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.

Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish

“…This pattern is in line with early observations of some badly reproducible banding patterns on less spiralized chromosomes [53][54][55][56]. The insufficient cytogenetic resolution in small-sized fish chromosomes can be augmented by the homogenizing effect of repetitive elements [46] that can be highly expanded in fish chromosomes, particularly in lineages with an additional whole-genome duplication [57]. The role of genome size can also be seen in the fact that in gar and other fishes and fish-like species with a rather larger genome (e.g., bowfin, lamprey, reedfish, sturgeon), at least four isofamilies could be identified with the sliding window size 100 kb (Figure 1 and Appendix B).…”

“…The natural clusters of GC% values were calculated for the following 13 fish and fish-like species, covering a broad part of basal vertebrate and ray-finned fish lineages: 1 ancelet (Branchiostoma floridae), 1 lamprey (Lethenteron reissneri), 1 skate (Amblyraja radiata), 1 reedfish (Erpetoichthys calabaricus), and 3 non-teleost ray-finned fish species, including 1 sturgeon (Acipenser ruthenus), 2 gar species (Atractosteus spatula and Lepisosteus oculatus), and the bowfin (Amia calva). Finally, five teleosts were analyzed, including one salmonid (Salmo salar) known for its salmonid-specific genome duplication and a high proportion of GC-rich repeats [57]. The remaining four teleosts were one eel (Anguilla anguilla), one platyfish (Xiphophorus maculatus), one perch (Perca fluviatilis), and one pike (Esox lucius).…”

Development and applications of chromosome-specific cytogenetic BAC-FISH probes in Larimichthys crocea

“…Currently, sequence-based methods have become powerful tools in the studies on chromosome evolution, but cytogenetic methods still played irreplaceable roles (Deakin et al, 2019;Gaffaroglu et al, 2020). In addition, more and more attentions were paid to link DNA sequence and chromosome structure to get comprehensive understanding in dynamic nature and evolution of chromosomes (Iannucci et al, 2021).…”

Fish Cytogenetics: Present and Future

“…In the Anatolian endemic flathead trout, Salmo platycephalus , the classical description of the karyotype was associated with a cytogenomic approach, that allowed the production of a prototypical virtual karyotype of Salmo trutta starting from high-quality genome data. This opens future perspectives not only for salmonid, but also for all vertebrates’ cytogenetics [ 27 ]. Finally, two papers used the cytogenomic approach, providing new perspectives on genome evolution in vertebrates.…”