Complete chloroplast genome sequence of <i>Pueraria thomsonii</i>, an important traditional Chinese medicine plant

Miao, Xiao-Rong; Niu, Junqi; Wang, Aiqin; Wang, Daobo; Fan, Jing

doi:10.1080/23802359.2019.1693301

Cited by 5 publications

(6 citation statements)

References 10 publications

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“…However, the CP genomes of P. lobata and P. thomsonii have not been thoroughly studied. The complete CP genome of P. thomsonii has been reported [19], and we can use these data for subsequent experimental comparison and verification, and to conduct further analysis for the identification of the two species. Therefore, the comparative analysis and marker development of CP genome of Pueraria DC.…”

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confidence: 99%

Chloroplast genomes of two Pueraria DC. species: sequencing, comparative analysis and molecular marker development

Yang

et al. 2021

FEBS Open Bio

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Puerariae lobatae radix (Ge-Gen in Chinese) and Puerariae thomsonii radix (Fen-Ge) are widely used as medicine and health products, particularly in Chinese medicine. Puerarin and daidzein are the primary bioactive compounds in Puerariae radix. These isoflavones have been used to treat cardiovascular and cerebrovascular diseases, hypertension, diabetes, and osteoporosis. The content of puerarin in Ge-Gen is about six times higher than that in Fen-Ge, so its use has a higher pharmacological effect. It is therefore of great importance to effectively distinguish between these two species. However, because their basal plants, P. lobata (Willd.) Ohwi and P. thomsonii Benth., possess an extremely similar appearance, and detecting the level of chemical constituents is just a rough distinction, it is necessary to develop more efficient identification approaches. Here the complete chloroplast genomes of P. lobata and P. thomsonii were deciphered, including sequencing, assembly, comparative analysis, and molecular marker development. The results showed that they are 153,393 and 153,442 bp in length, respectively; both contain 124 annotated genes, including eight encoding rRNA, 29 encoding tRNA, and 87 encoding proteins. Phylogenetic analysis showed that they form a clade, indicating that they originate from the same ancestor. After obtaining 10 intergenic/intronic regions with a genetic distance greater than 0.5 cm, primers were designed to amplify regions of high variability in P. lobata and P. thomsonii. Finally, a 60-bp differential base fragment, located in the intron of rpl16, was developed as a molecular marker to efficiently distinguish between these two species.Puerariae lobatae radix, known as Ge-Gen in Chinese, is a popular traditional Chinese herbal medicine that was first described in the Shennong Herbal Classic. The genus Pueraria DC. belongs to the Fabaceae family and comprises about 20 species worldwide. It is mainly distributed in East Asian countries, among which China is the distribution center, accounting for 11 species. The dried roots of Ge-Gen have been widely used for the treatment of influenza, muscle stiffness, and other sicknesses [1]. Owing to a multi-origin traditional Chinese medicine, there are two Pueraria species: Pueraria lobata (Willd.) Ohwi and Pueraria thomsonii Benth., whose roots were considered the main source of Ge-Gen because of the wide distribution and

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confidence: 99%

Chloroplast genomes of two Pueraria DC. species: sequencing, comparative analysis and molecular marker development

Yang

et al. 2021

FEBS Open Bio

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“…lobata and P. montana var. thomsonii [ 18 – 20 ]. The GC content of these plastomes was 35.4%, except for P. mirifica A. Shaw and Suvat that was 35.5%.…”

Section: Resultsmentioning

confidence: 99%

“…To better determine the phylogenetic position of P. montana var. lobata and other varieties, we reconstructed a phylogeny using 47 chloroplast genomes, including the representatives of the major subclades of legume species referring to the previous studies [ 16 , 18 – 20 ]. Twenty-one previously published plastomes were downloaded from the NCBI GenBank database ( https://www.ncbi.nlm.nih.gov/ ) (Table S8).…”

