Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis

Cui, Ning; Liao, Baosheng; Liang, Conglian; Li, Shifeng; Zhang, Hao; Xu, Jiang; Li, Xiwen; Chen, Shilin

doi:10.1016/s1875-5364(20)30068-6

Cited by 27 publications

(26 citation statements)

References 34 publications

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“…The highly variable regions of the cp genome can be used to identify closely related species and provide abundant information for further phylogenetic studies (Cui et al, 2020). Setting A. membranaceus var.…”

Section: Comparative Genome Analysis and Sequence Variationmentioning

confidence: 99%

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

Tian

et al. 2021

Front. Genet.

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Astragalus is the largest genus in Leguminosae. Several molecular studies have investigated the potential adulterants of the species within this genus; nonetheless, the evolutionary relationships among these species remain unclear. Herein, we sequenced and annotated the complete chloroplast genomes of three Astragalus species—Astragalus adsurgens, Astragalus mongholicus var. dahuricus, and Astragalus melilotoides using next-generation sequencing technology and plastid genome annotator (PGA) tool. All species belonged to the inverted repeat lacking clade (IRLC) and had similar sequences concerning gene contents and characteristics. Abundant simple sequence repeat (SSR) loci were detected, with single-nucleotide repeats accounting for the highest proportion of SSRs, most of which were A/T homopolymers. Using Astragalus membranaceus var. membranaceus as reference, the divergence was evident in most non-coding regions of the complete chloroplast genomes of these species. Seven genes (atpB, psbD, rpoB, rpoC1, trnV, rrn16, and rrn23) showed high nucleotide variability (Pi), and could be used as DNA barcodes for Astragalus sp. cemA and rpl33 were found undergoing positive selection by the section patterns in the coded protein. Phylogenetic analysis showed that Astragalus is a monophyletic group closely related to the genus Oxytropis within the tribe Galegeae. The newly sequenced chloroplast genomes provide insight into the unresolved evolutionary relationships within Astragalus spp. and are expected to contribute to species identification.

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Section: Comparative Genome Analysis and Sequence Variationmentioning

confidence: 99%

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

Tian

et al. 2021

Front. Genet.

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“…Salvia plants were selected referring to previous studies [22,[34][35][36][37] by considering extraordinary characteristics, including genetic diversity, global distribution and medicinal signi cance for treating cardiovascular diseases. The sample selection in this study was primarily based on the article by Xiao et al [13], and few other species with de nite applications were also supplemented in consideration of the species distribution and systematic taxonomy of Salvia.…”

Section: Plant Materials and Dna Extractionmentioning

confidence: 99%

“…The chloroplast (cp) genome of S. plebeia (NC050929) was assembled in our previous study [22]. Taking this work as a guidance, the DNA sample pre-treatment, whole genome sequencing, cp genome assembly, junction validation, and cp genome annotation were performed in turn.…”

Section: Sequencing Chloroplast Genome Assembly and Annotationmentioning

confidence: 99%

The Biology of Medicinal Resource Substitution in Salvia

Cui¹,

Chen²,

Bao-sheng³

et al. 2021

Preprint

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Background: The decrease of wild reserves and the sharp increase of market demand have led to resource substitution, but it is still not clear how to discover medicinal alternative resources. Here we reveal the biology of medicinal resource substitution in the case of Salvia.Methods: A hypothesis was put forward that phylogeny and ecology were the main factors which determined alternative species selection. Phylogenetic analysis was performed based on chloroplast genomes. Spatial climatic pattern was assessed through three mathematical models. Results: S. miltiorrhiza and alternative species were mainly located in Clade 3 in topology, and their growth environment was clustered into an independent group 3 inferred from Principal Component analysis. Correlation and Maxent major climate factor analyses showed that the ecological variations within each lineage were significantly smaller than the overall divergent between any two lineages. Mantel test reconfirmed the inalienability between phylogeny and ecology (P = 0.002). Only the species that are genetically and ecologically related to S. miltiorrhiza can form a cluster with it. Conclusion: Phylogenetic relationship and geographical climate work together to determine which species has the potential to be selected as substitutes. Other medicinal plants can learn from this biology towards developing alternative resources.

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“…Previous studies have shown that many types of secondary coumarin compounds that occur in M. exotica are widely used in the medical, spice, and seasoning industries. The chloroplast (cp) genome can be used as a tool for phylogenetic analysis, and it can be used for other usages such as species identification (Li et al 2015) or highly variable regions selection (Cui et al 2020). In the present study, we assembled the complete cp genome of M. exotica to provide genomic and genetic sources for further research.…”

mentioning

confidence: 99%

“… 2015 ) or highly variable regions selection (Cui et al. 2020 ). In the present study, we assembled the complete cp genome of M. exotica to provide genomic and genetic sources for further research.…”

mentioning

confidence: 99%

Characterization of the complete chloroplast genome of Murraya exotica (Rutaceae) from Yunnan Province, China

Zhou

2021

Mitochondrial DNA Part B

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Murraya exotica L. (Rutaceae) has important horticultural and medicinal values. Here, we reported the complete chloroplast (cp) genome of M. exotica using the next-generation sequencing method. The cp genome is 160,179 bp in length, including a large single-copy region (LSC, 87,726 bp), a small singlecopy region (SSC, 18,465 bp), and a pair of inverted repeats (IR) regions 26,994 bp. A maximum-likelihood phylogenomic analysis showed that M. exotica was sister to Murraya paniculate. These findings will provide useful information for further investigation of cp genome evolution in Murraya.

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Complete chloroplast genome of Salvia plebeia: organization, specific barcode and phylogenetic analysis

Cited by 27 publications

References 34 publications

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

Characterization and Comparative Analysis of Complete Chloroplast Genomes of Three Species From the Genus Astragalus (Leguminosae)

The Biology of Medicinal Resource Substitution in Salvia

Characterization of the complete chloroplast genome of Murraya exotica (Rutaceae) from Yunnan Province, China

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