The complete mitochondrial genome of Xiphister atropurpureus (Perciformes: Stichaeidae)

Abstract

Analysis of the marine black prickleback Xiphister atropurpureus Kittlitz using 76 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,518 bp in length and contains an origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Content and organization of the X. atropurpureus mitogenome is consistent with other teleost. Phylogenetic analysis of X. atropurpureus resolves it in a clade with another member of the Stichaeidae, Chirolophis japonicus Herzenstein.

Keywords:

• Mitogenome
• Stichaeidae
• xiphister
• Xiphisterinae
• zoarcales

The Stichaeidae fish family consists of entirely marine pricklebacks classified to six subfamilies, 35 genera, and 70 species (Eschmeyer & Fong 2017; Eschmeyer et al. 2017). Two mitogenomes have been deciphered for the family, these are Chirolophis japonicus subfamily Chirolophinae (Yang et al. 2016) and Leptoclinus maculatus Fries subfamily Lumpeninae (Swanburg et al. 2016). Here, we describe the mitogenome of X. atropurpureus, a member of the subfamily Xiphisterinae and common intertidal to subtidal species distributed from Kodiak Island, Alaska to Baja California, Mexico (Eschmeyer et al. 1983).

DNA was extracted from X. atropurpureus (Specimen Voucher- Hartnell College #262) collected from under a boulder in the mid intertidal at Pacific Grove, California (36°37′43.2″N, -121°55′17.5″W) following the protocol of Lindstrom et al. (2011). The 76 bp paired-end library construction and sequencing was performed by myGenomics, LLC (Alpharetta, GA) yielding 16,427,262 reads. The mitogenome was assembled by mapping the reads against the reference sequence Chirolophis japonicus (GenBank NC_028022) using the Medium-Low Sensitivity/Fast setting in Geneious 8.0 (Biomatters Limited, Auckland, New Zealand). The genes were annotated using MITOS (Bernt et al. 2013) and adjusted manually using NCBI ORF-finder (https://www.ncbi.nlm.nih.gov/orffinder/). Alignment of the mitogenome to other perciforms was accomplished with MAFFT (Katoh & Standley 2013). The maximum-likelihood analysis was performed using complete mitogenome sequences with RaxML (Stamatakis 2014) in Galaxy (Giardine et al. 2005; Blankenberg et al. 2010; Goecks et al. 2010) using the GTR + gamma model and 1000 fast bootstraps. The tree was visualized with TreeDyn 198.3 at Phylogeny.fr (Dereeper et al. 2008).

The mitogenome of X. atropurpureus (GenBank KY657279) is 16,518 bp in length, with a base composition of 25.4% A, 27.6% T, 18.7% G, and 28.3% C. It is highly conserved in organization, as is typical of animals (Boore 1999). The mitogenome contains 22 tRNA (trnL and trnS are duplicated), 2 rRNA (rrnL, rrnS), and 13 genes involved in electron transport and oxidative phosphorylation. All 13 genes start with the ATG initiation codon except cox1, which initiates with GTG. Most of the 13 genes terminate with the TAA stop codon, however, nd3 and cob terminate with TAG, and cox2 and nad4 with AGA. The nd6 gene and eight tRNAs encode on the light-strand, with the remaining genes encoding on the heavy strand. The OL is located between trnN and trnC, and is 38 bp in length, and the control region is 854 bp. Phylogenetic analysis of X. atropurpureus resolves it with two Stichaeids in a clade with C. japonicas, paraphyletic with respect to L. maculatus (Figure 1).

Figure 1. Maximum-likelihood phylogram of Xiphister atropurpureus and related teleost mitogenomes. Numbers along branches are RaxML bootstrap supports based on 1000 nreps (<75% support not shown). The legend below represents the scale for nucleotide substitutions.

Disclosure statement

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