Comparative and phylogenetic analysis of Platycarya longipes and related species based on the complete chloroplast genomes.

Abstract

Platycarya longipes is a dominant tree species in karst forests. Due to limited genomic information, its exact phylogenetic position within the family Juglandaceae remains unclear. In this study, the complete chloroplast genome (cp genome) of Platycarya longipes was de novo assembled using Illumina reads. This circular cp genome was 158 592 bp in length, consisting of an 88 066 bp large single-copy region, an 18 524 bp small single-copy region, and a total of 26 001 bp derived from a pair of inverted repeats (IRa and IRb), with an average GC content of 36.15%. It accommodated a total of 113 genes, including 80 protein-coding genes, 29 tRNAs, and 4 rRNAs. Additionally, within the genome, 49 long repeats and 66 simple sequence repeats, which could be utilized as molecular markers, were identified. In comparison to the related Platycarya strobilacea, the K_a/K_s substitution rate values of Platycarya longipes exhibited significant divergence, supporting the differentiation between the species. The conserved gene order and structure of the Platycarya longipes cp genome compared to other Juglandaceae members. Phylogenetic analysis using maximum likelihood and Bayesian inference methods with Fagales genomes showed a close relationship between Platycarya longipes and Platycarya strobilacea.