Nucleotide composition and codon usage across viruses and their respective hosts

Simón, Diego - Cristina, Juan - Musto, Héctor

Resumen:

The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.


Detalles Bibliográficos
2021
ANII: POS_NAC_2016_1_130463
Viral diversity
Base composition
GC-content
Compositional correlations
Codon usage
Inglés
Universidad de la República
COLIBRI
https://hdl.handle.net/20.500.12008/40863
Acceso abierto
Licencia Creative Commons Atribución (CC - By 4.0)
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author Simón, Diego
author2 Cristina, Juan
Musto, Héctor
author2_role author
author
author_facet Simón, Diego
Cristina, Juan
Musto, Héctor
author_role author
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collection COLIBRI
dc.contributor.filiacion.none.fl_str_mv Simón Diego, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.
Cristina Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares.
Musto Héctor, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.
dc.creator.none.fl_str_mv Simón, Diego
Cristina, Juan
Musto, Héctor
dc.date.accessioned.none.fl_str_mv 2023-10-30T15:50:49Z
dc.date.available.none.fl_str_mv 2023-10-30T15:50:49Z
dc.date.issued.none.fl_str_mv 2021
dc.description.abstract.none.fl_txt_mv The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.
dc.description.sponsorship.none.fl_txt_mv ANII: POS_NAC_2016_1_130463
dc.format.extent.es.fl_str_mv 9 h.
dc.format.mimetype.es.fl_str_mv application/pdf
dc.identifier.citation.es.fl_str_mv Simón, D, Cristina, J y Musto, H. "Nucleotide composition and codon usage across viruses and their respective hosts". Frontiers in Microbiology. [en línea] 2021, 12: 646300. 9 h. DOI: 10.3389/fmicb.2021.646300.
dc.identifier.doi.none.fl_str_mv 10.3389/fmicb.2021.646300
dc.identifier.issn.none.fl_str_mv 1664-302X
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12008/40863
dc.language.iso.none.fl_str_mv en
eng
dc.publisher.es.fl_str_mv Frontiers
dc.relation.ispartof.es.fl_str_mv Frontiers in Microbiology, 2021, 12: 646300.
dc.rights.license.none.fl_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
dc.source.none.fl_str_mv reponame:COLIBRI
instname:Universidad de la República
instacron:Universidad de la República
dc.subject.es.fl_str_mv Viral diversity
Base composition
GC-content
Compositional correlations
Codon usage
dc.title.none.fl_str_mv Nucleotide composition and codon usage across viruses and their respective hosts
dc.type.es.fl_str_mv Artículo
dc.type.none.fl_str_mv info:eu-repo/semantics/article
dc.type.version.none.fl_str_mv info:eu-repo/semantics/publishedVersion
description The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.
eu_rights_str_mv openAccess
format article
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identifier_str_mv Simón, D, Cristina, J y Musto, H. "Nucleotide composition and codon usage across viruses and their respective hosts". Frontiers in Microbiology. [en línea] 2021, 12: 646300. 9 h. DOI: 10.3389/fmicb.2021.646300.
1664-302X
10.3389/fmicb.2021.646300
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language eng
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publishDate 2021
reponame_str COLIBRI
repository.mail.fl_str_mv mabel.seroubian@seciu.edu.uy
repository.name.fl_str_mv COLIBRI - Universidad de la República
repository_id_str 4771
rights_invalid_str_mv Licencia Creative Commons Atribución (CC - By 4.0)
spelling Simón Diego, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.Cristina Juan, Universidad de la República (Uruguay). Facultad de Ciencias. Centro de Investigaciones Nucleares.Musto Héctor, Universidad de la República (Uruguay). Facultad de Ciencias. Instituto de Biología.2023-10-30T15:50:49Z2023-10-30T15:50:49Z2021Simón, D, Cristina, J y Musto, H. "Nucleotide composition and codon usage across viruses and their respective hosts". Frontiers in Microbiology. [en línea] 2021, 12: 646300. 