New insights into the interplay between codon bias determinants in plants
Identifieur interne : 000043 ( Pmc/Curation ); précédent : 000042; suivant : 000044New insights into the interplay between codon bias determinants in plants
Auteurs : S. Camiolo ; S. Melito ; A. PorcedduSource :
- DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes [ 1340-2838 ] ; 2015.
Abstract
Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.
Url:
DOI: 10.1093/dnares/dsv027
PubMed: 26546225
PubMed Central: 4675714
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">New insights into the interplay between codon bias determinants in plants</title>
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<front><div type="abstract" xml:lang="en"><p>Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.</p>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">DNA Res</journal-id>
<journal-id journal-id-type="iso-abbrev">DNA Res</journal-id>
<journal-id journal-id-type="publisher-id">dnares</journal-id>
<journal-id journal-id-type="hwp">dnares</journal-id>
<journal-title-group><journal-title>DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes</journal-title>
</journal-title-group>
<issn pub-type="ppub">1340-2838</issn>
<issn pub-type="epub">1756-1663</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">26546225</article-id>
<article-id pub-id-type="pmc">4675714</article-id>
<article-id pub-id-type="doi">10.1093/dnares/dsv027</article-id>
<article-id pub-id-type="publisher-id">dsv027</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Full Papers</subject>
</subj-group>
</article-categories>
<title-group><article-title>New insights into the interplay between codon bias determinants in plants</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Camiolo</surname>
<given-names>S.</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Melito</surname>
<given-names>S.</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Porceddu</surname>
<given-names>A.</given-names>
</name>
<xref ref-type="corresp" rid="cor1">*</xref>
</contrib>
<aff><addr-line>Dipartimento di Agraria, SACEG</addr-line>
,<institution>Università degli Studi di Sassari</institution>
,<addr-line>Sassari</addr-line>
,<country>Italy</country>
</aff>
</contrib-group>
<author-notes><corresp id="cor1"><label>*</label>
To whom correspondence should be addressed. Tel. +39 079 229224. Fax. +39 079 229222. E-mail: <email>aporceddu@uniss.it</email>
</corresp>
<fn id="AN1" fn-type="con"><p>Edited by Dr Satoshi Tabata</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>12</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="epub"><day>05</day>
<month>11</month>
<year>2015</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>05</day>
<month>11</month>
<year>2015</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>22</volume>
<issue>6</issue>
<fpage>461</fpage>
<lpage>470</lpage>
<history><date date-type="received"><day>30</day>
<month>6</month>
<year>2015</year>
</date>
<date date-type="accepted"><day>1</day>
<month>10</month>
<year>2015</year>
</date>
</history>
<permissions><copyright-statement>© The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</copyright-statement>
<copyright-year>2015</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:href="dsv027.pdf"></self-uri>
<abstract><p>Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these different factors influence codon usage is unknown, so we dissected the contribution of mutational bias and selection towards codon bias in genes from 15 eudicots, 4 monocots and 2 mosses. We analysed the frequency of mononucleotides, dinucleotides and trinucleotides and investigated whether the compositional genomic background could account for the observed codon usage profiles. Neutral forces such as mutational pressure and G|C-biased gene conversion appeared to underlie most of the observed codon bias, although there was also evidence for the selection of optimal translational efficiency and mRNA folding. Our data confirmed the compositional differences between monocots and dicots, with the former featuring in general a lower background compositional bias but a higher overall codon bias.</p>
</abstract>
<kwd-group><kwd>codon bias</kwd>
<kwd>mutational bias</kwd>
<kwd>translational selection</kwd>
<kwd>plant genetics</kwd>
</kwd-group>
</article-meta>
</front>
</pmc>
</record>
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