Complete mitochondrial genome of the endangered freshwater fish Microphysogobio rapidus (Cypriniformes, Cyprinidae) from Korea.

Microphysogobio rapidus is an endangered freshwater fish from Korea with a limited distribution in the Nakdong River. Here, we determined the mitochondrial genome of M. rapidus, which consisted of 16,603 bp with 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNA genes, and a control region (D-loop). The overall base composition of the complete genome was 29.96% A, 26.06% T, 17.24% G, and 26.74% C, with high A + T content of 56.02%.

Microphysogobio rapidus is an endemic freshwater species in Korea with a limited distribution in the Nakdong River. Its population is decreasing rapidly due to habitat destruction by human activity (Hong et al. 2017). In 2012, it was designated as a Korean endangered wild species class I (Ministry of Environment (ME) 2012). The complete mitochondrial genome was determined, providing basic data for conserving endangered species. A sample was collected from the Nam River, a tributary of the Nakdong River, and prepared for sequencing on an Illumina MiSeq instrument using the TruSeq Nano DNA kit (Illumina, San Diego, CA, USA). Extracted M. rapidus DNA is preserved at Soonchunhyang University, Republic of Korea (voucher number of SUC-7583).

The complete mitochondrial genome of M. rapidus (GenBank accession number MH713708) consisted of 16,603 bp, with 13 protein-coding, 2 ribosomal RNA (rRNA), and 22 transfer RNA (tRNA) genes and a control region (D-Loop). Except for the CO1 gene, which had a GTG start codon, the other 12 protein-coding genes (PCGs) started with ATG. The PCG ND1 terminated with TAG, a typical stop codon. Five PCGs (CO1, ATPase 8, ND4L, ND5, and ND6) were stopped with a complete ‘TAA,’ four PCGs (ND2, ATPase 6, ND3, and ND4) were stopped with an incomplete ‘TA-.’ Three PCGs (CO2, CO3, and Cytb) have an incomplete ‘T-,’ a common feature indicating the termination codon in Microphysogobio (Hwang et al. 2014; Park et al. 2016; Wang et al. 2016). The overall base composition of the M. rapidus genome was 29.96% A, 26.06% T, 17.24% G, and 26.74% C, with high A + T content of 56.02%. The ribosomal RNA (rRNA) consisted of 12S rRNA (959 bp) and 16S rRNA (1,690 bp). The control region (D-loop) was 926 bp in total length.

A molecular phylogenetic tree was constructed with the complete mitochondrial genomes of Microphysogobio species and the fish subfamily Gobioninae (Figure 1) using the maximum-likelihood method. In this study, M. rapidus was closely related to M. yaluensis.

Figure 1.

Molecular phylogenetic tree of the complete mitochondrial sequences of Microphysogobio species; the outgroup was the family Cyprinidae. The phylogenetic analysis used the maximum-likelihood method (1,000 bootstrap replicates), and the number at each node is the maximum-likelihood bootstrap proportion.