Insights into chloroplast genome structure and phylogenetic position of the Lacquer tree Toxicodendron trichocarpum (Anacardiaceae: Rhoideae)

Abstract

The lacquer tree Toxicodendron trichocarpum (Miq) Kuntze (Anacardiaceae: Rhoideae), which is known for its abundance of urushiol, produces a high-quality raw lacquer. There have been five complete chloroplast genomes reported in the genus Toxicodendron, while, only two T. trichocarpum genes were sequenced and used for phylogenetic and biogeographic analysis. In this study, we sequenced the T. trichocarpum whole genome on the Illumina HiSeq 4000 platform and investigated its complete chloroplast genome characteristics. Our results showed that the length of the chloroplast genome of T. trichocarpum was 159,959 bp with a GC content of 37.9%. The genome was found to comprise a large single-copy region (LSC) spanning 87,964 bp, a small single-copy region (SSC) of 18,979 bp, and two inverted repeat regions (IRa/IRb) of equal length, each measuring 26,508 bp. A total of 134 genes were annotated, consisting of 89 protein-coding genes, 37 tRNA genes and eight rRNA genes. Altogether, 84 chloroplast simple sequence repeats (SSRs) were identified, predominantly composed of single nucleotides (A/T), with a clear preference for A/T. By comparing the chloroplast genomes of the genus Toxicodendron, six relatively highly variable regions were identified for future molecular marker development. Phylogenetic analyses conducted within the tribe Rhoideae strongly supported the monophyly of the genus Toxicodendron. The species T. trichocarpum was sister to T. diversilobum, with a high level of support at 99%, forming a clade with T. griffithii and T. vernicifluum. Divergence time estimation suggested that Toxicodendron was originated at 42.47 mya (95% HPD: 41.99–42.99 mya) and T. trichocarpum occurred concomitantly with the sister species T. diversilobum at approximately 16.33 mya. We first reported the complete chloroplast genome of T. trichocarpum and comparative analysis of the Toxicodendron species, which will provide valuable genomic information for accurate classification and evolutionary process of this important taxa in the future.