The complete chloroplast genome of an endangered species in Korea, Halenia corniculata (L.) Cornaz (Gentianaceae)

Abstract

Halenia corniculata, characterized by having yellow corollas with spurs at the base within Halenia, is an endangered species in Korea, which represents the southern limit of the distribution range of the species. We present the complete chloroplast genome of H. corniculata. Its length is 153,198 bp and it has four subregions; 83,252 bp of large-single-copy and 18,372 bp of small-single-copy regions are separated by 25,787 bp of inverted repeat, including 130 genes (85 protein-coding genes, 8 rRNAs, and 37 tRNAs). Phylogenetic trees show that H. corniculata is a sister to S. bimaculata, nested within Swertia, consistent with previous phylogenetic studies.

Keywords:

• Halenia corniculata
• chloroplast genome
• Gentianaceae
• endangered species
• Korea

Halenia Borkh. (Gentianaceae) consists of approximately 40 annual or perennial species distributed in eastern Europe, East Asia, and the Americas (von Hagen and Kadereit 2003). Halenia is the only member in Gentianaceae that has spurred corollas, and it is shown as monophyletic within the family (von Hagen and Kadereit 2002). Halenia species have been used as herbal medicine sources to treat hepatic diseases, such as hepatitis and jaundice, in East Asia (Yang et al. 1991). Halenia corniculata (L.) Cornaz, distributed in northeastern China, Mongolia, Korea, northern Japan, and the Russian Far East, is one of two Asian species and is distinguished from the Himalayan H. elliptica D. Don by having yellow corollas and linear-lanceolate calyxes (Toyokuni and Yamazaki 1993; Ho and Pringle 1995; Park 2007). H. corniculata is listed as an endangered species in Korea by the Ministry of the Environment of Korea (http://species.nibr.go.kr). Only a few populations with less than 100 individuals have been reported in Korea. These populations, which can be found in open meadow-like habitats at high elevations on mountains, are threatened by habitat destruction and over-collection.

To understand its genetic background, we determined its complete chloroplast genome. The total DNA of H. corniculata isolated from Mt. Hwaaksan, Korea (Voucher in the Herbarium of the National Institute of Biological Resources, Korea (KB); [Oh 7377]) was extracted from fresh leaves using a DNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). The genome was sequenced using HiSeq4000 of Macrogen Inc., Korea, and de novo assembly and confirmation were performed with Velvet 1.2.10 (Zerbino and Birney 2008), SOAP GapCloser 1.12 (Zhao et al. 2011), BWA 0.7.17 (Li 2013), and SAMtools 1.9 (Li et al. 2009). Geneious R11 11.0.5 (Biomatters Ltd., Auckland, New Zealand) was used for annotation based on the Swertia mussotii chloroplast genome (NC031155; Xiang et al. 2016).

The chloroplast genome of H. corniculata (GenBank accession is MK606372) is 153,198 bp (GC ratio is 38.2%) and has four subregions: 83,252 bp of large-single-copy (LSC: 36.4%) and 18,372 bp of small-single-copy (SSC: 32.2%) regions are separated by 25,787 bp of an inverted repeat (IR: 43.4%). It contains 130 genes (85 protein-coding genes, 8 rRNAs, and 37 tRNAs); 19 genes (8 protein-coding gene, 4 rRNAs, and 7 tRNAs) are duplicated in the IR regions.

Complete or partial chloroplast genomes from H. corniculata, 3 Swertia chloroplast genomes, and 12 Gentiana genomes as outgroups were aligned using MAFFT 7.388 (Katoh and Standley 2013). Phylogenetic trees using maximum likelihood and neighbor-joining methods were drawn by MEGA X (Kumar et al. 2018). The phylogenetic trees show that H. corniculata is a sister to S. bimaculata, nested within Swertia (Figure 1), in good agreement with a previous phylogenetic analysis of Swertiinae (von Hagen and Kadereit 2002). In addition, two major clades in Gentiana correspond to the findings of a previous phylogeny study (Mishiba et al. 2009). The sample of H. corniculata in this study, which represents the southernmost population of the species, will contribute to a better understanding of its haplotype diversity and conservation biology.

Figure 1. A Neighbor-joining tree (with 10,000 bootstrap replicates) of Halenia, Swertia, and Gentiana chloroplast genomes from Gentianaceae: H. corniculata (MK606372 in this study), S. bimaculata (MH394374), S. mussotii (NC031155), S. verticillifolia (MF795137), G. macrophylla (NC035719), G. straminea (NC027441), G. obconica (NC037981), G. oreodoxa (NC037982), G. veitchiorum (NC037985), G. ornata (NC037983), G. caelestis (NC037979), G. hexaphylla (NC037980), G. stipitata (NC037894), G. officinalis (NC039574), G. siphonantha (NC039573), and G. dahurica (NC039572). Phylogenetic tree based on maximum likelihood (with 1000 replicates) produced a tree nearly identical to the NJ tree. The numbers below the branches indicate the corresponding bootstrap support values from the neighbor joining and maximum likelihood methods.

Disclosure statement

No potential conflict of interest was reported by the authors.

Additional information

Funding

This study was supported by a Daejeon University research grant (2016).