Chromosomes and constitutive heterochromatin distribution in Arctic charr, Salvelinus alpinus (L.) (Pisces: Salmonidae)

Cytogenetic investigation of Arctic char × brook trout F1, F2 and backcross hybrids revealed remnants of the chromosomal rearrangements

Arctic char (Salvelinus alpinus) and brook trout (Salvelinus fontinalis) hybridize and their offspring is viable and fertile. This may be a real treat for the native European stocks of Arctic char which gene pools might be unintendedly contaminated with the genetic elements of brook trout. On the other hand, hybrids of these two species are appreciated by customers and have some potential for the aquaculture. Moreover, Salvelinus hybrids and backcross individuals are interesting models in the research focused on influence of hybridization on the genomic organization and chromosome rearrangements. Thus, the main goal of the present study was to examine chromosomes of Arctic char × brook trout F₁, F₂ hybrids and backcross individuals and compare with genomic information concerning parental species to recognize karyotypic changes provoked by the hybridization events. Application of conventional and molecular (FISH) techniques allow to identify characteristic chromosomes for both parental species in the hybrid progeny and show multiplicity of cytotypes among different types of crosses with variability in structure and number of chromosome (81–85) and chromosome arm (99–101). Chromosome fragment was detected in the karyotype of one F₁ and one backcross individual and the presence of one triploid (3n) fish was documented. Occurrence of chromosomes containing internally located telomeric sequences (ITS) inherited after brook trout or both parental species was shown in F₁ and backcross progeny. Moreover, additional CMA₃-positive signal on chromosome from Arctic char pair no. 2 in F₁ fish and interstitially located active NOR visible on subtelo-acrocentric (F₂ hybrid) and acrocentric (Sf × H individual) chromosomes were detected. Described polymorphic chromosomes together with specific, interstitial location of CMA₃-positive found in F₂ and Sf × H hybrids and DAPI-positive regions observed in H × Sa fish at different uniarmed chromosomes pair presumably are remnants of chromosomal rearrangements. Provided results strongly indicate that the hybridization process influenced the genome organization in the Salvelinus hybrid progeny.

A SNP Based Linkage Map of the Arctic Charr (Salvelinus alpinus) Genome Provides Insights into the Diploidization Process After Whole Genome Duplication

Diploidization, which follows whole genome duplication events, does not occur evenly across the genome. In salmonid fishes, certain pairs of homeologous chromosomes preserve tetraploid loci in higher frequencies toward the telomeres due to residual tetrasomic inheritance. Research suggests this occurs only in homeologous pairs where one chromosome arm has undergone a fusion event. We present a linkage map for Arctic charr (Salvelinus alpinus), a salmonid species with relatively fewer chromosome fusions. Genotype by sequencing identified 19,418 SNPs, and a linkage map consisting of 4508 markers was constructed from a subset of high quality SNPs and microsatellite markers that were used to anchor the new map to previous versions. Both male- and female-specific linkage maps contained the expected number of 39 linkage groups. The chromosome type associated with each linkage group was determined, and 10 stable metacentric chromosomes were identified, along with a chromosome polymorphism involving the sex chromosome AC04. Two instances of a weak form of pseudolinkage were detected in the telomeric regions of homeologous chromosome arms in both female and male linkage maps. Chromosome arm homologies within the Atlantic salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) genomes were determined. Paralogous sequence variants (PSVs) were identified, and their comparative BLASTn hit locations showed that duplicate markers exist in higher numbers on seven pairs of homeologous arms, previously identified as preserving tetrasomy in salmonid species. Homeologous arm pairs where neither arm has been part of a fusion event in Arctic charr had fewer PSVs, suggesting faster diploidization rates in these regions.

C, Q, and restriction enzyme banding of the chromosomes in brook trout (Salvelinus fontinalis) and Arctic charr (Salvelinus alpinus)

The brook trout (Salvelinus fontinalis) and the Arctic charr (Salvelinus alpinus) represent different phylogenetic lines of the salmonid fish genus Salvelinus. Chromosome banding studies utilizing C, Q, and restriction enzymes reveal differences between the two species for the amount and sequence composition of their heterochromatic DNA. Arctic charr, the more recently evolved of the two species, possesses more C and Q bands than the brook trout. With the exception of Alu I, the banding patterns produced by restriction enzymes bear a close resemblance to the C band pattern. Alu I eliminates staining from large pericentromeric regions, including the centromeric heterochromatin, in the chromosomes of both species and from some telomeric regions in Arctic charr. These findings show that the evolutionary divergence of the Arctic charr from the brook trout has been accompanied by accumulation of heterochromatic DNA and subsequent sequence divergence.

Molecular characterization and cytogenetic analysis of highly repeated DNAs of lake trout, Salvelinus namaycush

The chromosomes of lake trout (Salvelinus namaycush) contain a considerable amount of heterochromatin located at the centromeres and/or telomeres of several chromosomes, including a sex-specific block located distally on the X chromosome. In order to investigate further the repetitive DNAs of lake trout, genomic DNA from a female was size fractionated (<600 bp) with the restriction endonuclease AluI and fragments were cloned into the bacteriophage M13. A total of 42 clones were isolated. Relative copy number of individual inserts within the lake trout genome was estimated by Southern analysis. Twelve clones were determined to be highly repetitive and were chosen for further investigation. Inserts of these clones contained sequences similar to the AluI/RsaI, EcoRI/DraI, DraI/BstEII, and MboI/BglII families reported from Arctic char (Salvelinus alpinus). The chromosomal location of several of these fragments was determined in lake trout by fluorescence in situ hybridization (FISH). Two related AluI/RsaI sequences (Type A, approximately 140 bp, and Type B,approximately 120 bp) showed differential hybridization. Type A hybridized to the centromeres of all metacentric as well as several acrocentric chromosomes. Type B hybridized to the centromeres of most acrocentric chromosomes. A sequence with homology to the EcoRI/DraI family hybridized to the centromeres of several acrocentric chromosomes. Sequences with partial similarity to the DraI/BstEII family hybridized to the major rDNA sites (nucleolar organizer regions, NORs) and several minor telomeric sites. The interstitial and telomeric heterochromatin of lake trout, including that of the X chromosome, appears to comprise sequences belonging to the MboI/BglII family.