First report of three complete mitochondrial genomes of the long-finned charr Salvethymus svetovidovi Chereshnev et Skopetz, 1990 (Salmoniformes: Salmonidae) with phylogenetic consideration

Complete mitochondrial genomes of Gritzenko's charr Salvelinus gritzenkoi and Miyabe charr Salvelinus malma miyabei and their interpretation regarding intraspecific taxonomy

BACKGROUND

Salvelinus is one the most species-rich genera of salmonids (Salmoniformes: Salmonidae), and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new charr species. However, current reference databases contain limited mitochondrial genome information on narrow-ranged, endemic charrs with disputable origin and systematic status. More comprehensive mitochondrial genome-based phylogenetics will help enhance understanding of the relationship and delineate charr species.

METHODS AND RESULTS

In the present study, the complete mitochondrial genomes of three taxa (S. gritzenkoi, S malma miyabei, and S. curilus) were sequenced (PCR and Sanger dideoxy sequencing) and compared with those of other charr species whose mitochondrial genomes are already reported. Results indicate that the mitochondrial genomes of the three taxa were similar in length (16,652 bp and 16,653 bp for S. curilus and S. malma miyabei, to 16,658 bp for S. gritzenkoi). Analyses of nucleotide composition showed that the newly sequenced five mitochondrial genomes skewed strongly towards high AT (54.4%) content, which is typical of Salvelinus. No large deletions and insertions were found in the mitochondrial genomes, including samples from isolated populations. Heteroplasmy associated with single-nucleotide substitution in the ND1 gene was found in one case (S. gritzenkoi). In maximum likelihood and Bayesian inference trees, S. gritzenkoi and S malma miyabei were clustered with S. curilus with strong branch support. Our results provide the basis for a possible reclassification of S. gritzenkoi to S. curilus.

CONCLUSION

The results of this study may be useful for future genetic studies on charrs of the genus Salvelinus toward the in-depth phylogenetic study and proper assessment of the conservation status of the disputed taxa.

Salmonidae Genome: Features, Evolutionary and Phylogenetic Characteristics

The salmon family is one of the most iconic and economically important fish families, primarily possessing meat of excellent taste as well as irreplaceable nutritional and biological value. One of the most common and, therefore, highly significant members of this family, the Atlantic salmon (Salmo salar L.), was not without reason one of the first fish species for which a high-quality reference genome assembly was produced and published. Genomic advancements are becoming increasingly essential in both the genetic enhancement of farmed salmon and the conservation of wild salmon stocks. The salmon genome has also played a significant role in influencing our comprehension of the evolutionary and functional ramifications of the ancestral whole-genome duplication event shared by all Salmonidae species. Here we provide an overview of the current state of research on the genomics and phylogeny of the various most studied subfamilies, genera, and individual salmonid species, focusing on those studies that aim to advance our understanding of salmonid ecology, physiology, and evolution, particularly for the purpose of improving aquaculture production. This review should make potential researchers pay attention to the current state of research on the salmonid genome, which should potentially attract interest in this important problem, and hence the application of new technologies (such as genome editing) in uncovering the genetic and evolutionary features of salmoniforms that underlie functional variation in traits of commercial and scientific importance.

Complete mitochondrial genomes of the Arctic charr Salvelinus alpinus alpinus Linnaeus (Salmoniformes: Salmonidae)

The complete mitochondrial genomes were sequenced in three individuals of Arctic charr Salvelinus alpinus alpinus. The genome sequences were 16,655 and 16,657 bp in length, and the gene arrangement, composition, and size are very similar to the charr genomes published previously. The difference between the three genomes studied is low, 0.09%. The level of sequence divergence between S. alpinus alpinus and S. alpinus oquassa inferred from the complete mitochondrial genomes is relatively low (0.36%), indicating recent divergence of the taxa and/or potential historical hybridization between different lineages upon secondary contact.

Complete mitochondrial genome and phylogenetic position of the Levanidov's charr Salvelinus levanidovi Chereshnev, Skopetz et Gudkov, 1989 (Salmoniformes, Salmonidae)

The complete mitochondrial genome was sequenced in Levanidov’s charr Salvelinus levanidovi. The genome sequences are 16,624 bp, and the gene arrangement, composition, and size are similar to the charr genomes. The level of divergence between S. levanidovi and charr belonging to the genus Salvelinus was in the range from 4.80% to 3.65%. Molecular phylogeny provides new evidence that S. levanidovi is closely related to the common ancestor of the genus Salvelinus. The present study confirms that S. fontinalis, S. levanidovi, S. leucomaensis, and S. namaycus form a basal group of taxa, each of them belongs to an independent evolutionary line.