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Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes

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dc.rights.license CC BY eng
dc.contributor.author Symonová, Radka cze
dc.contributor.author Suh, Alexander cze
dc.date.accessioned 2020-06-07T20:51:16Z
dc.date.available 2020-06-07T20:51:16Z
dc.date.issued 2019 eng
dc.identifier.issn 1759-8753 eng
dc.identifier.uri http://hdl.handle.net/20.500.12603/335
dc.description.abstract Background: Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected. Results: The genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. nonrepetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome. Conclusion: Our results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation. eng
dc.format p. "Article Number: 49" eng
dc.language.iso eng eng
dc.publisher BMC eng
dc.relation.ispartof Mobile DNA, volume 10, issue: 1 eng
dc.subject Teleost fish eng
dc.subject Transposon eng
dc.subject GC content eng
dc.subject Genome evolution eng
dc.subject Nucleotide composition eng
dc.subject teleosta cze
dc.subject transpozon cze
dc.subject GC obsah cze
dc.subject evoluce genomu cze
dc.subject složení nukleotidů cze
dc.title Nucleotide composition of transposable elements likely contributes to AT/GC compositional homogeneity of teleost fish genomes eng
dc.title.alternative Nukleotidové složení transpozonů pravděpodobně přispívá k AT/GC homogenitě genomů teleostních ryb cze
dc.type article eng
dc.identifier.obd 43875813 eng
dc.identifier.doi 10.1186/s13100-019-0195-y eng
dc.description.abstract-translated Background: Teleost fish genome size has been repeatedly demonstrated to positively correlate with the proportion of transposable elements (TEs). This finding might have far-reaching implications for our understanding of the evolution of nucleotide composition across vertebrates. Genomes of fish and amphibians are GC homogenous, with non-teleost gars being the single exception identified to date, whereas birds and mammals are AT/GC heterogeneous. The exact reason for this phenomenon remains controversial. Since TEs make up significant proportions of genomes and can quickly accumulate across genomes, they can potentially influence the host genome with their own GC content (GC%). However, the GC% of fish TEs has so far been neglected. Results: The genomic proportion of TEs indeed correlates with genome size, although not as linearly as previously shown with fewer genomes, and GC% negatively correlates with genome size in the 33 fish genome assemblies analysed here (excluding salmonids). GC% of fish TE consensus sequences positively correlates with the corresponding genomic GC% in 29 species tested. Likewise, the GC contents of the entire repetitive vs. nonrepetitive genomic fractions correlate positively in 54 fish species in Ensembl. However, among these fish species, there is also a wide variation in GC% between the main groups of TEs. Class II DNA transposons, predominant TEs in fish genomes, are significantly GC-poorer than Class I retrotransposons. The AT/GC heterogeneous gar genome contains fewer Class II TEs, a situation similar to fugu with its extremely compact and also GC-enriched but AT/GC homogenous genome. Conclusion: Our results reveal a previously overlooked correlation between GC% of fish genomes and their TEs. This applies to both TE consensus sequences as well as the entire repetitive genomic fraction. On the other hand, there is a wide variation in GC% across fish TE groups. These results raise the question whether GC% of TEs evolves independently of GC% of the host genome or whether it is driven by TE localization in the host genome. Answering these questions will help to understand how genomic GC% is shaped over time. Long-term accumulation of GC-poor(er) Class II DNA transposons might indeed have influenced AT/GC homogenization of fish genomes and requires further investigation. cze
dc.publicationstatus postprint eng
dc.peerreviewed yes eng
dc.source.url https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-019-0195-y cze
dc.relation.publisherversion https://mobilednajournal.biomedcentral.com/track/pdf/10.1186/s13100-019-0195-y eng
dc.rights.access Open Access eng


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