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.

Plastid genomes of the North American Rhus integrifolia-ovata complex and phylogenomic implications of inverted repeat structural evolution in Rhus L.

“…While the sampling of 52 plastomes in the current study does not capture the species richness of this diverse order, it does provide support for higher-level relationships based on the plastomes included, and further enables a robust framework for comparative plastid genomics in the order. In fact, the relationships among sapindalean families recovered in the current study are corroborated by another recent study based on complete plastome sequences in Wang et al (2020), here with the addition of two plastomes from Nitrariaceae (Nitraria L. and Peganum L.), which were not included in the aforementioned study.…”

“…While most of the deep branch support values in that study were moderate to high, the placement of Biebersteiniaceae and Nitrariaceae among other members of Sapindales received no support. Additionally, there was moderate support for Meliaceae as sister to Simaroubaceae, whereas in the current study and in that of Wang et al (2020), both based on complete plastome data, Meliaceae is supported as sister to Simaroubaceae + Rutaceae. The topology from the current study among families is also identical to that in (Li et al, 2019b) based on coding regions of the plastome.…”

Plastome comparative genomics in maples resolves the infrageneric backbone relationships

“…In all other Sapindaceae surveyed (listed above), infA also appears as a pseudogene suggesting that it became obsolete in the ancestor of this family or perhaps of Sapindales. It has been reported as missing or as a pseudogene, in several genera of Meliaceae ( Mader et al, 2018 ), Simaroubaceae ( Saina et al, 2018 ), Nitrariaceae ( Lu et al, 2017 ), and Anacardiaceae ( Wang et al, 2020 ). The loss of this gene from cpDNA has been documented in many other angiosperm lineages, and there is even indication of its transfer to the nuclear genome in a number of species ( Daniell et al, 2016 ; Millen et al, 2001 ).…”

“…The pattern of codon usage in Acer plastomes is very similar to that of other members of Sapindales. The three most frequent codons (AUU, AAA, and GAA) and the least frequent (UGC, AGC, and CGC) are shared, for example, with Ailanthus (Simaroubaceae), Nitraria (Nitrariaceae) and Toxicodendron (Anacardiaceae) (Lu et al, 2017;Saina et al, 2018;Wang et al, 2020). The most commonly specified amino acids, leucine and isoleucine, are also the most commonly specified in these and many other plant genera (Li et al, 2018;Silva et al, 2018;Yang et al, 2018).…”

The complete chloroplast genome sequence of Toxicodendron succedaneum (Anacardiaceae)

“…In Australia and New Zealand, T. succedaneum is planted as an ornamental plant for its beautiful autumn foliage. Recently, the complete chloroplast (cp) genome of Chinese lacquer tree (T. vernicifluum) has been reported (Zhong et al 2019;Wang et al 2020). However, plastid genome sequences of most Toxicodendron species remain unknown.…”