Abstract
Peucedanum chujaense is a newly discovered species of Apiaceae and is endemic to southern and western islands in Korea. In this study, complete chloroplast genome sequence of P. chujaense was characterized through de novo assembly with next-generation sequencing data. The chloroplast genome is 147,839 bp long and has a typical quadripartite organization consisting of a large single copy, a small single copy, and a pair of inverted repeats. The chloroplast genome harbored 80 protein-coding genes, 29 tRNA genes, and 4 rRNA genes.
Peucedanum chujaense K. Kim, S.H. Oh, C.S. Kim and C.W Park is a newly discovered species in Peucedanum sect. Oreoselinum (Adan.) Rchb. (Kim et al. Citation2019). It is endemic to Korea and restricted to southern and western islands of Korean Peninsula. The genus Peucedanum L. (Apiaceae) consists approximately 120 species, and many species of the genus Peucedanum have been widely used as drug in traditional medicinal practices in Mediterranean area, Europe, and Asia (Leporatti and Ivancheve Citation2003; Morioka et al. Citation2004; Sarkahil Citation2014). They contain phytochemicals such as coumarins and essential oils which play a fundamental role to treat asthma, hepatic injury, or allergy (Aida et al. Citation1998; Zhao et al. Citation1999; Ciesla et al. Citation2009; Skalicka-Woźniak et al. Citation2009; Sarkahil Citation2014). Meanwhile, the genus Peucedanum is known as heterogenous and the relationships between infrageneric taxa are mostly uncertain because they exhibit great morphological variations (Shneyer et al. Citation2003). Furthermore, previous phylogenetic studies showed the genus Peucedanum is paraphyletic and tried to divide the genus Peucedanum into several smaller groups (Reduron et al. Citation1997; Spalik et al. Citation2004; Winter et al. Citation2008).
In this study, we determined the chloroplast (cp) genome of P. chujaense to contribute to the classification and development of DNA markers for the authentication of Peucedanum species. The specimen was collected from Sinyang-ri, Hachujado Island, Jeju-shi, Jeju-do, Korea, and the voucher specimen (K. Kim et al. 1611) is deposited at herbarium of Seoul National University (SNU). Total genomic DNA was prepared and sequenced by the Illumina MiSeq platform (Illumina Inc., San Diego, CA) and obtained high-quality paired-end reads of ca. 2.0 Gb. The complete cp genome of P. chujaense was revealed to GenBank (Accession no. MT233391), as described previously (Kim et al. Citation2015).
The cp genome was 147,839 bp in length with 37.4% overall GC content. The cp genome structure of P. chujaense has the typical quadripartite organization featuring two copies (IRa and IRb) of IR regions (18,457 bp) that are separated by a large single copy (LSC) region (93,335 bp), and a small single copy (SSC) region (17,590 bp). The total number of identified genes encoded is 113 genes containing of 80 protein-coding genes, 29 tRNA genes, and 4 rRNA genes.
To investigate phylogenetic relationship of P. chujaense between relative taxa in Apiaceae, maximum-likelihood (ML) tree was constructed. The ML analysis was conducted with 66 common protein-coding gene sequences of P. chujaense which are obtained in this study and 17 taxa which are obtained from GenBank. Outgroup includes two species of Aralia (A. continentalis) and Panax (P. japonicus) in Araliaceae, which is the most likely sister group of Apiaceae (). The ML tree showed that P. chujaense is mostly related to the species of Angelica among the 17 related taxa (). This newly reported chloroplast genome sequence provides a significant foundation for the identification and genotyping of Peucedanum species.
Figure 1. Maximum-likelihood (ML) tree based on 66 chloroplast protein-coding genes of 20 species including P. chujaense. Sequences of 66 chloroplast protein-coding gene from 20 species were aligned using MAFFT (http://mafft.cbrc.jp/alignment/server/index.html… ) and used to generate ML phylogenetic tree by MEGA 7.0 (Kumar et al. Citation2016).
Disclosure statement
No potential conflict of interest was reported by the author(s).
Data availability
The data that support the findings of this study are available from the corresponding author on request.
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References
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