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Advances in vertebrate (cyto)genomics shed new light on fish compositional genome evolution
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SYSNO ASEP 0583820 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Advances in vertebrate (cyto)genomics shed new light on fish compositional genome evolution Author(s) Matoulek, M. (CZ)
Ježek, B. (CZ)
Vohnoutová, M. (CZ)
Symonová, Radka (BC-A) RID, ORCIDNumber of authors 4 Article number 244 Source Title Genes. - : MDPI
Roč. 14, č. 2 (2023)Number of pages 16 s. Language eng - English Country CH - Switzerland Keywords base composition ; compositional cytogenomics ; genome evolution Subject RIV EH - Ecology, Behaviour OECD category Other biological topics Method of publishing Open access Institutional support BC-A - RVO:60077344 UT WOS 000939064500001 EID SCOPUS 85148873460 DOI 10.3390/genes14020244 Annotation 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. Workplace Biology Centre (since 2006) Contact Dana Hypšová, eje@eje.cz, Tel.: 387 775 214 Year of Publishing 2024 Electronic address https://doi.org/10.3390/genes14020244
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