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. 2022 Aug 12;7(8):1477–1478. doi: 10.1080/23802359.2021.1915198

The complete chloroplast genome of a medical herb, Gentianopsis paludosa (Hook. f.) Ma (Gentianaceae), from Qinghai-Tibet Plateau in China

Hongyu Wang a, Jinping Li a, Yang Zeng a,b, Ruifeng Zhang a, Junyan Zhang a, Likuan Liu a,✉
PMCID: PMC9377260  PMID: 35979391

Abstract

Gentianopsis paludosa (Hook. f.) Ma (Gentianaceae) is one of the genuine medicinal materials in Qinghai-Tibet Plateau, China. Here we report the first chloroplast (cp) genome of G. paludosa using Illumina NovaSeq 6000 platform. The length of its complete cp genome is 151,568 bp, containing four sub-regions; a large single copy region (LSC) of 82,834 bp and a small single copy region (SSC) of 17,928 bp are separated by a pair of inverted repeat regions (IRs) of 25,403bp. The complete cp genome of G. paludosa contains 130 genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The overall GC content of the cp genome is 37.8%. The phylogenetic analysis, based on 23 cp genomes, suggested that G. paludosa is closely related to G. grandis (H. Smith) Ma and Swertia species.

Keywords: Gentianopsis paludosa, chloroplast genome, Gentianaceae, Qinghai-Tibet Plateau, phylogenetic trees

Gentianopsis Ma (Gentianaceae) includes about 24 species distributed in the Asia, Europe, North America. There are only five Gentianopsis species distributed in China (He 1988). G. paludosa, known as the ‘Tibetan capillaris’, using whole herb as medicine, is one of the common Tibetan herbal medicines used in the treatment of gallbladder and liver diseases (Song 1986). It is mainly distributed in flood land, forest margins and meadows area (altitude 1180–4600 m) in Tibet, Qinghai, Sichuan, Yunnan Provinces and other places in north of China (Yang 1991; He 1988).

To study the systematic position and genetic background of G. paludosa, we sequenced the G. paludosa DNA and obtained its complete chloroplast (cp) genome. The voucher specimen of G. paludosa was collected from the riverside in the Yuer village in Xianmi township, Menyuan County, Qinghai Province, China, on August 11 in 2019 (alt. 2683 m, E101°58′6.69″, N37°16′41.76″), and the specimen deposited at Herbarium, School of Life Sciences, Zhengzhou University, the voucher number is ZZU2019-6306. The total DNA was isolated from leaf materials of the voucher specimen using the plant genomic DNA extraction kit (Solarbio LIFE SCIENCES, China). The DNA concentration and quality were then measured by NanoDrop2000c micro-uv spectrophotometer (Thermo Scientific, America). The DNA was sequenced at Novogene Biotech Co. (Beijing, China) using the Illumina NovaSeq 6000 platform with a 150-bp shotgun library. Finally, 2.34 G of 150-bp paired-end raw reads of G. paludosa were obtained, processed and assembled following the method of Nicolas et al. (2017). The raw sequencing reads is deposited in SRA, and the number is PRJNA656080. The assembled contigs were mapped to the reference cp genome (G. grandis, GenBank accession no. NC_049879) and annotated using Geneious Prime software(https://www.geneious.com). The border regions between the large single copy region (LSC), the small single copy region (SSC) and two inverted repeat regions (IRs) were validated by PCR amplifications and Sanger sequencing. The complete cp genome of G. paludosa is 151,568bp in length, and it released to NCBI (GenBank accession no.MT921831). It contains two IRs of 25,403 bp, separated by a LSC of 82,834bp and a small SSC of 17,928bp. The cp genome of G. paludosa is comprised of 130 genes, including 85 protein-coding genes, 8 rRNA genes, and 37 tRNA genes. The overall GC content of the cp genome is 37.8%, while the corresponding values of the LSC, SSC, and IR regions are 35.8%, 31.8%, and 43.3%.

The cp genome of G. paludosa and 22 cp genome sequences (downloaded from GenBank) were aligned using MAFFT (Katoh and Standley 2013) and then constructed phylogenetic trees using neighbor-joining (NJ) and maximum likelihood (ML) methods in MEGA7 (Kumar et al. 2016). Rhodiola rosea (Crassulaceae) and Haloxylon persicum (Chenopodiaceae) were selected as outgroups. The results showed that G. paludosa was sister group to G. grandis and they were close related to Halenia corniculata (Figure 1). The phylogenetic analysis was consistent with previous studies (Park et al. 2019; Chassot et al. 2001).

Figure 1.

Figure 1.

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Phylogenetic tree of 23 species based on complete chloroplast genome sequences using NJ (with 1000 replicates) and ML (with 1000 replicates) methods. The numbers below the branches indicate the corresponding bootstrap support values from the ML and NJ trees. Haloxylon persicum (NC_027669) and Rhodiola rosea (NC_041671) are outgroups.

Funding Statement

This work was supported by the Natural Science Foundation of Qinghai Provincial Science and Technology Department, China [2017-ZJ-742], Chun Hui Program of Ministry of Education of China [Z2019070], The support from the innovative team of comprehensive utilization and Development of medicinal plant resources.

Disclosure statement

No potential conflict of interest was reported by the authors.

Data availability statement

The data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/), under the accession no. MT921831. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA656080, SRR13089735, and SAMN15770945 respectively.

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

The data that support the findings of this study are openly available in GenBank of NCBI at (https://www.ncbi.nlm.nih.gov/), under the accession no. MT921831. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA656080, SRR13089735, and SAMN15770945 respectively.

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