Comparative Chloroplast Genome Analysis of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae): East-West Divergence within Its Range in China

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species known for the production of raw lacquer. Here, we investigated the intraspecific chloroplast (cp) genome variability of T. vernicifluum using two available and five newly sequenced cp genomes. We found that each of the seven cp genomes encoded 87 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analyses based on protein-coding genes indicated that the four individuals from western China formed a monophyletic group sister to the cluster containing the three individuals from eastern China. The cp genomes from western China exhibited a larger genome length and longer large single-copy (LSC), small single-copy (SSC), and inverted repeat (IR) regions than those from eastern China. A total of 466 single nucleotide polymorphisms (SNPs) and 141 insertion-deletion mutations were detected among the seven cp genomes, most of which were found between the eastern and western lineages. The two groups exhibited a similar number of microsatellites, long repeats, and tandem repeats. Notably, complementary repeat sequences were only found in the IRs of the individuals from eastern China, while reverse repeat sequences were only detected in the LSC of the individuals from western China. Eight intraspecific mutational hotspots were also identified, including six intergenic regions (trnF-ndhJ, rpl32-trnL, ccsA-ndhD, trnH-psbA, psbC-trnS, and trnL-trnF) and two gene regions (rpl32 and rps19). The genomic resources presented in this study will be useful for further studies on evolutionary patterns and resource protection of T. vernicifluum.