Chloroplast genome phylogeny and codon preference of Docynia longiunguis

Abstract:

Docynia longiunguis is a plant uniquely present in China and is of high edible and medicinal value. The analysis of its chloroplast genome will help clarify the phylogenetic relationship among Docynia and facilitate the development and utilization of D. longiunguis resources. Based on the alignment of chloroplast genome sequences of related species, the phylogeny and codon preference were analyzed. The total length of D. longiunguis chloroplast genome sequence was 158 914 bp (GenBank accession number is MW367027), with an average GC content of 36.7%. The length of the large single-copy (LSC), the small single-copy (SSC), and inverted repeats (IRs) are 87 020 bp, 19 156 bp, and 26 369 bp, respectively. A total of 102 functional genes were annotated, including 72 protein-coding genes, 26 tRNA genes, and 4 rRNA genes. The best model for constructing phylogenetic tree was TVM+F+R2. D. longiunguis and Docynia indica were clustered into a single group, while Docynia and Malus were clustered into a single group. Comparison of the chloroplast genome sequences of D. longiunguis and its five related species revealed that trnY (GUA)-psbD, ndhC-trnV (UAC), accD-psaI, psbZ-trnfM (CAU), ndhF-trnL gene regions varied greatly. The nucleic acid diversity analysis showed that there were 11 high variation areas with nucleotide variability > 0.01, all were located in the LSC and SSC regions. Except for D. longiunguis, the trnH genes in other sequences were located at the IRs/LSC junction and did not cross the boundary. Codon preference analysis showed that D. longiunguis chloroplast genome has the largest number of isoleucine (Ile) codons, up to 1 205. D. longiunguis has the closest genetic relationship with Malus baccata, Malus sieboldii, Malus hupehensis and Chaenomeles sinensis. Its chloroplast genome codon prefers to end with A/T. The chloroplast genome of D. longiunguis and other Rosaceae chloroplast genomes showed great differences in gene distribution in four boundary regions, while relatively small differences from the chloroplast genomes of Docynia delavayi and D. indica of the same genus were observed. The genome annotation, phylogenetic analysis and sequence alignment of chloroplast genome of D. longiunguis may facilitate the identification, development and utilization of this species.