The complete mitochondrial genome of the endangered freshwater fish Kichulchoia brevifasciata in Korea

Abstract Kichulchoia brevifasciata is an endangered fish that is distributed across the Goheung Peninsula, South Korea. This is the first report of the complete mitochondrial genome of K. brevifasciata, which consists of 16,646 bp with 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome is A (29.57%), T (28.08%), G (16.54%), and C (25.80%), with a high A + T content of 57.65%. Phylogenetic analysis showed that K. brevifasciata was most closely related to K. multifasciatas.

Kichulchoia brevifasciata is a dwarf loach with a total length of less than 70 mm (Ko and Bang 2014). It is an endemic species of Korea and belongs to the Cobitidae family. K. brevifasciata inhabits rivers with high flow rates and riverbeds made of gravel, and its distribution is limited to the Goheung Peninsula, Geogeumdo and Geumodo Island . The Republic of Korea Ministry of Environment designated K. brevifasciata as an endangered wildlife class II species due to environmental pollution and river development, but its habitat continued to decline and it was upgraded to endangered wildlife class I in 2017 (Kim and Park 2012). In this study, we report the complete mitogenome of K. brevifasciata, which will aid conservation of this species.
K. brevifasciata was collected from the Sinpyeongcheon Stream under a collection permit issued by the Ministry of Environment in Korea. K. brevifasciata genomic DNA was extracted from the caudal fin using the Genomic DNA Prep Kit (Biofact, Korea), and the extracted genomic DNA was stored at Soonchunhyang University. The complete mitochondrial DNA sequence was sequenced using the MGISEQ-2000 protocol (MGI, China) according to the MGI Easy DNA Library Prep Kit (MGI) manual. The raw K. brevifasciata sequencing data were assembled using Geneious (ver. 11.0.3) software and annotated using the MITOS web server (Bernt et al. 2013). The complete mitochondrial DNA sequence of K. brevifasciata was deposited in GenBank with accession number MW092826.
A phylogenetic tree was constructed using the Neighbor-Joining method (10,000 bootstrap replications) in MEGA X software (Kumar et al. 2018) based on the 13 protein coding genes of the Cobitidae family, with species of genera Barbatula and Sinogastromyzon as the outgroups (Figure 1). The phylogenetic tree includes clades 1 and 2, and clade 1 is classified into species of the genus Misgurnus, Cobitis, Kichulchoia, Iksookimia, and Niwaella. Clade 1 did not form a single lineage due to the presence of species belonging to the genus Misgurnus, which experienced mitochondrial introgression. Additionally, in clade 1, Cobitis, Kichulchoia, Iksookimia, and Niwaella did not form a single lineage as in previous studies (Park et al. 2018), presumably due to mitochondrial introgression (Kwan et al. 2019). Phylogenetic analyses based on nuclear genes are needed to create a single phylogenetic tree of the Cobitidae (Kwan et al. 2018). The genus Koreocobitis of clade 2 formed a strong single lineage, whereas the genus Misgurnus did not form a single lineage due to the presence of some species belonging to the genus Paramisgurnus. According to Slechtov a et al. (2008), Misgurnus and Paramisgurnus phylogeny should be studied by investigating mitochondrial introgression following intergenus hybrid formation. In the phylogenetic tree, K. brevifasciata is the closest related species to K. multifasciata, and the mitochondrial genome of K. brevifasciata is expected to provide an important genetic resource for molecular phylogenetic and conservation studies.

Disclosure statement
The authors report no conflicts of interests. The authors alone are responsible for the content and writing of this article.

Funding
This study was supported by Soonchunhyang University Research Fund.

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. MW092826. The associated BioProject, SRA, and Bio-Sample numbers are PRJNA687292, SRX9720364 and SAMN17141013, respectively.