The complete chloroplast genome sequences of three Clematis species (Ranunculaceae)

Abstract

Clematis is an important horticultural and medicinal genus in Ranunculaceae. Here, we report three complete chloroplast genome sequences of C. acerifolia, C. smilacifolia, and C. uncinata. The chloroplast genomes were found to be 159,552 bp, 159,624 bp, and 159,524 bp in length, and GC contents were 37.9, 37.9, and 38.0%, respectively. The sequence of each species contained 112 unique genes, including 29 tRNA, 4 rRNA, and 79 protein-coding genes. These chloroplast genome sequences provide knowledge to the genetic variations and evolution of Clematis and Ranunculaceae.

Keywords:

• Clematis
• complete chloroplast genome
• phylogeny
• Ranunculaceae

Clematis is one of the largest genera in the buttercup family (Ranunculaceae) with about 300 species distributed worldwide (Tamura 1995; Johnson 1997; Wang and Li 2005). Many Clematis species are traditional chinese medicines (TCM) and their garden hybrids are popular to gardeners. Here, we report three complete chloroplast genome sequences of Clematis. Among them, C. acerifolia is an endangered species narrowly endemic to Beijing (López-Pujol et al. 2005), C. uncinata is an important TCM species (Li et al. 2014), and C. smilacifolia is rare in southern China (Wang 2006).

Fresh young leaves of Clematis acerifolia, C. smilacifolia, and C. uncinata were collected from Shidu, Beijing (N 39°38′51″, E 115°35′58″), Longzhou, Guangxi (N 22°18′57″, E 106°55′24″, and Guilin, Guanxi (N 25°13′52″, E 110°12′31″, respectively. Voucher specimens were deposited in the Herbarium of Beijing Forestry University (BJFC) (under collection numbers of L. Xie 2012008, L. Xie 20151206, and L. Xie 20151171). Genomic DNAs were extracted using CTAB method (Doyle and Doyle 1987), and 2 × 150 bp pair end sequencing was performed on an Illumina HiSeq 4000 platform at Novogene (http://www.novogene.com, China). We used map function of Geneious R11 (Kearse et al. 2012) to extract chloroplast reads using published chloroplast genome from Clematis as references. Filtered chloroplast reads were used for de novo assembly with Geneious R11. Gaps were bridged using fine tuning function of Genious R11. The three chloroplast sequences were then annotated using Plann (Huang and Cronk 2015) and annotations were verified by Genious R11.

The plastome of C. acerifolia was 159,552 bp in length containing a large single-copy (LSC) region of 79,315 bp, a small single-copy (SSC) region of 18,145 bp, and two inverted repeats (IR) of 31,046 bp. The genome contained 112 functional genes, including 79 protein-coding genes, 29 tRNA genes, and 4 rRNA genes. The sequence GC content was 37.9%. The length of plastome sequence of C. smilacifolia was 159,624 bp, which consisted of contained LSC region of 79,398 bp, SSC region of 18,125 bp, and IR regions of 31,050 bp. Gene numbers and GC content were detected in the same way as C. acerifolia. In C. uncinata, the plastome sequence was 159,524 bp in length. The LSC, SSC, and IR regions were 79,349 bp, 18,099 bp, and 31,038 bp, respectively. The gene numbers were the same with the other two tested species and the GC content was 38.0%. Gene inversions, transpositions, and IR expansion of the three samples were consistent with (Liu, Ding et al. 2018; Liu, He et al. 2018).

Complete chloroplast genome sequences of the other genera of Ranunculaceae available from GenBank were mined for phylogenomic analysis. Bayesian inference and parsimony analyses were conducted for phylogeny reconstruction (Figure 1). The sequence alignment and all the settings of parsimony and Bayesian analyses were the same with Liu, Ding et al. 2018a. Phylogenetic framework of Clematis as well as Ranunculaceae were consistent with previous studies (Miikeda et al. 2006; Wang et al. 2009; Xie et al. 2011; Lehtonen et al. 2016; Jiang et al. 2017; Liu, Ding et al. 2018; Liu, He et al. 2018).

Figure 1. Bayesian phylogram of Clematis as well as Ranunculaceae species inferred from the complete plastome sequences. Branches with 100% PP value and 100 parsimony bootstrap value are shown in bold lines.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by the Medium- and Long-term Scientific Study Projects for Young Teachers of Beijing Forestry University [grant no. 2015ZCQ-BH-03 to Lei Xie], the National Natural Science Foundation of China [grant no. 31670207 to Lei Xie], and the Beijing Natural Science Foundation [grant no. 5182016 to Lei Xie].