The first complete chloroplast genome sequence of a medicinal goldthread species, Coptis omeiensis (Ranunculaceae)

Abstract

Coptis omeiensis, as an important Chinese medicinal plant, has been endangered because of overharvesting. To better understand and protect this species, we report the first complete chloroplast genome sequence of C. omeiensis. The chloroplast genome was found to be 154,684 bp in length, and GC content was 38.2%, with large and small single copy regions (LSC with 85,099 bp and SSC with 17,239 bp in length) separated by two Inverted repeat regions (IRs with 26,173 bp). Meanwhile, the sequence contained 113 genes, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. The phylogeny of Ranunculaceae based on the complete cp genomes of 27 related taxa was also presented in this study.

Keywords:

• Coptis
• endangered plant
• complete chloroplast genome
• phylogeny
• Ranunculaceae

The goldthread genus Coptis is a small genus with about 15 species in Ranunculaceae and famous for its great pharmaceutical importance (Xiang et al. 2016, 2018). Coptis omeiensis (Chen) C. Y. Cheng is restricted to the mountain cliffs in central Sichuan Province, China, at the altitude of 1000–1700 m. Due to its medicinal importance, this species has been harvested for hundreds of years, and its wild population have been shrinking dramatically (Qin et al. 2011). In order to better understand and protect this species, we reported and characterized the first complete chloroplast genome of C. omeiensis by the next-generation sequencing technology. Furthermore, a phylogenomic analysis of Ranunculaceae was also presented.

Dried leaves of C. omeiensis was collected from Mt. Emei, Sichuan, China. Voucher specimen (Z.M. Liang 2018015) was deposited in the Herbarium of Beijing Forestry University (BJFC). Total genomic DNA was extracted using a CTAB method (Doyle and Doyle 1987). DNA libraries preparation and 2 × 150 bp pair-end sequencing were performed on an Illumina Hi-Seq 4000 platform at Novogene (http://www.novogene.com, China). Chloroplast reads were extracted using published references (Mamut et al. 2018; Zhang et al. 2018), and then de novo assembly was done by Geneious R11 (Kearse et al. 2012). The annotation was performed using Plann (Huang and Cronk 2015), and then verified manually. The plastome sequence was deposited in GenBank (accession number: MK600514).

The plastome sequence of C. omeiensis was 154,684 bp in length, containing two single copy regions (LSC with 85,099 bp and SSC with 17,239 bp) separated by two inverted repeat regions (IRs with 26,173 bp). The sequence GC content was 38.2%, with IR regions having higher GC content (43.1%) than LSC (36.4%) and SSC (32.3%). The cp genome contained 113 genes, including 79 protein-coding, 30 tRNA, and 4 rRNA genes. Among them, 12 protein-coding (atpF, ndhA, ndhB, petB, petD, rpl2, rpoC1, rps16, rpl16) and 6 tRNA genes (trnA-UGC, trnG-GCC, trnI-GAU, trnK-UUU, trnL-UAA and trnV-UAC) contained a single intron, while three protein-coding genes (clpP, ycf3, rps12) possessed two introns. Of these, the gene rps12 was a trans-spliced gene.

Complete cp genome sequences of other 23 Ranunculaceae species and three outgroup taxa were mined from GenBank (Figure 1). The Bayesian inference (BI), maximum-likelihood (ML) and parsimony (MP) analyses were conducted for phylogeny reconstruction. BI analysis was performed in MrBayes 3.2.3 (Ronquist et al. 2012), with ngen =20,000,000, samplefreq =5000. ML analysis was implemented in RAxML-HPC 8.2.10 (Stamatakis 2014) on CIPRES cluster (https://www.phylo.org/), employing the GTR + G model and 1000 bootstrap replicates. MP analysis was carried out in PAUP* 4.0b10 (Swofford 2003), with 2000 replicates of random addition and 1000 bootstrap replicates. The phylogenetic framework was consistent with the previous phylogenetic studies on Ranunculaceae (Cossard et al. 2016; Liu et al. 2018; Mamut et al. 2018; Zhang et al. 2018; Zhai et al. 2019). Subfamily Coptidoideae diverged early from the family. Within Coptis, C. omeiensis was sister to C. chinensis (Figure 1).

Figure 1. The plastid phylogenomic tree of Coptis omeiensis as well as other Ranunculaceae species inferred from Bayesian analysis. Branches with 100% PP value, 100 likelihood 100 parsimony bootstrap values are shown in bold lines. Otherwise, MP bootstrap values/ML bootstrap values are shown above and pp values are below each branch.

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], Science & Technology Basic Resources Investigation Program of China [grant no. 2017FY100100], the National Natural Science Foundation of China [grant no. 31670207 to Lei Xie], and the Error! Hyperlink reference not valid. [grant no. 5182016 to Lei Xie].