Halibut mitogenomics : a study of the complete mitochondrial genome sequences of Atlantic, Pacific and Greenland halibut

Abstract

The complete mitochondrial DNA sequence was determined in four individuals of Atlantic halibut (Hippoglossus hippoglossus), Pacific halibut (Hippoglossus stenolepis) and Greenland halibut (Reinhardtius hippoglossoides) respectively. Thirteen protein-coding genes, twentytwo tRNA genes, two rRNA genes and a large non-coding control region were identified, and the conserved vertebrate gene order was confirmed. Extensive length variation of the mtDNA genome was observed, due to variations in copy number of a 61 bp heteroplasmic repeated motif in the control region. Furthermore, 800 bp from the mtDNA genes ND2, COI and control region respectively was sequenced in 30 individuals from the Atlantic halibut broodstock at Mørkvedbukta Reseach Station. In addition, approximately 13420 bp from Common sole (Solea vulgaris), 15012 bp from European plaice (Pleuronectes platessa) and 7678 bp from Turbot (Scophthalmus maximus) were determined. The overall genetic variation based on the number of nucleotide substitutions was greatest in Greenland halibut, followed by Pacific halibut and Atlantic halibut. The control region and some of the ND genes had the highest nucleotide diversity, while the rRNA genes and ATP8 (Pacific and Greenland halibut) were most conserved. Four amino acid substitutions between the three halibut species in ND5, with a negative mutation matrix score suggest that these substitutions could have an impact on functional and structional properties of the gene. Phylogenetic investigations based on the complete mtDNA genome revealed that Atlantic halibut and Pacific halibut are closely related species, potentially separated at the sub-species level. Of all other available mtDNA genomes Greenland halibut is the closest relative to the Hippoglossus genus. Furthermore, Atlantic- and Pacific halibut was estimated to have separated 2 Ma, while divergence between Greenland halibut and the Hippoglossus genus took place approximately 6 million years ago.