Present and Future Salmonid Cytogenetics

Abstract

Salmonids are extremely important economically and scientifically; therefore, dynamic developments in their research have occurred and will continue occurring in the future. At the same time, their complex phylogeny and taxonomy are challenging for traditional approaches in research. Here, we first provide discoveries regarding the hitherto completely unknown cytogenetic characteristics of the Anatolian endemic flathead trout, Salmo platycephalus, and summarize the presently known, albeit highly complicated, situation in the genus Salmo. Secondly, by outlining future directions of salmonid cytogenomics, we have produced a prototypical virtual karyotype of Salmo trutta, the closest relative of S. platycephalus. This production is now possible thanks to the high-quality genome assembled to the chromosome level in S. trutta via soft-masking, including a direct labelling of repetitive sequences along the chromosome sequence. Repetitive sequences were crucial for traditional fish cytogenetics and hence should also be utilized in fish cytogenomics. As such virtual karyotypes become increasingly available in the very near future, it is necessary to integrate both present and future approaches to maximize their respective benefits. Finally, we show how the presumably repetitive sequences in salmonids can change the understanding of the overall relationship between genome size and G+C content, creating another outstanding question in salmonid cytogenomics waiting to be resolved.

Keywords: FISH; NOR phenotype; Salmo platycephalus; chromosome banding; cytotaxonomy of trout; rDNA.

Figure 1

Giemsa stained metaphase plate and the corresponding karyotype of Salmo platycephalus. m, metacentric; st, subtelocentric; a, acrocentric chromosomes. Bar equals 10 µm.

Figure 2

Chromosome analyses of Salmo platycephalus. (a,b) Giemsa-stained metaphases corresponding to (d,e) panels; (c) DAPI/CMA₃ fluorescence, DAPI stained chromosomes (green), CMA₃ signals of GC-rich regions (red); (d) DAPI stained chromosomes (blue), telomere repeat hybridization signals (green); (e) DAPI stained chromosomes (blue), 28S rDNA (green, indicated by arrows), 5S rDNA hybridization signals (red, indicated by arrowheads); (f) Ag-NOR impregnation showing the active major rDNA unit corresponding to the 28S rDNA sites. Bar equals 10 µm.

Figure 3

Virtual karyotype of Salmo trutta shows the haploid set of size-sorted chromosomes. The colour scale represents the proportion of repetitive (green) and non-repetitive (red) sequences. The y axis of each chromosome represents the scale of GC%. The karyotype based on cytogenetics in S. trutta enables us to roughly identify only the first three chromosomes according to their size—the largest acrocentric, the largest sub-telocentric and probably the largest metacentric chromosome. According to Ensembl, the 5S rDNA bearing chromosomes are chromosome No. 1 (the main site visualized also by FISH, blue arrow), i.e., the fourth largest chromosome, and chromosome No. 20 (orange arrow), which has a single 5S rDNA sequence.

Figure 4

Scatter plot showing the relationship between GC% and genome size in salmonids and other teleosts. Data from https://www.ncbi.nlm.nih.gov/genome/browse#!/overview/.