Section: Methodsmentioning

confidence: 99%

Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence

et al. 2023

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Background Pueraria montana var. lobata (kudzu) is an important food and medicinal crop in Asia. However, the phylogenetic relationships between Pueraria montana var. lobata and the other two varieties (P. montana var. thomsonii and P. montana var. montana) remain debated. Although there is increasing evidence showing that P. montana var. lobata adapts to various environments and is an invasive species in America, few studies have systematically investigated the role of the phylogenetic relationships and evolutionary patterns of plastomes between P. montana var. lobata and its closely related taxa. Results 26 newly sequenced chloroplast genomes of Pueraria accessions resulted in assembled plastomes with sizes ranging from 153,360 bp to 153,551 bp. Each chloroplast genome contained 130 genes, including eight rRNA genes, 37 tRNA genes, and 85 protein-coding genes. For 24 newly sequenced accessions of these three varieties of P. montana, we detected three genes and ten noncoding regions with higher nucleotide diversity (π). After incorporated publically available chloroplast genomes of Pueraria and other legumes, 47 chloroplast genomes were used to construct phylogenetic trees, including seven P. montana var. lobata, 14 P. montana var. thomsonii and six P. montana var. montana. Phylogenetic analysis revealed that P. montana var. lobata and P. montana var. thomsonii formed a clade, while all sampled P. montana var. montana formed another cluster based on cp genomes, LSC, SSC and protein-coding genes. Twenty-six amino acid residues were identified under positive selection with the site model. We also detected six genes (accD, ndhB, ndhC, rpl2, rpoC2, and rps2) that account for among-site variation in selective constraint under the clade model between accessions of the Pueraria montana var. lobata clade and the Pueraria montana var. montana clade. Conclusion Our data provide novel comparative plastid genomic insights into conservative gene content and structure of cp genomes pertaining to P. montana var. lobata and the other two varieties, and reveal an important phylogenetic clue and plastid divergence among related taxa of P. montana come from loci that own moderate variation and underwent modest selection.

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“…Although Egan and Pan divided it into a new genus of Haymondia based on morphological characters and phylogenetic studies (Egan and Pan 2015;Egan et al 2016), it was still incomplete in molecular biology research. The accurate identification of H. wallichii can ensure the quality of H. wallichii (Miao et al 2019) and different molecular techniques may lead to different phylogenetic results (Zhang et al 2020). Therefore, the study reported the complete chloroplast genome of the H. wallichii, and revealed its phylogenetic relationship with other Fabaceae plants to lay the foundation for future research of Haymondia.…”

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confidence: 98%

“…The accurate identification of H. wallichii can ensure the quality of H. wallichii (Miao et al. 2019 ) and different molecular techniques may lead to different phylogenetic results (Zhang et al. 2020 ).…”

mentioning

confidence: 99%

The first complete chloroplast genome of Haymondia wallichii (Fabaceae) and its phylogenetic analysis

Xian-jun

Xia

Yuan

et al. 2021

Mitochondrial DNA Part B

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Haymondia wallichii DC. was a scandent shrub. In this study, we sequenced the complete chloroplast (cp) genome of H. wallichii to investigate its phylogenetic relationship in Fabaceae. The total length of the cp genome was 153,668 bp, consisted of a large single copy (LSC) region of 84,310 bp, a small single copy (SSC) region of 17,918 bp, and a pair of inverted repeat regions (IRs) of 25,720 bp. The genome contained 132 genes, namely 37 tRNA genes, 87 protein-coding genes, and 8 rRNA genes. The overall GC content was 35.4%. The phylogenetic analysis indicated H. wallichii was closely related to Pueraria montana var. thomsonii and Pueraria montana var. lobata.

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Complete chloroplast genome sequence of Pueraria thomsonii, an important traditional Chinese medicine plant

Cited by 5 publications

References 10 publications

Chloroplast genomes of two Pueraria DC. species: sequencing, comparative analysis and molecular marker development

Chloroplast genomes of two Pueraria DC. species: sequencing, comparative analysis and molecular marker development

Comparative plastomes of Pueraria montana var. lobata (Leguminosae: Phaseoleae) and closely related taxa: insights into phylogenomic implications and evolutionary divergence

The first complete chloroplast genome of Haymondia wallichii (Fabaceae) and its phylogenetic analysis

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