Complete mitochondrial genome of Stichaeus grigorjewi Herzenstein, 1890 (Zoarcales: Stichaeidae)

Abstract

The complete mitochondrial genome of Stichaeus grigorjewi (Zoarcales: Stichaeidae) was sequenced for the first time based on the 27 pairs of newly designed primers using Sanger dideoxy sequencing method. Genome structure is consistent with standard scheme known for the vertebrates including 13 gene fragments, two rRNAs, 22 tRNAs, and control region. Moreover, it has additional tRNAs with atypical codons. These features were previously found in Xiphister atropurpureus, which shows the closest position to S. grigorjewi as seen from the phylogram built on the sequences of complete mitochondrial genome.

Keywords:

• Mitogenome
• annotation
• phylogeny

Zoarcales is a perciform infraorder (Teleostei) comprising about 405 species of coldwater marine fishes (Nelson et al. 2016) whose rank and taxonomic composition could be reevaluated in the light of recent molecular phylogenetic findings (Miya et al. 2003; Near et al. 2012; Radchenko 2015; Radchenko 2016; Turanov et al. 2017). Currently, a less is known about mitochondrial genomics of zoarcoids. However, recently based on the available sequences of complete mitochondrial genome (e.g., Johnstone et al. 2007; Swanburg et al. 2016; Yang et al. 2016; Ayala et al. 2017) obvious constrains were found on the nucleotide variation in the control region versus protein-coding genes (Turanov et al. 2018). In addition, mitochondrial genomics approaches have provided the opportunity to resolve phylogeographic issues of some endangered zoarcoid species (Lait and Carr 2018), demonstrating the possibility of forthcoming extension of its applications for these and other fish taxa. In the current short note, we describe the first complete mitochondrial genome of S. grigorjewi, the prickleback fish (Zoarcales: Stichaeidae) distributed along the coast of the Sea of Japan, Yellow Sea, and the Sea of Okhotsk (Parin et al. 2014; Fricke et al. 2018).

Total genomic DNA was extracted from the white muscle tissue of the female specimen (MIMB 36611) collected in Vostok Bay of the Sea of Japan (42.89° N, 132.73° E) by gill nets in April 26, 2017. The mitochondrial genome was obtained using Sanger dideoxy sequencing method based on the set of newly designed universal primers by which 27 overlapping regions were amplified (sequences are available upon request). Primer design was performed using Sliding Window-Based PSO Algorithm (Yang et al. 2011) based on the sequences available in GenBank for zoarcoids. This approach was recently applied to obtain mitochondrial genome sequences for some fishes (Balakirev, Kravchenko, et al. 2018; Balakirev, Romanov, et al. 2018).

The resulted chromatograms were assembled into mitochondrial genome fragments using Geneious Trial (Kearse et al. 2012). Then, the produced consensus sequence of complete genome was annotated using MitoAnnotator online pipeline (Iwasaki et al. 2013) and MITOS Web Server (Bernt et al. 2013). To clarify the relative position of S. grigorjewi within zoarcoids, we reconstructed NJ-phylogenetic tree using APE R package (Paradis et al. 2004). The tree was built based on the sequence matrix consisted of 13 zoarcoid species together with Hypoptychus dybowskii as outgroup with prior alignment in MEGA 6.0 (Tamura et al. 2013) using Muscle algorithm (Edgar 2004). TrN + G+I nucleotide substitution model implemented in the analysis was found through “modeltest” function of APE.

The mitochondrial genome of S. grigorjewi (GenBank accession number MK240352) is 16,531 bp long, with following overall nucleotide base composition: T (27.5%), C (28.1%), A (26.6%), and G (17.8%). Genome annotation resulted in 13 protein genes where ND6 (and eight tRNAs) reside on the light-strand. All other genes encoding on the heavy strand. It contains 22 tRNAs together with additional tRNA-Leu and tRNA-Ser fragments both maintaining atypical codons as it was also revealed in Xiphister atropurpureus (Ayala et al. 2017). There were found two typical rRNAs (16S rRNA and 12S rRNA) and control region, 862 pb in length.

Molecular phylogenetic reconstruction (Figure 1) shows that S. grigorjewi is most closely related to X. atropurpureus and C. japonicus comprising distinct clade within zoarcoids.

Figure 1. NJ-phylogenetic tree demonstrating the relationships among zoarcoid fishes built on complete sequences of mitochondrial genome. Numbers in nodes indicate support values based on 1000 replicates of non-parametric bootstrap test in order NJ/ML.

Disclosure statement

The authors have no conflicts of interest to declare. The authors are solely responsible for the content and the writing of this paper.

Additional information

Funding

This research was partially supported by Russian Foundation for Basic Research [project no. 16-34-00298, connected with genome annotation and molecular phylogenetics] and by Far Eastern Branch of the Russian Academy of Sciences in the framework of the Federal Program of Base Research [#18-4-040].