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

ABSTRACT: The complete mitochondrial genome was sequenced in three individuals of long-finned charr Salvethymus svetovidovi from Lake El'gygytgyn (Chukotka Peninsula, Russia). The genome sequences are 16,655?bp in size and the gene arrangement, composition, and size are similar to the charr genomes published previously. The difference between the three genomes studied is low, 0.07%. Our results support the phylogenetic closeness of Sl. svetovidovi with representatives of the genus Salvelinus and their origin from a common ancestor. A placement of Sl. svetovidovi in the phylogenetic tree is strictly defined and this taxon should be included in the genus Salvelinus.

SUBMITTER: Oleinik AG

PROVIDER: S-EPMC7687372 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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

Oleinik Alla G AG Skurikhina Lubov A LA Kukhlevsky Andrey D AD Semenchenko Alexander A AA

Mitochondrial DNA. Part B, Resources 20190713 2

The complete mitochondrial genome was sequenced in three individuals of long-finned charr Salvethymus svetovidovi from Lake El'gygytgyn (Chukotka Peninsula, Russia). The genome sequences are 16,655 bp in size and the gene arrangement, composition, and size are similar to the charr genomes published previously. The difference between the three genomes studied is low, 0.07%. Our results support the phylogenetic closeness of Sl. svetovidovi with representatives of the genus Salveli ...[more]

PMID: 33365584

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Project description:BackgroundSalmonids are regarded as 4R derivative species, having experienced 4 whole genome duplication events in their ancestry. Many duplicated chromosome regions still share extensive homology with one another which is maintained primarily through male-based homeologous chromosome pairings during meiosis. The formation of quadrivalents during meiosis leads to pseudolinkage. This phenomenon is more prevalent within 5 of the 12 ancestral teleost linkage groups in salmonids.ResultsWe constructed a genetic linkage map for brook charr and used this in combination with the genetic map from Arctic charr, to make comparisons with the genetic map of rainbow trout. Although not all chromosome arms are currently mapped, some homologous chromosome rearrangements were evident between Arctic charr and brook charr. Notably, 10 chromosome arms in brook charr representing 5 metacentric chromosomes in Arctic charr have undergone rearrangements. Three metacentrics have one arm translocated and fused with another chromosome arm in brook charr to a make a new metacentrics while two metacentrics are represented by 4 acrocentric pairs in brook charr. In two cases (i.e., BC-4 and BC-16), an apparent polymorphism was observed with the identification of both a putative metacentric structure (similar to metacentric AC-4 = BC-4 and a joining of acrocentric AC-16 + one arm of AC-28 = BC-16), as well as two separate acrocentric linkage groups evident in the mapping parents. Forty-six of the expected 50 karyotypic arms could be inter-generically assigned. SEX in brook charr (BC-4) was localized to the same homologous linkage group region as in Arctic charr (AC-4). The homeologous affinities detected in the two charr species facilitated the identification of 20 (expected number = 25) shared syntenic regions with rainbow trout, although it is likely that some of these regions were partial or overlapping arm regions.ConclusionsInter-generic comparisons among 2 species of charr (genus Salvelinus) and a trout (genus Oncorhynchus) have identified that linkage group arm arrangements are largely retained among these species. Previous studies have revealed that up to 7 regions of high duplicate marker retention occur between Salmo species (i.e., Atlantic salmon and brown trout) and rainbow trout, with 5 of these regions exhibiting higher levels of pseudolinkage. Pseudolinkage was detected in the charr species (i.e., BC-1/21, AC-12/27, AC-6/23, = RT-2p/29q, RT-12p/16p, and RT-27p/31p, respectively) consistent with three of the five 'salmonid-specific' pseudolinkage regions. Chromosome arms with the highest number of duplicated markers in rainbow trout are the linkage group arms with the highest retention of duplicated markers in both charr species.

Project description:Considerable research efforts have focused on elucidating the systematic relationships among salmonid fishes; an understanding of these patterns of relatedness will inform conservation- and fisheries-related issues, as well as provide a framework for investigating evolutionary mechanisms in the group. However, uncertainties persist in current Salmonidae phylogenies due to biological and methodological factors, and a comprehensive phylogeny including most representatives of the family could provide insight into the causes of these difficulties. Here we increase taxon sampling by including nearly all described salmonid species (n = 63) to present a time-calibrated and more complete portrait of Salmonidae using a combination of molecular markers and analytical techniques. This strategy improved resolution by increasing the signal-to-noise ratio and helped discriminate methodological and systematic errors from sources of difficulty associated with biological processes. Our results highlight novel aspects of salmonid evolution. First, we call into question the widely-accepted evolutionary relationships among sub-families and suggest that Thymallinae, rather than Coregoninae, is the sister group to the remainder of Salmonidae. Second, we find that some groups in Salmonidae are older than previously thought and that the mitochondrial rate of molecular divergence varies markedly among genes and clades. We estimate the age of the family to be 59.1 MY (CI: 63.2-58.1 MY) old, which likely corresponds to the timing of whole genome duplication in salmonids. The average, albeit highly variable, mitochondrial rate of molecular divergence was estimated as ~0.31%/MY (CI: 0.27-0.36%/MY). Finally, we suggest that some species require taxonomic revision, including two monotypic genera, Stenodus and Salvethymus. In addition, we resolve some relationships that have been notoriously difficult to discern and present a clearer picture of the evolution of the group. Our findings represent an important contribution to the systematics of Salmonidae, and provide a useful tool for addressing questions related to fundamental and applied evolutionary issues.

Dataset Information

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

Publications

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

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