The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae)

Abstract

The complete mitochondrial genome of the black surfperch, Embiotoca jacksoni: Selection and substitution rates among surfperches (Embiotocidae) The complete 16,515 bp nucleotide sequence of the mitochondrial genome was determined for the black surfperch, Embiotoca jacksoni (Perciformes: Embiotocidae). The black surfperch mitochondrial genome contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, and the non-coding control region (Dloop), the gene order of which is identical to that observed in most vertebrates. The protein-coding gene sequences of E. jacksoni mitochondrial DNA were compared with two other embiotocid surfperches with available complete mitochondrial genomes, Cymatogaster aggregata and Ditrema temminckii. Across all mitochondrial protein-coding genes in surfperches the weighted average substitution rate was 2.079% per My and average dN/dS ratios for each protein-coding gene ranged from 0.016 in CytB to 0.608 in ND3. Substitution rates and dN/dS ratios were relatively high for ATP8 compared to other protein-coding genes. Although most protein-coding genes showed signals of purifying selection, we found evidence for positive selection in ND3 in E. jacksoni.

Reference Genome of the Black Surfperch,Embiotoca jacksoni(Embiotocidae, Perciformes), a California Kelp Forest Fish That Lacks a Pelagic Larval Stage

“…The base composition of the final assembly version is A = 34.62%, C = 26.37%, G = 12.65%, T = 26.34%, and consists of 22 unique transfer RNAs and 13 protein coding genes. This was identical in size and organization to a previously published mitochondrial genome ( Longo et al 2016 ). The two genomes differed by 15 base pair substitutions, which included 12 transitions and 3 transversions.…”

A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage

“…The generated consensus sequence was then used as a scaffold on which to map the paired short-read data for polishing, again using the Geneious mapper. This consensus sequence was then annotated using E. jacksoni reference annotations from GenBank accession NC_029362.1 ( Longo et al 2016 ) to identify potential spurious frameshift mutations and stop codons introduced by sequencing and/or assembly errors. We identified a total of 3 stop codons, one each in the coding sequences of the ND2, COI, and ND4 genes, which were all caused by incorrect calling of the length of mononucleotide repeats.…”