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

The organization of the genome nucleotide (AT/GC) composition in vertebrates remains poorly understood despite the numerous genome assemblies available. Particularly, the origin of the AT/GC heterogeneity in amniotes, in comparison to the homogeneity in anamniotes, is controversial. Recently, severa...

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Autores principales: Vohnoutová, Marta, Sedláková, Anastázie, Symonová, Radka
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10487504/
https://www.ncbi.nlm.nih.gov/pubmed/37685974
http://dx.doi.org/10.3390/ijms241713167
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author Vohnoutová, Marta
Sedláková, Anastázie
Symonová, Radka
author_facet Vohnoutová, Marta
Sedláková, Anastázie
Symonová, Radka
author_sort Vohnoutová, Marta
collection PubMed
description The organization of the genome nucleotide (AT/GC) composition in vertebrates remains poorly understood despite the numerous genome assemblies available. Particularly, the origin of the AT/GC heterogeneity in amniotes, in comparison to the homogeneity in anamniotes, is controversial. Recently, several exceptions to this dichotomy were confirmed in an ancient fish lineage with mammalian AT/GC heterogeneity. Hence, our current knowledge necessitates a reevaluation considering this fact and utilizing newly available data and tools. We analyzed fish genomes in silico with as low user input as possible to compare previous approaches to assessing genome composition. Our results revealed a disparity between previously used plots of GC% and histograms representing the authentic distribution of GC% values in genomes. Previous plots heavily reduced the range of GC% values in fish to comply with the alleged AT/GC homogeneity and AT-richness of their genomes. We illustrate how the selected sequence size influences the clustering of GC% values. Previous approaches that disregarded chromosome and genome sizes, which are about three times smaller in fish than in mammals, distorted their results and contributed to the persisting confusion about fish genome composition. Chromosome size and their transposons may drive the AT/GC heterogeneity apparent on mammalian chromosomes, whereas far less in fishes.
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spelling pubmed-104875042023-09-09 Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish Vohnoutová, Marta Sedláková, Anastázie Symonová, Radka Int J Mol Sci Article The organization of the genome nucleotide (AT/GC) composition in vertebrates remains poorly understood despite the numerous genome assemblies available. Particularly, the origin of the AT/GC heterogeneity in amniotes, in comparison to the homogeneity in anamniotes, is controversial. Recently, several exceptions to this dichotomy were confirmed in an ancient fish lineage with mammalian AT/GC heterogeneity. Hence, our current knowledge necessitates a reevaluation considering this fact and utilizing newly available data and tools. We analyzed fish genomes in silico with as low user input as possible to compare previous approaches to assessing genome composition. Our results revealed a disparity between previously used plots of GC% and histograms representing the authentic distribution of GC% values in genomes. Previous plots heavily reduced the range of GC% values in fish to comply with the alleged AT/GC homogeneity and AT-richness of their genomes. We illustrate how the selected sequence size influences the clustering of GC% values. Previous approaches that disregarded chromosome and genome sizes, which are about three times smaller in fish than in mammals, distorted their results and contributed to the persisting confusion about fish genome composition. Chromosome size and their transposons may drive the AT/GC heterogeneity apparent on mammalian chromosomes, whereas far less in fishes. MDPI 2023-08-24 /pmc/articles/PMC10487504/ /pubmed/37685974 http://dx.doi.org/10.3390/ijms241713167 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Vohnoutová, Marta
Sedláková, Anastázie
Symonová, Radka
Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
title Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
title_full Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
title_fullStr Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
title_full_unstemmed Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
title_short Abandoning the Isochore Theory Can Help Explain Genome Compositional Organization in Fish
title_sort abandoning the isochore theory can help explain genome compositional organization in fish
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10487504/
https://www.ncbi.nlm.nih.gov/pubmed/37685974
http://dx.doi.org/10.3390/ijms241713167
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