Analysis of chloroplast genome features of endangered and rare plant Camellia minima

Abstract

Camellia minima, a rare and endangered species of sect. Chrysantha, has not been previously explored in terms of its chloroplast genome. Utilizing the Illumina HiSeq 2000 platform, the chloroplast genome sequence of C. minima was sequenced, assembled, annotated, and analysed. The results were as follows: (1) The chloroplast genome of C. minima was 156 961 bp in length, embodied a typical tetrad structure, and contained 136 annotated genes, including 87 protein-coding genes, 41 tRNA genes, and 8 rRNA genes. (2) The analysis identified 66 SSR loci and 39 repetitive sequences. (3) Codons prefered to use codons ending in A/U. Comprehensive effective number of codons (ENC) mapping, PR2-plot, and neutral analyses suggested natural selection as a primary factor shaping codon usage patterns. (4) Boundary analysis showed variation in the length and position of the ycf1 gene among different species of yellow Camellia. (5) Phylogenetic analysis of the chloroplast genomes of published sect. Chrysantha species revealed that C. minima was most closely related to C. micrantha. This study provides crucial references for exploring species evolution and enhancing exogenous gene expression, establishing a theoretical foundation for the conservation and utilization of species of sect. Chrysantha in the future.

Keywords

• camellia minima
• chloroplast genome
• characteristic analysis
• phylogenetic analysis
• codon preference