9 h. DOI: 10.3389/fmicb.2021.646300.1664-302Xhttps://hdl.handle.net/20.500.12008/4086310.3389/fmicb.2021.646300The genetic material of the three domains of life (Bacteria, Archaea, and Eukaryota) is always double-stranded DNA, and their GC content (molar content of guanine plus cytosine) varies between ≈ 13% and ≈ 75%. Nucleotide composition is the simplest way of characterizing genomes. Despite this simplicity, it has several implications. Indeed, it is the main factor that determines, among other features, dinucleotide frequencies, repeated short DNA sequences, and codon and amino acid usage. Which forces drive this strong variation is still a matter of controversy. For rather obvious reasons, most of the studies concerning this huge variation and its consequences, have been done in free-living organisms. However, no recent comprehensive study of all known viruses has been done (that is, concerning all available sequences). Viruses, by far the most abundant biological entities on Earth, are the causative agents of many diseases. An overview of these entities is important also because their genetic material is not always double-stranded DNA: indeed, certain viruses have as genetic material single-stranded DNA, double-stranded RNA, single-stranded RNA, and/or retro-transcribing. Therefore, one may wonder if what we have learned about the evolution of GC content and its implications in prokaryotes and eukaryotes also applies to viruses. In this contribution, we attempt to describe compositional properties of ∼ 10,000 viral species: base composition (globally and according to Baltimore classification), correlations among non-coding regions and the three codon positions, and the relationship of the nucleotide frequencies and codon usage of viruses with the same feature of their hosts. This allowed us to determine how the base composition of phages strongly correlate with the value of their respective hosts, while eukaryotic viruses do not (with fungi and protists as exceptions). Finally, we discuss some of these results concerning codon usage: reinforcing previous results, we found that phages and hosts exhibit moderate to high correlations, while for eukaryotes and their viruses the correlations are weak or do not exist.Submitted by Parodi Mónica (mparodi@fcien.edu.uy) on 2023-10-26T18:18:12Z No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103389fmicb2021646300.pdf: 1041146 bytes, checksum: 63a8e6707886f2e2d8ea4b531a0fcdd2 (MD5)Approved for entry into archive by Faget Cecilia (lfaget@fcien.edu.uy) on 2023-10-30T14:39:35Z (GMT) No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103389fmicb2021646300.pdf: 1041146 bytes, checksum: 63a8e6707886f2e2d8ea4b531a0fcdd2 (MD5)Made available in DSpace by Seroubian Mabel (mabel.seroubian@seciu.edu.uy) on 2023-10-30T15:50:49Z (GMT). No. of bitstreams: 2 license_rdf: 24251 bytes, checksum: 71ed42ef0a0b648670f707320be37b90 (MD5) 103389fmicb2021646300.pdf: 1041146 bytes, checksum: 63a8e6707886f2e2d8ea4b531a0fcdd2 (MD5) Previous issue date: 2021ANII: POS_NAC_2016_1_1304639 h.application/pdfenengFrontiersFrontiers in Microbiology, 2021, 12: 646300.Las obras depositadas en el Repositorio se rigen por la Ordenanza de los Derechos de la Propiedad Intelectual de la Universidad de la República.(Res. Nº 91 de C.D.C. de 8/III/1994 – D.O. 7/IV/1994) y por la Ordenanza del Repositorio Abierto de la Universidad de la República (Res. 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- Universidad de la Repúblicafalse
spellingShingle Nucleotide composition and codon usage across viruses and their respective hosts
Simón, Diego
Viral diversity
Base composition
GC-content
Compositional correlations
Codon usage
status_str publishedVersion
title Nucleotide composition and codon usage across viruses and their respective hosts
title_full Nucleotide composition and codon usage across viruses and their respective hosts
title_fullStr Nucleotide composition and codon usage across viruses and their respective hosts
title_full_unstemmed Nucleotide composition and codon usage across viruses and their respective hosts
title_short Nucleotide composition and codon usage across viruses and their respective hosts
title_sort Nucleotide composition and codon usage across viruses and their respective hosts
topic Viral diversity
Base composition
GC-content
Compositional correlations
Codon usage
url https://hdl.handle.net/20.500.12008/40863