Characterization of the complete chloroplast genome sequence of Hemsleya zhejiangensis (cucurbitaceae), a rare and endangered wild plant species in Zhejiang province, China

Abstract

Hemsleya zhejiangensis is a rare and endangered plant species which is listed as a key protected wild plant in Zhejiang province, China. In our present study, we assembled the complete chloroplast (CP) genome of H. zhejiangensis using high-throughput sequencing data. The whole genome sequence of H. zhejiangensis is 157,289 bp in size, with a GC content of 37.1%. Sequencing analyses reveal that the CP genome encodes 133 genes, including 84 protein-coding genes, 8 rRNA genes, 37 tRNA genes, and four pseudogenes. Phylogenetic analysis results indicate that H. zhejiangensis is clustered with H. lijiangensis, with a support value of 100%, and they are sister to the three Gynostemma species.

The genus Hemsleya belongs to the family Cucurbitaceae and is comprised of about 27 plant species which are distributed in subtropical or tropical Asia (Wu et al. 2011). Hemsleya zhejiangensis is a plant with enlarged tubers, slender stems, and 5–9 foliolates. Hemsleya zhejiangensis is a wild plant species of extremely small population with fewer than 5000 individuals, and it is now listed as a key protected species in Zhejiang province, China. Hemsleya zhejiangensis is mainly distributed in counties of Taishun, Longyou, Jingning, and Yunhe, and it is used as a medicinal herb in fork medicine for treating enteritis, bacillary dysentery, coronary heart disease, and tracheitis (Zheng 1985; Yang et al. 2014). In our present study, we assembled the complete chloroplast (CP) genome of H. zhejiangensis, and phylogenetic analysis was performed to understand its relationship with other species.

Leaf samples were collected from Guanshan (27°53′42′′N, 119°31′51′′E), Yunhe county, Zhejiang province, China. A voucher specimen designated CHS2019022 is stored at the Molecular Biology Laboratory in Taizhou University. Genomic DNA isolation was performed following the CTAB-based method by Doyle and Doyle (1987), and a DNA library for high-throughput sequencing was then constructed following manufacturer's instructions. Totally, 6.8 Gb raw reads were generated using an Illumina Hiseq X Ten platform, and the clean reads were used for de novo assembly by a Perl program namely NOVOPlasty (Dierckxsens et al. 2017). Dual Organellar GenoMe Annotator (DOGMA) (Wyman et al. 2004) was applied to annotate the CP genome. tRNAscan-SE and ARAGORN were used for prediction of tRNAs (Lowe and Eddy 1997; Laslett and Canback 2004).

The results indicated that the whole CP genome of H. zhejiangensis (GenBank accession: MN414239) was 157,289 bp in length. The quadripartite structure was comprised of a large single copy, a small single copy, and two inverted repeats, and their sizes were 86,536 bp, 26,233 bp, and 44,520 bp, respectively. The CP genome encoded 133 genes, including 84 protein-coding genes, 37 tRNA genes, eight rRNA genes, and four pseudogenes (psbC, psbL, infA, and ycf1). Three protein-coding genes, clpP, rps12, and ycf3, had two introns, while other 16 genes (atpF, ndhA, ndhB, petB, petD, rpl2, rpl16, rpoC1, rps12, rps16, trnA-UGC, trnG-UCC, trnI-GAU, trnk-UUU, trnL-UAA, and trnV-UAC) contained only one intron.

To reveal the phylogenetic status with other related plant species, whole genome sequences of Platycodon grandiflorus (Campanulaceae) and 20 Cucurbitaceae plants were obtained from National Center for Biotechnology Information. The 20 Cucurbitaceae plants included species from genera of Hemsleya, Gynostemma, Momordica, Siraitia, Coccinia, Lagenaria, Citrullus, Hodgsonia, Trichosanthes, Cucurbita, Cucumis. A phylogenetic tree was generated by the maximum likelihood method (ML) using PhyML 3.1 (Guindon et al. 2010). The best DNA evolution model was GTR + G + I, which was computed by jModelTest 2 (Darriba et al. 2012). The phylogenomic analysis results revealed that the 22 plants were divided into 12 groups. Hemsleya zhejiangensis was closely related to H. lijiangensis, with a bootstrap support of 100%, and they were grouped with three Gynostemma species, with 100% bootstrap support (Figure 1).

Figure 1.

A maximum likelihood tree based on the complete chloroplast genome sequences of Hemsleya zhejiangensis and other Cucurbitaceae species, with Platycodon grandiflorus (Campanulaceae) as the outgroup. The numbers next to nodes are bootstrap support values.

Disclosure statement

No potential conflict of interest was reported by the authors.