Mitochondrial genome assembly of the Chinese endemic species of Camellia luteoflora and revealing its repetitive sequence mediated recombination, codon preferences and MTPTs

Abstract

Camellia luteoflora Y.K. Li ex Hung T. Chang & F.A. Zeng belongs to the Camellia L. genus (Theaceae Mirb.). As an endemic, rare, and critically endangered species in China, it holds significant ornamental and economic value, garnering global attention due to its ecological rarity. Despite its conservation importance, genomic investigations on this species remain limited, particularly in organelle genomics, hindering progress in phylogenetic classification and population identification. In this study, we employed high-throughput sequencing to assemble the first complete mitochondrial genome of C. luteoflora and reannotated its chloroplast genome. Through integrated bioinformatics analyses, we systematically characterized the mitochondrial genome's structural organization, gene content, interorganellar DNA transfer, sequence variation, and evolutionary relationships.Key findings revealed a circular mitochondrial genome spanning 587,847 bp with a GC content of 44.63%. The genome harbors70 unique functional genes, including 40 protein-coding genes (PCGs), 27 tRNA genes, and 3 rRNA genes. Notably, 9 PCGs contained 22 intronic regions. Codon usage analysis demonstrated a pronounced A/U bias in synonymous codon selection. Structural features included 506 dispersed repeats and 240 simple sequence repeats. Comparative genomics identified 19 chloroplast-derived transfer events, contributing 29,534 bp (3.77% of total mitochondrial DNA). RNA editing prediction revealed 539 C-to-T conversion events across PCGs. Phylogenetic reconstruction using mitochondrial PCGs positioned C. luteoflora in closest evolutionary proximity to Camellia sinensis var. sinensis. Selection pressure analysis (Ka/Ks ratios < 1 for 11 PCGs) and nucleotide diversity assessment (Pi values: 0-0.00711) indicated strong purifying selection and low sequence divergence.This study provides the first comprehensive mitochondrial genomic resource for C. luteoflora, offering critical insights for germplasm conservation, comparative organelle genomics, phylogenetic resolution, and evolutionary adaptation studies in Camellia species.

Keywords: Camellia luteoflora; Homologous recombination; Mitochondrial genome; RNA editing events.

Fig. 1

Mitochondrial genome assembly results of Camellia luteoflora. (A: Mitochondrial genome map; B: Field photo of Camellia luteoflora; The genes located in the upper region of linear molecules and within the interior of circular molecules represent genes transcribed in a clockwise direction, while thegenes in the lower region of linear molecules and the genes on the outside of circular molecules represent genes transcribed in a counterclockwise direction. Genes with different functions were depicted using different colors.)

Fig. 2

Camellia luteoflora recombination mediated by repetitive sequences. (The yellow rectangles indicate repetitive sequences at branch points. A: the initial structure of the genome is branching; B: the complete linear sequence of the genome branching unraveling; C: the four substructures arising from two pairs of repetitive sequences in the genome.)

Fig. 3

Repetitive sequences of Camellia luteoflora mitochondrial genome. (A: Distribution of repetitive sequences; B: length of forward repetitive sequence and palindromic sequence; C: proportion of six SSR types; D: number of SSR repetitive sequence types)

Fig. 4

Use of relative synonymous codons in the mitochondrial genomes of Camellia luteoflora

Fig. 5

Fragments of Camellia luteoflora converted from chloroplasts to mitochondria

Fig. 6

Prediction of RNA editing sites for PCGs in the mitochondrial genome of Camellia luteoflora. (A: number of RNA editing sites for each gene; B: type of amino acid conversion C: percentage of hydrophilic and hydrophobic amino acids before RNA editing; D: percentage of hydrophilic and hydrophobic amino acids after RNA editing.)

Fig. 7

Box plots of Ka/Ks ratios of Camellia luteoflora with six plants

Fig. 8

Nucleotide diversity values of Camellia luteoflora with six species

Fig. 9

Phylogenetic relationships of Camellia luteoflora mitochondrial genomes. ( phylogenetic tree constructed on the basis of 28 protein coding genes)

Fig. 10

Phylogenetic relationships of Camellia luteoflora chloroplast genomes. (phylogenetic tree constructed on the chloroplast genome)