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First complete chloroplast genome of the rare medicinal plant Schnabelia tetrodonta.

ABSTRACT: Schnabelia tetrodonta is a medicinal plant used in traditional Chinese medicine. However, the molecular biology data of the species was too scarce to bioprospect the medicinal species. In this study, the first complete chloroplast genome (cp) of S. tetrodonta was sequenced and assembled based on the next generation sequencing. The cp genome is 157,004 bp in length, including a large single-copy (LSC) region of 83,605 bp, a small single-copy (SSC) region of 36,899 bp, and a pair of inverted repeat (IR) regions of 18,250 bp each. The genome encodes 134 genes, including 90 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The GC content of whole genome is 37.80%. The phylogenetic analysis based on 20 complete cp sequences (19 genome sequences from the Teucrioideae of Lamiaceae and an outgroup of Ipomoea purpurea) revealed that S. tetrodonta was closely related to S. oligophylla.

SUBMITTER: Ren F

PROVIDER: S-EPMC8462896 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature

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First complete chloroplast genome of the rare medicinal plant Schnabelia tetrodonta.

Ren Fengming F Wang Liqiang L Zhuo Wei W Lu Shenge S Zhu Xiaofu X Liu Chao C Yang Meisen M

Mitochondrial DNA. Part B, Resources 20210920 10

Schnabelia tetrodonta is a medicinal plant used in traditional Chinese medicine. However, the molecular biology data of the species was too scarce to bioprospect the medicinal species. In this study, the first complete chloroplast genome (cp) of S. tetrodonta was sequenced and assembled based on the next generation sequencing. The cp genome is 157,004 bp in length, including a large single-copy (LSC) region of 83,605 bp, a small single-copy (SSC) region of 36,899 bp, and a pair of ...[more]

PMID: 34568558

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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

First complete chloroplast genome of the rare medicinal plant Schnabelia tetrodonta.

Publications

First complete chloroplast genome of the rare medicinal plant <i>Schnabelia tetrodonta</i>.

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