Complete Chloroplast Genome Sequence of Chinese Lacquer Tree (Toxicodendron vernicifluum, Anacardiaceae) and Its Phylogenetic Significance

Abstract

Chinese lacquer tree (Toxicodendron vernicifluum) is an important commercial arbor species widely cultivated in East Asia for producing highly durable lacquer. Here, we sequenced and analyzed the complete chloroplast (cp) genome of T. vernicifluum and reconstructed the phylogeny of Sapindales based on 52 cp genomes of six families. The plastome of T. vernicifluum is 159,571 bp in length, including a pair of inverted repeats (IRs) of 26,511 bp, separated by a large single-copy (LSC) region of 87,475 bp and a small single-copy (SSC) region of 19,074 bp. A total of 126 genes were identified, of which 81 are protein-coding genes, 37 are transfer RNA genes, and eight are ribosomal RNA genes. Forty-nine mononucleotide microsatellites, one dinucleotide microsatellite, two complex microsatellites, and 49 long repeats were determined. Structural differences such as inversion variation in LSC and gene loss in IR were detected across cp genomes of the six genera in Anacardiaceae. Phylogenetic analyses revealed that the genus Toxicodendron is closely related to Pistacia and Rhus. The phylogenetic relationships of the six families in Sapindales were well resolved. Overall, this study providing complete cp genome resources will be beneficial for determining potential molecular markers and evolutionary patterns of T. vernicifluum and its closely related species.

Figure 1

Gene map of Toxicodendron vernicifluum chloroplast genome. Genes shown inside the circle are transcribed clockwise and those outside are transcribed counterclockwise. Genes of different functions are color-coded. The darker gray in the inner circle shows the GC content, while the lighter gray shows the AT content.

Figure 2

Visualization of alignment of the six Anacardiaceae species using mVISTA, with T. vernicifluum as the reference. The horizontal axis indicates the coordinates within the chloroplast genome. The vertical scale represents the percentage of identity, ranging from 50% to 100%. The gray arrows above the alignment indicate the genes' orientations.

Figure 3

Nucleotide diversity (P_i) values among the six Anacardiaceae species.

Figure 4

Gene map and MAUVE alignment of six Anacardiaceae chloroplast genomes. Within each of the alignment, local collinear blocks are represented by blocks of the same color connected by lines.

Figure 5

Comparison of IR-SC border positions across chloroplast genomes of six Anacardiaceae species. Genes are denoted by colored boxes. The gaps between the genes and the boundaries are indicated by the base lengths (bp).

Figure 6

Bayesian-inference (BI) and maximum likelihood (ML) analyses based on the chloroplast genome sequences of 52 species from six families in Sapindales and two outgroups of Brassicales and Huerteales. Above each node, the first number indicates the Bayesian posterior probability (PP), and the second number indicates the ML bootstrap value (BS). Nodes with posterior probability of 1 and bootstrap value of 100 are not labeled.