Characterization of the complete chloroplast genome of Clematoclethra scandens subsp. actinidioides (Actinidiaceae).

Clematoclethra scandens subsp. actinidioides (Actinidiaceae) is an endemic medicinal species in China. Here, we first sequenced and characterized the complete chloroplast genome of C. scandens subsp. actinidioides. The chloroplast genome was 159,341 bp in length, containing a large single-copy of 88,351 bp and a small single-copy of 21,580 bp separated by a pair of identical inverted repeat regions of 24,705 bp each. A total of 131 genes were identified, including 84 protein-coding genes, 39 tRNA, and eight rRNA genes. The phylogenetic analysis of C. scandens subsp. actinidioides showed a relatively close relationship with Clematoclethra scandens subsp. hemsleyi.

Clematoclethra scandens subsp. actinidioides (Maximowicz) Y. C. Tang & Q. Y. Xiang 1890 is an endemic medicinal plant in the family Actinidiaceae, which is distributed in the temperate and subtropical regions in central and western China (Li et al. 2007; Yang et al. 2014). The roots of C. scandens subsp. actinidioides have long been used as an important traditional medicinal to treat chronic hepatitis, rheumatic arthritis, and hernia (Song et al. 2001). Previous studies have focused on the chemical composition, pollen morphology, and taxonomy for this species (Yang et al. 2014; Xiao et al. 2015). Due to its various flavonoids and triterpenoids, C. scandens subsp. actinidioides not only has a high medicinal value, but also has scientific research value as an endemic species (Xiao et al. 2015). Herein, we first sequenced and assembled the complete chloroplast genome of C. scandens subsp. actinidioides and analyzed its phylogenetic relationship.

The fresh leaves from a wild single tree of C. scandens subsp. actinidioides were collected from Feng River, Shaanxi Province (108°48′16.76″E, 33°50′22.77″N) and the voucher specimens were stored at Xi’an Botanical Herbarium under accession number XBH20200822 (http://www.xazwy.com/; Yongpeng Wu, Email: 43566351@qq.com). Total genomic DNA was extracted using CTAB method (Doyle and Doyle 1987) and sequenced with Illumina Hiseq 4000 platform. The chloroplast genome was de novo assembled using Novoplasty (Dierckxsens et al. 2019). The annotation was performed with the online annotation tool CPGAVAS2 (Shi et al. 2019). Phylogenetic analyses were carried out by maximum likelihood (ML) using MEGA v7.0 (Kumar et al. 2016) with 1000 bootstrap replicates.

The chloroplast genome of C. scandens subsp. actinidioides was a typical quadripartite circular molecule with a length of 159,341 bp, including a large single-copy region (LSC) of 88,351 bp and a small single-copy region (SSC) of 21,580 bp, and two 24,705 bp inverted repeat regions (IRs). A total of 131 genes were annotated, containing 84 protein-coding genes, 39 tRNA genes, and eight rRNA genes. Unexpectedly, we observed the chloroplast genome lacks clpP gene, which is consistent with C. scandens subsp. hemsleyi chloroplast genome in the genus Clematoclethra (Wang et al. 2016). The overall GC content of C. scandens subsp. actinidioides plastid genome is 38.3%, while the corresponding values of LSC, SSC, and IR regions are 38.9%, 37.1%, and 37.5%, respectively.

To confirm the phylogenetic position of C. scandens subsp. actinidioides, 14 chloroplast genome sequences of Actinidiaceae, Lardizabalaceae, and Passifloraceae were aligned by MEGA v7.0 (Kumar et al. 2016). The result indicated that C. scandens subsp. actinidioides was found to be relatively closely related to C. scandens subsp. hemsleyi chloroplast compared to other species of Actinidia genera in Actinidiaceae (Figure 1). The chloroplast genome information reported in this study provided fundamental data for the bioinformatics and systematics of the Actinidiaceae.

Figure 1.

Phylogenetic tree produced by maximum-likelihood (ML) analysis based on 15 chloroplast genome sequences. The following sequences were used: Actinidia melanandra MK863365 (Zhao et al. 2019), Actinidia deliciosa NC026691, Actinidia chinensis NC026690, Actinidia callosa var. henryi NC043861 (Wu et al. 2019), Actinidia arguta NC034913, Actinidia polygama NC031186 (Wang et al. 2016), Actinidia valvata NC050357 (Wang et al. 2016), Actinidia tetramera NC031187 (Wang et al. 2016), Clematoclethra scandens subsp. hemsleyi KX345299 (Wang et al. 2016), Saurauia tristyla MG912839, Saurauia tristyla NC044098, Akebia trifoliata NC029427 (Sun et al. 2016), Decaisnea insignis NC035941 (Li et al. 2017), Passiflora caerulea MT884000, and Clematoclethra scandens subsp. actinidioides OL457297.