Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution
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 contra...
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| Format: | Article |
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MDPI AG
2023-01-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/2/244 |
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| author | Dominik Matoulek Bruno Ježek Marta Vohnoutová Radka Symonová |
| author_facet | Dominik Matoulek Bruno Ježek Marta Vohnoutová Radka Symonová |
| author_sort | Dominik Matoulek |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-11T08:47:51Z |
| format | Article |
| id | doaj.art-5c8dfdd2305b4d40811b9f565eee8d47 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T08:47:51Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-5c8dfdd2305b4d40811b9f565eee8d472023-11-16T20:40:18ZengMDPI AGGenes2073-44252023-01-0114224410.3390/genes14020244Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome EvolutionDominik Matoulek0Bruno Ježek1Marta Vohnoutová2Radka Symonová3Department of Physics, Faculty of Science, University of Hradec Králové, 500 03 Hradec Králové, Czech RepublicFaculty of Informatics and Management, University of Hradec Králové, Rokitanského 62, 500 02 Hradec Králové, Czech RepublicDepartment of Computer Science, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech RepublicDepartment of Computer Science, Faculty of Science, University of South Bohemia, Branišovská 1760, 370 05 České Budějovice, Czech RepublicCytogenetic 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.https://www.mdpi.com/2073-4425/14/2/244compositional cytogenomicsAT/GC evolutionGC contentgenome evolutionGC landscape pipeline |
| spellingShingle | Dominik Matoulek Bruno Ježek Marta Vohnoutová Radka Symonová Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution Genes compositional cytogenomics AT/GC evolution GC content genome evolution GC landscape pipeline |
| title | Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution |
| title_full | Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution |
| title_fullStr | Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution |
| title_full_unstemmed | Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution |
| title_short | Advances in Vertebrate (Cyto)Genomics Shed New Light on Fish Compositional Genome Evolution |
| title_sort | advances in vertebrate cyto genomics shed new light on fish compositional genome evolution |
| topic | compositional cytogenomics AT/GC evolution GC content genome evolution GC landscape pipeline |
| url | https://www.mdpi.com/2073-4425/14/2/244 |
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