The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

Department of Bioinformatics Wissenschaftszentrum Weihenstephan Technische Universität München 80333 Freising Germany

Department of Marine Biology and Ecology Institute of Oceanography Faculty of Oceanography and Geography University of Gdansk 80 309 Gdansk Poland

Faculty of Science University of Hradec Kralove 500 03 Hradec Králové Czech Republic

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

Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution

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