The complete chloroplast genome sequence of <i>Toxicodendron succedaneum</i> (Anacardiaceae)

Wang, Lu; He, Na; Li, Yao; Fang, Yanming; Zhang, Feilong

doi:10.1080/23802359.2020.1756956

Cited by 6 publications

(3 citation statements)

References 7 publications

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“…In this study, we sequenced and annotated the cp genomes of four Toxicodendron accessions and compared their characteristics with those of six other related species from Toxicodendron . Like other angiosperms, Toxicodendron cp genome is a circular double-standed DNA molecular, exhibiting a conserved quadripartite structure [ 24 , 25 , 36 ], and the ten cp genomes were relatively conserved, which is consistent with the slow rates of sequence and structure evolution of plant plastomes [ 37 , 38 ]. The cp genomes ranged from 158,221 bp (triploid T. vernicifluum ) to 159,710 bp [ T. vernicifluum and T. succedaneum (Ts)], with a difference in size of 1489 bp.…”

Section: Discussionmentioning

confidence: 84%

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

Qiao

Zhou

et al. 2023

BMC Genomics

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Background Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared it with related species of Toxicodendron genus based on chloroplast genome and SSR markers. Results The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 132 genes including 87 protein-coding genes, 37 tRNA genes and 8 rRNA genes were identified in the triploid T. vernicifluum. Among these, 16 genes were duplicated in the IR regions, 14 genes contain one intron, while three genes contain two introns. After nucleotide substitutions, seven small inversions were analyzed in the chloroplast genomes, eight hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi. Moreover, phylogenetic clustering based on the SSR markers showed that all the samples of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the samples of T. vernicifluum and T. succedaneum in another group, which is consistent with the cp genome and morphological analysis. Conclusions The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum.

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Section: Discussionmentioning

confidence: 84%

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

Qiao

Zhou

et al. 2023

BMC Genomics

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“…These cp genomes ranged from 158,221 bp (triploid T. vernici uum) to 159,710 bp (T. vernici uum) and comprised all the four major components of chloroplast genome architecture. The size of genome, content of GC, length of IR, LSC, and SSC regions and gene content exposed high similarity among the genomes, suggesting that Toxicodendron species shared low diversity [24][25]35]. 116 genes, including 82 protein coding genes, 30 tRNA genes and four RNA genes were annotated in triploid T. vernici uum cp genome.…”

Section: Discussionmentioning

confidence: 99%

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

Qiao

Zhou

et al. 2022

Preprint

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Background: Toxicodendron vernicifluum, belonging to the family Anacardiaceae, is an important commercial arbor species, which can provide us with the raw lacquer, an excellent adhesive and painting material used to make lacquer ware. Compared with diploid, triploid lacquer tree has a higher yield of raw lacquer and stronger resistance to stress. Triploid T. vernicifluum was a newly discovered natural triploid lacquer tree. However, the taxonomy of triploid T. vernicifluum has remained uncertain. Here, we sequenced and analyzed the complete chloroplast (cp) genome of triploid T. vernicifluum and compared with T. vernicifluum cv. Dahongpao, T. vernicifluum cv. Hongpigaobachi, T. vernicifluum and T. succedaneum based on chloroplast genome and SSR markers. Results: The plastome of triploid T. vernicifluum is 158,221 bp in length, including a pair of inverted repeats (IRs) of 26,462 bp, separated by a large single-copy region of 86,951 bp and a small single-copy region of 18,346 bp. In total, 116 unique genes including 82 protein-coding genes, 30 tRNA genes and 4 rRNA genes were identified in the triploid T. vernicifluum. After nucleotide substitutions, small inversions were analyzed in the chloroplast genomes, five hotspot regions were found, which could be useful molecular genetic markers for future population genetics. Phylogenetic analyses showed that triploid T. vernicifluum was a sister to T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi.Moreover, phylogenetic clustering based on the SSR markers showed that all the individuals of triploid T. vernicifluum, T. vernicifluum cv. Dahongpao and T. vernicifluum cv. Hongpigaobachi in one group, while the individuals of T. vernicifluum and T. succedaneumin another group. Conclusions: The current genomic datasets provide pivotal genetic resources to determine the phylogenetic relationships, variety identification, breeding and resource exploitation, and future genetic diversity-related studies of T. vernicifluum.

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“…Finally, we obtained a dataset for 449 T. vernicifluum trees (333 wild trees and 116 cultivated trees) sampled from 79 sites, including 397 trees from 47 sites in China, 46 trees from 30 sites in Japan, and six trees from two sites in South Korea ( Table 1 ). Furthermore, we also compiled the sequence data for five congeners that were used as outgroups, including T. succedaneum ( Suzuki et al, 2014 ; Wang et al, 2020b ), T. sylvestre ( He et al, 2020 ), T. trichocarpum ( Suzuki et al, 2014 ), T. radicans ( Suzuki et al, 2014 ), and T. griffithii ( Li et al, 2020 ). GenBank accession numbers for all the samples analyzed in this study were listed in Supplementary Table S1 .…”

Section: Methodsmentioning

confidence: 99%

Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species (Toxicodendron vernicifluum, Anacardiaceae) in East Asia

Wang

Noshiro

et al. 2022

Front. Plant Sci.

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Species’ phylogeographic patterns reflect the interplay between landscape features, climatic forces, and evolutionary processes. Here, we used two chloroplast DNA (cpDNA) markers (trnL and trnL-F) to explore the role of stepped geomorphology in shaping the phylogeographic structure of Toxicodendron vernicifluum, an economically important tree species widely distributed in East Asia. The range-wide pattern of sequence variation was analyzed based on a dataset including 357 individuals from China, together with published sequences of 92 individuals mainly from Japan and South Korea. We identified five chloroplast haplotypes based on seven substitutions across the 717-bp alignment. A clear east-west phylogeographic break was recovered according to the stepped landforms of mainland China. The wild trees of the western clade were found to be geographically restricted to the “middle step”, which is characterized by high mountains and plateaus, while those of the eastern clade were confined to the “low step”, which is mainly made up of hills and plains. The two major clades were estimated to have diverged during the Early Pleistocene, suggesting that the cool glacial climate may have caused the ancestral population to retreat to at least two glacial refugia, leading to allopatric divergence in response to long-term geographic isolation. Migration vector analyses based on the outputs of ecological niche models (ENMs) supported a gradual range expansion since the Last Interglacial. Mountain ranges in western China and the East China Sea land bridge were inferred to be dispersal corridors in the western and eastern distributions of T. vernicifluum, respectively. Overall, our study provides solid evidence for the role of stepped geomorphology in shaping the phylogeographic patterns of T. vernicifluum. The resulting east-west genetic discontinuities could persist for a long time, and could occur at a much larger scale than previously reported, extending from subtropical (e.g., the Xuefeng Mountain) to warm-temperate China (e.g., the Taihang Mountain).

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The complete chloroplast genome sequence of Toxicodendron succedaneum (Anacardiaceae)

Cited by 6 publications

References 7 publications

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

Chloroplast genome sequence of triploid Toxicodendron vernicifluum and comparative analyses with other lacquer chloroplast genomes

Stepped Geomorphology Shaped the Phylogeographic Structure of a Widespread Tree Species (Toxicodendron vernicifluum, Anacardiaceae) in East Asia

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