The complete chloroplast genome of Dipelta yunnanensis (Caprifoliaceae), a vulnerable plant in China

Abstract

Dipelta yunnanensis (Caprifoliaceae) is a medicinal plant endemic to China. It has been included in the Chinese Species Red List and is also listed as a vulnerable species in the IUCN Red List. In this study, we determined the complete chloroplast (cp) genome sequence of Dipelta yunnanensis using Illumina paired-end sequencing. The whole cp genome was 155,359 bp in length, consisting of a pair of inverted repeat regions of 23,397 bp, a small single-copy region of 19,098 bp, and a large single-copy region of 89,467 bp. The genome encoded 128 unique genes including 82 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the genome was 38.4%. Phylogenetic analysis with the reported chloroplast genomes of Dipsacales revealed that D. yunnanensis had a close relationship with Kolkwitzia amabilis. The chloroplast genome sequence of D. yunnanensis offers a useful resource for future conservation genetics and phylogenetic studies.

Keywords:

• Chloroplast genome
• Dipelta yunnanensis
• phylogenetic analysis

Dipelta yunnanensis is a deciduous shrub belonging to the genus Dipelta of family Caprifoliaceae (Yang and Landrein 2011) and mainly distributed in Yunnan, Hubei, Sichuan, China. It is of great value in landscape design and its root is used as a traditional Chinese medicine to treat measles, pruritus, and Damp-Heat syndrome (Wang 2014). Recently, the natural populations of D. yunnanensis have been declining dramatically due to the excessive deforestation and continuous deterioration of habitats. It has been classified as a vulnerable plant listed in the category of the Red List of biodiversity in China and International Union for Conservation of Nature and Natural Resources (http://rep.iplant.cn/prot/Dipelta%20yunnanensis). To date, only SSR and AFLP markers have been developed to identify the interspecific relationships in Dipelta (Liu et al. 2013), and genomic information of the genus is lacking for further study. Here we characterized the complete chloroplast genome of D. yunnanensis based on the whole-genome Illumina sequencing dataset to obtain genomic information for conservation studies and to explore its phylogenetic placement within Dipsacales.

Fresh leaves of D. yunnanensis were collected from Shangri-la, (Yunnan, China; 100.05°E, 27.19°N), and the voucher (2018JH15) was deposited at the Evolutionary Botany Laboratory (EBL), Northwest University. Genomic DNA isolated with DNAquick Plant System (Tiangen Biotech (Beijing) CO. LTD) was sequenced using the Illumina HiSeq 2500 platform in Biomarker Technologies CO, China. The raw reads were trimmed using NGSQC Toolkit_v.2.3.3 with the default parameters (Patel and Jain 2012). Subsequently, the clean reads were used to perform referenced-guided assembly using MIRA 4.0.2 (Chevreux et al. 2004) and MITObim v1.8 (Hahn et al. 2013) with cp genome of Dipelta floribunda (NC_037955) as the reference. Assembled plastome was annotated using Geneious R v9.0.5 (Kearse et al. 2012) by aligning to the reference plastome. The consensus sequences were imported into the online program Dual Organellar Genome Annotator DOGMA (Wyman et al. 2004) for gene annotation.

The complete chloroplast genome of D. yunnanensis (GenBank accession no. MK002702) was 155,359 bp in length, comprising of a large single copy (LSC) region of 89,467 bp, a small single copy (SSC) region of 19,098 bp, and a pair of inverted repeat (IR) regions of 23,397 bp. The overall GC content was 38.4% with the corresponding values in the LSC, SSC, and IR region of 36.5%, 33.1%, and 44.2%, respectively. The chloroplast genome contained 128 genes including 82 protein-coding genes, 37 tRNA genes, and 8 rRNA genes.

In order to understand the phylogenetic relationship between D. yunnanensis and its related species, we selected 10 published cp genomes of Caprifoliaceae and six Adoxaceae species as outgroup. The whole plastome sequences were aligned with MAFFT 7.310 (Katoh and Standley 2016), and the maximum likelihood (ML) tree was reconstructed by RAxML v 7.2.8 (Stamatakis 2006) with 1000 bootstrap replicates. The result indicated that D. yunnanensis was sister to D. floribunda and closely related to Kolkwitzia amabilis. Both of the two genera are classified into the new genus Linnaea (Christenhusz 2013) (Figure 1).

Figure 1. ML phylogenetic tree of 17 species in Dipsacales constructed by the whole chloroplast genomes. Numbers above nodes were the bootstrap values based on 1000 replicates.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

The study is supported by the National Natural Sciences Foundation of China (31670219, 31870321) and Natural Science Basic Research Plan in Shaanxi Province of China (2018JM3010).