Complete mitochondrial genome of the Ukrainian nine-spined stickleback Pungitius platygaster (Gasterosteiformes, Gasterosteidae)

Abstract

The complete mitochondrial genome of the Ukrainian nine-spined stickleback Pungitius platygaster was obtained using massive parallel sequencing of genomic DNA. The mitogenome sequence was 16 570 bp long, and the gene order and contents were identical to those of other sequenced Pungitius mitogenomes. In a phylogenetic analysis, the mitogenome of P. platygaster clustered with other Pungitius mitogenomes, yet being clearly distinct from those of P. pungitius, P. sinensis and P. kaibarae.

Keywords:

• Caspian nine-spined stickleback
• Gasterosteidae
• genome
• mtDNA
• Pungitius platygaster

The Ukrainian nine-spined stickleback P. platygaster is morphologically one of the most easily identifiable sticklebacks in the genus Pungitius (Keivany & Nelson 2000). Hence, most taxonomic treatments recognize it as a valid species, rather than a subspecies of P. pungitius (Wootton 1984; Keivany & Nelson 2000; Mattern 2007). However, in contrast to most other species in this genus, the genetics of this species is poorly studied. To the best of our knowledge, the only genetic studies of this species involved phylogenetic analysis of mitochondrial DNA (mtDNA) fragments by Geiger et al. (2014) and Wang et al. (2015). Access to the complete mitogenome of this species might be helpful in piecing together the evolutionary affinities and biogeographic history of this species which (together with P. hellenicus) has an enigmatic southern distribution at the Black Sea, Sea of Azov, Aral Sea and Caspian Sea basins. All other members of the genus have much more northern distribution ranges (Wootton 1976, 1984).

We sequenced the genomic DNA of P. platygaster collected from the River Loudias drainage in Greece (40°50′N, 22°18'E) on the Illumina HiSeq2000 platform with 100 paired-end strategy. A total of 11.8 million reads were aligned against the P. sinensis mitogenome (Hwang et al. 2012a) with bwa-0.5.10 (Li & Durbin 2009). Mean sequence coverage across the genome was 27.58 reads per base pair and 100% of the reference genome had one-fold coverage (72.61% of the bases had ≥20-fold coverage). The consensus sequence of the P. platygaster mitochondrial genome was exported with samtools 1.2 (Li et al. 2009) and manually checked. The complete mitochondrial genome of P. platygaster is 16 570 bp (GenBank Accession No. KT989570), consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. The order and direction of these genes were identical to those of other Gasterosteidae fishes (Miya et al. 2001; Kawahara et al. 2009; Hwang et al. 2012a, 2012b). Of the 13 protein-coding genes, four (ND2, COII, ND4 and Cytb) showed an incomplete stop codon. The base composition of the entire mitochondrial genome was 27.8% for A, 26.6% for T, 17.2% for G and 28.4% for C. The phylogenetic position of P. platygaster in Gasterosteidae fishes was investigated based on a maximum likelihood tree constructed with the 37 genes (15 583 bp in total) using RAxML v.8.0 under the GTR + GAMMA model (37 gene partitions and 100 thorough bootstrap replicates; Stamatakis 2014). P. platygaster was phylogenetically positioned with other Pungitius species (i.e., P. pungitius, P. sinensis and P. kaibarae), but showed clear albeit shallow divergence from them (Figure 1). Nucleotide identity in the 37 gene regions of P. platygaster was 95.7%, 95.6% and 93.0% in comparison with those of P. pungitius (GenBank Accession No. AB445130; Kawahara et al. 2009), P. sinensis (EU332748; Hwang et al. 2012a) and P. kaibarae (EU332749; Hwang et al. 2012b), respectively.

Figure 1. A maximum likelihood tree inferred from 37 mitochondrial genes among nine Gasterosteidae and an outgroup species. Bootstrap support is indicated at nodes. GenBank accession numbers are indicated in brackets.

Acknowledgements

We thank Jacquelin De Faveri for linguistic corrections. Pekka Ellonen, Laura Häkkinen, Tiina Hannunen and Sami Karja are thanked for help with laboratory and bioinformatic work. The sequencing was conducted at the Finnish Institute for Molecular Medicine.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.

Funding information

This study was supported by grants (108601 & 118673) from the Academy of Finland, the Ministry of Culture of the Czech Republic (DKRVO 2015/15, National Museum, 00023272) and by the institutional resources of the Ministry of Education, Youth, and Sports of the Czech Republic.