The complete chloroplast genome sequence of coastal psammophyte, Ixeris repens (Asteraceae, subtribe Crepidinae), in Korea

Abstract We report the first complete chloroplast genome sequence of psammophyte, Ixeris repens, on the coastal dunes in Korea. The complete plastid genome is 153,017 bp in total length, with one large single copy (LSC; 84,242 bp), one small single copy (SSC; 18,495 bp), and two inverted repeat (IR) regions (IRa and IRb, each with 25,140 bp). The overall GC content is 37.6% and the genome contains 130 genes, including 85 protein-coding, 37 transfer RNA and 8 ribosomal RNA genes. Phylogenetic analysis based on 17 representative plastomes of the family Asteraceae suggests that Ixeris repens is sister to congeneric species I. polycephala with strong bootstrap support (100%) and also that monophyletic Ixeris is sister to the clade containing Taraxacum, Youngia, Lapsanastrum, and Crepidiastrum.

The genus Ixeris comprises close to ten species and is centered in East Asia, extending to South and Southeast Asia. Based on carpological and cytological investigations, a taxonomic revision of Ixeris and its relatives was provided by Kawano (1990a, b, c, 1992), which is largely in agreement with the narrow generic concept of Nakai (1920). Of six Ixeris species in Korea, I. repens (L.) A.Gray shows very wide geographic distribution, ranging from Indochina (Cambodia, Thailand, Vietnam, and Laos) through Taiwan, China, Japan, Korea to the Russia Far East (Kamchatka). Ixeris repens can be found commonly on the coastal dunes of western and southeastern parts of the Korean Peninsula as well as on Jeju-do Island. As one of vulnerable coastal species, nearly 18% of reduction in the potential distribution area of I. repens and future potential distribution shift toward the northern parts along the east coast in the Korean Peninsula have been suggested (Park and Choi 2020). Although phylogenetic relationships within Ixeris haven not been fully determined, nrDNA ITS sequence data showed that I. repens is closely related to I. stolonifera A.Gray, which occurs in open mountain slopes and disturbed areas (Nakamura et al. 2014). In this study, we assembled the first complete plastome of I. repens, analyzed available plastomes of Ixeris and related genera, and assessed its phylogenetic position and intergeneric relationships within the subtribe Crepidinae.
The maximum likelihood (ML) analysis with 1,000 bootstrap replications was conducted using IQ-TREE v.1.6.7 (Nguyen et al. 2015). Seventeen representative species of Asteraceae (16 from tribe Cichorieae and one outgroup from tribe Astereae), including I. repens, were aligned using MAFFT v.7 (Katoh and Standley 2013). Aster tataricus (tribe Astereae) was used as an outgroup. The ML tree (Figure 1) showed that the genus Ixeris is a monophyletic and I. repens is closely related to I. polycephala, only available congeneric species with the complete plastome sequence. Based on currently all available plastome sequences of the five major clades within the subtribe Crepidinae (a total of five genera), the ML tree suggested that the subtribe Crepidinae is monophyletic (100% bootstrap support, BS) and that Lactucinae is sister to the Crepidinae (96% BS). A sister relationship between Hyoseridinae and Hypochaeridinae, albeit very weakly (53% BS), was suggested ( Figure 1). Within the Crepidinae, the Crepidiastrum-Lapsanastrum-Youngia clade recognized by Kilian et al. (2009) was strongly supported (100% BS), while the Ixeris-Ixeridium-Taraxacum clade was not supported. Rather, the complete plastome phylogeny suggested that Taraxacum is more closely related to the genera of Crepidinae than to genus Ixeris. The plastid phylogenomic study based on much broader species coverage among subtribes of Cichorieae as well as within subribe Crepidinae will shed light on overall intersubtribal relationships within and phylogenetic and biogeographic history of genus Ixeris and related genera, respectively.

Disclosure statement
No potential competing interest was reported by the author(s).

Funding
This work was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2016R1A6A1A05011910).

Data availability statement
The genome sequence data that support the findings of this study are openly available in GenBank of NCBI at https://www.ncbi.nlm.nih.gov/ under the accession no. MW092111. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA697908, SRR13590698, and SAMN17676084, respectively.