The first complete chloroplast genome of Vicatia thibetica de Boiss.: genome features, comparative analysis, and phylogenetic relationships

Guan, Yunhui; Liu, Wenwen; Duan, Baozhong; Zhang, Haizhu; Chen, Xu-bing; Wang, Ying; Xia, Conglong

doi:10.1007/s12298-022-01154-y

Cited by 9 publications

(4 citation statements)

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“…Compared with the traditional DNA fragments, the cp genome was relatively conserved and slightly varied, which has been applied to many research fields, such as species identification and the development of molecular markers (Abdullah et al, 2020;Li et al, 2022;Wang et al, 2022). The method has been widely used for identifying Paris, Polygonatum, Vicatia, and their adulterants (Guan et al, 2022;Jiang et al, 2022;Wang et al, 2022). Recently, although the complete cp genomes of Phyllanthaceae species have been reported and the high-resolution phylogenetic tree was reconstructed (Rehman et al, 2021), the purpose of this study was to clarify the genome evolution in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference.…”

Section: Introductionmentioning

confidence: 99%

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

et al. 2023

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BackgroundPhyllanthus urinaria L. is extensively used as ethnopharmacological material in China. In the local marketplace, this medicine can be accidentally contaminated, deliberately substituted, or mixed with other related species. The contaminants in herbal products are a threat to consumer safety. Due to the scarcity of genetic information on Phyllanthus plants, more molecular markers are needed to avoid misidentification.MethodsIn this study, the complete chloroplast genome of nine species of the genus Phyllanthus was de novo assembled and characterized.ResultsThis study revealed that all of these species exhibited a conserved quadripartite structure, which includes a large single copy (LSC) region and small single copy (SSC) region, and two copies of inverted repeat regions (IRa and IRb), which separate the LSC and SSC regions. And the genome structure, codon usage, and repeat sequences were highly conserved and showed similarities among the nine species. Three highly variable regions (trnS-GCU-trnG-UCC, trnT-UGU-trnL-UAA, and petA-psbJ) might be helpful as potential molecular markers for identifying P. urinaria and its contaminants. In addition, the molecular clock analysis results showed that the divergence time of the genus Phyllanthus might occur at ~ 48.72 Ma.ConclusionThis study provides valuable information for further species identification, evolution, and phylogenetic research of Phyllanthus.

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Section: Introductionmentioning

confidence: 99%

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

et al. 2023

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“…The average size of cp genomes in Stemona was larger than its sister genus Croomia [ 30 ]. As most reported in other land plants, the LSC region has a relatively higher length variation compared with the IR and SSC regions, suggesting the IR and SSC regions were more conservative [ 31 ]. The GC content of the chloroplast genome ranged from 24.78% to 57.664%; the average of this occupied 36.82 % [ 32 ].…”

Section: Discussionmentioning

confidence: 89%

The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

Wei

Li²

2022

Genes

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Stemona parviflora is an endangered species, narrowly endemic to Hainan and Southwest Guangdong. The taxonomic classification of S. parviflora remains controversial. Moreover, studying endangered species is helpful for current management and conservation. In this study, the first complete chloroplast genome of S. parviflora was assembled and compared with other Stemona species. The chloroplast genome size of S. parviflora was 154,552 bp, consisting of 87 protein-coding genes, 38 tRNA genes, 8 rRNA genes, and one pseudogene. The ψycf1 gene was lost in the cp genome of S. sessilifolia, but it was detected in four other species of Stemona. The inverted repeats (IR) regions have a relatively lower length variation compared with the large single copy (LSC) and small single copy (SSC) regions. Long repeat sequences and simple sequence repeat (SSR) were detected, and most SSR were distributed in the LSC region. Codon usage bias analyses revealed that the RSCU value of the genus Stemona has almost no difference. As with most angiosperm chloroplast genomes, protein-coding regions were more conservative than the inter-gene spacer. Seven genes (atpI, ccsA, cemA, matK, ndhA, petA, and rpoC1) were detected under positive selection in different Stemona species, which may result from adaptive evolution to different habitats. Phylogenetic analyses show the Stemona cluster in two main groups; S. parviflora were closest to S. tuberosa. A highly suitable region of S. parviflora was simulated by Maxent in this study; it is worth noting that the whole territory of Taiwan has changed to a low fitness area and below in the 2050 s, which may not be suitable for the introduction and cultivation of S. parviflora. In addition, limited by the dispersal capacity of S. parviflora, it is necessary to carry out artificial grafts to expand the survival areas of S. parviflora. Our results provide valuable information on characteristics of the chloroplast genome, phylogenetic relationships, and potential distribution range of the endangered species S. parviflora.

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“…Compared with the traditional DNA fragments, the cp genome was relatively conserved and slightly varied, which has been applied to many research fields, such as species identification and the development of molecular markers . The method has been widely used for identifying Paris, Polygonatum, Vicatia, and their adulterants (Guan et al, 2022;Jiang et al, 2022;. Recently, although the complete cp genomes of Phyllanthaceae species have been reported and the high-resolution phylogenetic tree was reconstructed (Rehman et al, 2021), the purpose of this study was to clarify the genome evolution in Phyllanthaceae and identify the polymorphic loci for phylogenetic inference.…”

Section: Application Of Chloroplast Genome In the Identification Of P...mentioning

confidence: 99%

Structural Variation of the Chloroplast Genome and Related Bioinformatics Tools

Kong

2024

Frontiers Research Topics

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Frontiers is more than just an open access publisher of scholarly articles: it is a pioneering approach to the world of academia, radically improving the way scholarly research is managed. The grand vision of Frontiers is a world where all people have an equal opportunity to seek, share and generate knowledge. Frontiers provides immediate and permanent online open access to all its publications, but this alone is not enough to realize our grand goals. Frontiers journal seriesThe Frontiers journal series is a multi-tier and interdisciplinary set of openaccess, online journals, promising a paradigm shift from the current review, selection and dissemination processes in academic publishing. All Frontiers journals are driven by researchers for researchers; therefore, they constitute a service to the scholarly community. At the same time, the Frontiers journal series operates on a revolutionary invention, the tiered publishing system, initially addressing specific communities of scholars, and gradually climbing up to broader public understanding, thus serving the interests of the lay society, too. Dedication to qualityEach Frontiers article is a landmark of the highest quality, thanks to genuinely collaborative interactions between authors and review editors, who include some of the world's best academicians. Research must be certified by peers before entering a stream of knowledge that may eventually reach the public -and shape society; therefore, Frontiers only applies the most rigorous and unbiased reviews. Frontiers revolutionizes research publishing by freely delivering the most outstanding research, evaluated with no bias from both the academic and social point of view. By applying the most advanced information technologies, Frontiers is catapulting scholarly publishing into a new generation. What are Frontiers Research Topics?Frontiers Research Topics are very popular trademarks of the Frontiers journals series: they are collections of at least ten articles, all centered on a particular subject. With their unique mix of varied contributions from Original Research to Review Articles, Frontiers Research Topics unify the most influential researchers, the latest key findings and historical advances in a hot research area.

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The first complete chloroplast genome of Vicatia thibetica de Boiss.: genome features, comparative analysis, and phylogenetic relationships

Cited by 9 publications

References 50 publications

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

Application of chloroplast genome in the identification of Phyllanthus urinaria and its common adulterants

The Complete Chloroplast Genome of Endangered Species Stemona parviflora: Insight into the Phylogenetic Relationship and Conservation Implications

Structural Variation of the Chloroplast Genome and Related Bioinformatics Tools

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