Cytogenetic and compositional studies considered fish genomes rather poor in guanine-cytosine content (GC%) because of a putative "sharp increase in genic GC% during the evolution of higher vertebrates". However, the available genomic data have not been exploited to confirm this viewpoint. In contrast, further misunderstandings in GC%, mostly of fish genomes, originated from a misapprehension of the current flood of data. Utilizing public databases, we calculated the GC% in animal genomes of three different, technically well-established fractions: DNA (entire genome), cDNA (complementary DNA), and cds (exons). Our results across chordates help set borders of GC% values that are still incorrect in literature and show: (i) fish in their immense diversity possess comparably GC-rich (or even GC-richer) genomes as higher vertebrates, and fish exons are GC-enriched among vertebrates; (ii) animal genomes generally show a GC-enrichment from the DNA, over cDNA, to the cds level (i.e., not only the higher vertebrates); (iii) fish and invertebrates show a broad(er) inter-quartile range in GC%, while avian and mammalian genomes are more constrained in their GC%. These results indicate no sharp increase in the GC% of genes during the transition to higher vertebrates, as stated and numerously repeated before. We present our results in 2D and 3D space to explore the compositional genome landscape and prepared an online platform to explore the AT/GC compositional genome evolution.

Department of Bioinformatics Wissenschaftszentrum Weihenstephan Technische Universität München 85354 Freising Germany

Department of Computer Science Faculty of Science University of South Bohemia Branišovská 1760 370 05 České Budějovice Czech Republic

Department of Physics Faculty of Science University of Hradec Králové 500 03 Hradec Králové Czech Republic

Faculty of Informatics and Management University of Hradec Králové Rokitanského 62 500 02 Hradec Králové Czech Republic

Institute of Hydrobiology Biology Centre of the Czech Academy of Sciences 370 05 České Budějovice Czech Republic

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