complete mitochondrial genome in Calophyllaceae, it can be used as a reference genome for other medicinal plant species within the family for future genetic studies.

Figure 1

The circular map of Calophyllum soulattri mitochondrial genome. The gray arrows show the direction of transcription. Genes inside the circle are transcribed clockwise while genes outside the circle are transcribed counterclockwise. The gray bars inside the circle represent the GC content of the sequence.

Figure 2

Distribution of protein-coding genes in the mitogenomes of representative species in the order Malpighiales. Red boxes indicate that the gene is present while white boxes indicate that the gene is absent. Calophyllum soulattri is labelled with an asterisk (*).

Figure 3

Codon usage bias of the mitochondrial PCGs of Calophyllum soulattri. The RSCU refers to relative synonymous codon usage. Codon families are labelled on the x-axis. Values on top of the bars refer to amino acid usage.

Figure 4

Repetitive elements in the mitochondrial genome of Calophyllum soulattri. (a) Abundance of simple sequence repeats (SSRs), and (b) the number and types of dispersed repeats ($\ge$30bp) identified in C. soulattri mitochondrial genome.

Figure 5

Circular map showing the distribution of MTPTs on the mitochondrial genome of Calophyllum soulattri. The blue and green outer arcs represent the mitochondrial genome (mt) and chloroplast genome (cp), respectively. The gray links in the inner circle represent the MTPTs on C. soulattri mitochondrial genome.

Figure 6

Number of RNA editing sites identified in the PCGs of Calophyllum soulattri mitochondrial genome. The abscissa shows the name of the genes, while the ordinate shows the number of edited sites.

Figure 7

The Ka/Ks ratios for 29 protein-coding genes of Calophyllum soulattri. The red broken line represents Ka/Ks ratio of 1.0, indicating neutral selection.

Figure 8

Phylogenetic tree of 14 plant species from the order Malpighiales and two non-Malpighiales species inferred from IQ-TREE and MrBayes based on 25 concatenated orthologous mitochondrial PCGs with the best-fit partitioning strategy. Two species from Fabaceae (Caragana spinosa and Echinosophora koreensis) were used as outgroups. Values inside parenthesis beside branches are SH-aLRT/UFBoot/PP support. The tree scale indicates the number of nucleotide substitutions per site. The mitochondrial genome obtained from this study was highlighted in bold.