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The complete chloroplast genome of Rubus setchuenensis, an edible and medicinal dual-purpose wild plant.

ABSTRACT: Rubus setchuenensis Bureau et Franch. is important in phylogeny and evolution amongst genus Rubus L. (Rosaceae) plants. The chloroplast genome of R. setchuenensis reported in this study is 156,231 bp in size, with an average GC content of 37.19%. The complete chloroplast genome has a typical quadripartite structure, including a large single copy (LSC) region (85,829 bp) and a small single copy (SSC) region (18,860 bp), which are separated by a pair of inverted repeats (IRs, 25,771 bp). This plastome contains 129 different genes, including 85 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The phylogenetic analysis of 20 chloroplast genomes from genera Fragaria, Rosa and Rubus of the family Rosaceae suggested that R. setchuenensis clustered into one clade with the other three species of section Malachobatus Focke, and then grouped with four species of section Idaeobatus Focke, while species from Fragaria and Rosa were classified into a group, separately.

SUBMITTER: Zhu YA

PROVIDER: S-EPMC8788380 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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The complete chloroplast genome of Rubus setchuenensis, an edible and medicinal dual-purpose wild plant.

Zhu Ying-An YA Li Chunhua C Wang Shiyu S Lei Liping L Xiao Jingxiu J

Mitochondrial DNA. Part B, Resources 20220124 1

Rubus setchuenensis Bureau et Franch. is important in phylogeny and evolution amongst genus Rubus L. (Rosaceae) plants. The chloroplast genome of R. setchuenensis reported in this study is 156,231 bp in size, with an average GC content of 37.19%. The complete chloroplast genome has a typical quadripartite structure, including a large single copy (LSC) region (85,829 bp) and a small single copy (SSC) region (18,860 bp), which are separated by a pair of inverted repeats (IRs, ...[more]

PMID: 35087936

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Project description:Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.

Dataset Information

The complete chloroplast genome of Rubus setchuenensis, an edible and medicinal dual-purpose wild plant.

Publications

The complete chloroplast genome of <i>Rubus setchuenensis</i>, an edible and medicinal dual-purpose wild plant.

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