Characterization of the complete chloroplast genome of sorrel (<i>Rumex acetosa</i>)

Gui, Ling‐Jian; Jiang, Shaofeng; Wang, Huaiping; Nong, Dong-Xin; Liu, Yingying

doi:10.1080/23802359.2018.1501297

Cited by 5 publications

(8 citation statements)

References 19 publications

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“…The plastomes in Calligonum are highly conserved and ranged in size of 161,184 to 162,535 bp. When compared to the plastomes of the other Polygonaceae genera (e.g., Fagopyrum [30], Rumex [31], Oxyria [32]), all the plastomes generated in this study exhibited typical plastome structure, gene order and content (Fig. 1).…”

Section: Plastome Featuresmentioning

confidence: 79%

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Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

Song

Burgess

et al. 2020

BMC Plant Biol

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Background: Calligonum (Polygonaceae) is distributed from southern Europe through northern Africa to central Asia, and is typically found in arid, desert regions. Previous studies have revealed that standard DNA barcodes fail to discriminate Calligonum species. In this study, the complete plastid genomes (plastome) for 32 accessions of 21 Calligonum species is sequenced to not only generate the first complete plastome sequence for the genus Calligonum but to also 1) Assess the ability of the complete plastome sequence to discern species within the group, and 2) screen the plastome sequence for a cost-effective DNA barcode that can be used in future studies to resolve taxonomic relationships within the group. Results: The whole plastomes of Calligonum species possess a typical quadripartite structure. The size of the Calligonum plastome is approximately 161 kilobase pairs (kbp), and encodes 113 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Based on ML phylogenetic tree analyses, the complete plastome has higher species identification (78%) than combinations of standard DNA barcodes (rbcL + matK + nrITS, 56%). Five newly screened gene regions (ndhF, trnS-G, trnC-petN, ndhF-rpl32, rpl32-trnL) had high species resolution, where ndhF and trnS-G were able to distinguish the highest proportion of Calligonum species (56%). Conclusions: The entire plastid genome was the most effective barcode for the genus Calligonum, although other gene regions showed great potential as taxon-specific barcodes for species identification in Calligonum.

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Section: Plastome Featuresmentioning

confidence: 79%

“…1). In addition, the GC content of Calligonum (37.50%) was similar to that of Fagopyrum (37.80-38.0%) [30], Rumex acetosa (37.20%) [31], and equal to that of Oxyria sinensis (37.50%) [32]. Inverted repeat (IR) contraction and expansion is a common evolutionary phenomenon and may cause variation in plastome length [33].…”

Section: Plastome Featuresmentioning

confidence: 82%

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

Song

Burgess

et al. 2020

BMC Plant Biol

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“…Forst.) Meisn ( Schuster et al, 2018 ), Oxyria sinensis Hemsl ( Luo et al., 2017 ), Rumex japonicus Houtt ( Gurusamy et al., 2020 ), R. acetosa L. ( Gui et al., 2018 ) and R. palmatum L. ( Fan et al., 2016 ). A total of 12 plastomes were used for final analyses.…”

Section: Methodsmentioning

confidence: 99%

Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

Yang

Liu

et al. 2021

Plant Diversity

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The phylogenetic position of the monotypic woody Parapteropyrum (Polygonaceae) remains controversial. Parapteropyrum has been thought to be closely related to the woody genera of the tribe Atraphaxideae, although some evidence indicates that it nests within the herbal buckwheat genus Fagopyrum of tribe Polygoneae. In this study, we used plastome data to determine the phylogenetic position of Parapteropyrum ( Fagopyrum ) tibeticum . Different reference species were used to assemble plastomes of three species currently placed in the tribe Ataphaxideae: Parapteropyrum ( Fagopyrum ) tibeticum , Atraphaxis bracteata and Calligonum ebinuricum . Once assembled, plastomes were characterized and compared to plastomes of 12 species across the family Polygonaceae. Phylogenetic analyses of Polygonaceae were performed using whole plastome, all plastome genes, and single-copy genes. Plastomes assembled using different reference plastomes did not differ; however, annotations showed small variation. Plastomes of Parapteropyrum ( Fagopyrum ) tibeticum , A. bracteata and C. ebinuricum have the typical quadripartite structure with lengths between 159,265 bp and 164,270 bp, and a total number of plastome genes of about 130. Plastome microsatellites (SSR) ranged in number from 48 to 77. Maximum Likelihood and Bayesian analyses of three plastome data sets consistently nested Parapteropyrum within the genus Fagopyrum . Furthermore, our analyses indicated that sampled woody genera of the family Polygonaceae are polyphyletic. Our study provides strong evidence that the woody Parapteropyrum tibeticum , which is distantly related to woody genera sampled here, should be taxonomically placed under Fagopyrum as Fagopyrum tibeticum .

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“…The clean data was de novo assembled using NOVOPlasty v3.1 CONTACT Xiaoxuan Tian tian_xiaoxuan@tjutcm.edu.cn Tianjin State Key Laboratory of Modern Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Poyang Lake Road 10, Tianjin 301617, China (Dierckxsens et al 2017) and GetOrganelle pipeline (Jin et al 2018). Then, the resulting contigs were identified and rearranged by mapping to reference genome Rumex acetosa (Gui et al 2018) (Accession number: MH359405). Annotation of the chloroplast genome was performed using CpGAVAS2 (Shi et al 2019) and GeSeq (Tillich et al 2017).…”

mentioning

confidence: 99%

“…Then, the resulting contigs were identified and rearranged by mapping to reference genome Rumex acetosa (Gui et al. 2018 ) (Accession number: MH359405). Annotation of the chloroplast genome was performed using CpGAVAS2 (Shi et al.…”

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confidence: 99%

The complete chloroplast genome of a medicinal resource plant (Rumex crispus)

Tan

Gao

Yang

et al. 2019

Mitochondrial DNA Part B

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Rumex crispus has high medicinal value which belongs to the family Polygonaceae. We sequenced the complete chloroplast genome of R. crispus, which is 158,851 bp in length. A total of 111 unique genes have been predicted in the chloroplast genome of this species, consisting of 77 protein-coding sequences, 30 tRNA and 4 rRNA genes. A maximum likelihood (ML) phylogenetic tree based on 80 proteincoding genes of 18 Polygonaceae species showed the phylogenetic position of R. crispus within the family Polygonaceae. These results facilitate population and biological studies of R. crispus and benefit further investigations of this important species.

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Characterization of the complete chloroplast genome of sorrel (Rumex acetosa)

Cited by 5 publications

References 19 publications

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

Complete plastome sequencing resolves taxonomic relationships among species of Calligonum L. (Polygonaceae) in China

Plastome and phylogenetic relationship of the woody buckwheat Fagopyrum tibeticum in the Qinghai-Tibet Plateau

The complete chloroplast genome of a medicinal resource plant (Rumex crispus)

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