The complete chloroplast genome of Tibetan medicine Gentianopsis paludosa.

Gentianopsis paludosa (Mum.) Ma is an important species in Tibetan folk medicine, but its wild populations are shrinking roughly due to the increasing demand for it. Gentianopsis paludosa is presently at risk of over-exploitation, so it needs urgent conservation. Here, we report the complete sequence of the chloroplast genome of G. paludosa. The genome was 51,121 bp in length with 129 genes comprising 84 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of G. paludosa chloroplast genome was is 36.67%. The phylogenomic analysis suggested that G. paludosa forms a clade with species in Halenia and Swertia, indicating that the G. paludosa is more closely related to Halenia and Swertia than that of Gentiana.

Gentianopsis paludosa (Mum.) Ma, belonging to the family Gentianaceae, is an important species in Tibetan folk medicine. Tibetan people called it jiadi, jihedou, etc. (Lu et al. 2016). Its natural range is on the Qinghai-Tibetan Plateau of China with a high altitude (2500–4500 m) (Liu 1996). The whole herb of G. paludosa is widely used for treatment of conjunctivitis, hepatitis, nephritis, gastroenteritis, dyspepsia, fever, influenza, and diarrhea due to the high levels of oleanolic acid, gentiopicrin, and swertiamarin contained in G. paludosa (Guo 1987; Tu et al. 2005; Cai et al. 2009). Moreover, researchers found that G. paludosa had anti-diarrhea and antibacterial activity (Wang et al. 2005), which promoted the increasing demand for it. As a result of the increasing demand for it, G. paludosa is presently at risk of over-exploitation (Liu 1996). To date, previous studies of G. paludosa have mainly focused on chemical composition (Wang et al. 2005; Vaidya et al. 2009), genetic diversity (Yu et al. 2012), pharmacodynamics (Lu et al. 2017), and others (Xue and Li 2011). Thus, it is useful to know more genetic information about G. paludosa to carry out conservation, genetic improvement, and sustainable management for this risk species.

We sampled the wild individual of G. paludosa from Xinping village (101°37.556′ E, 36°34.460′ N, 2510 m), Huangzhong country in Qinghai province of China (Voucher specimen: QHGC20190824, HNWP). Genome DNA was extracted using modified CTAB method, which was fragmented to construct paired-end (PE) libraries. Genome sequences were screened out and assembled with the SPAdes. And then, annotation was performed with DOGMA. The annotated genomic sequence had been submitted to GenBank with the accession number SRR10572767.

The complete chloroplast genome length of G. paludosa is 151,121 bp, consisting of two inverted repeats (IR, 25,224 bp) separated by a large single copy region (LSC 82,813 bp) and a small single copy region (SSC 17,860 bp). The overall CC content is 36.67%. The chloroplast genome includes a total of 129 functional genes including 84 protein-coding genes, 37 tRNA and eight rRNA. A total of 18 genes were duplicated in the IR regions including seven tRNA, four rRNA, and seven protein-coding genes. The genome organization, gene/intron content, and gene relative positions of the newly sequenced plastid genome were almost identical to other Gentianaceae species.

We used the complete chloroplast genomes of G. paludosa and 18 other species from Gentianaceae to reconstruct the Phylogenetic tree. And, Carissa macrocarpa (Apocynaceae) was used as an outgroup. Maximum-likelihood (ML) analysis demonstrated that G. paludosa formed a clade with species in Halenia and Swertia with high bootstrap values (Figure 1), indicating that the G. paludosa was more closely related to Halenia and Swertia than that of Gentiana.

Figure 1.

Maximum-likelihood phylogenetic tree based on 20 complete chloroplast genome sequences.