Characterization of the chloroplast genome of a relict tree, Pterocarya fraxinifolia (Juglandaceae), and its comparative analysis

The rare, vulnerable relict species Pterocarya fraxinifolia is among the last surviving tree species growing in small, scattered populations in the southern Caucasus region; P. fraxinifolia grows up to 1000 m in plain forests and is threatened by habitat loss and environmental changes. Here, we sequenced and annotated the chloroplast genome of P. fraxinifolia from Hyrcanian forests and compared it to the chloroplast genomes of five other Pterocarya species. The evolutionary relationships of P. fraxinifolia were subsequently evaluated using the chloroplast genomes and individual chloroplast loci. The chloroplast genome of P. fraxinifolia was 160,086 bp in length, comprising 128 genes and a typical quadripartite structure. A comparative analysis of the six Pterocarya species revealed limited nucleotide diversity and structural variations in genes. The bulk of the 68 loci identified by SSR analysis comprised A/T repeats. Codon bias analysis revealed strong purifying selection, with the ndhF gene showing the highest Ka/Ks ratio. Our phylogenetic analysis revealed Pterocarya as a sister to the genus Juglans and a distinct subclade within Pterocarya.