PoplarV1, Main, Exploration, bibRecord, 002346

Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence.

Identifieur interne : 002346 ( Main/Exploration ); précédent : 002345; suivant : 002347

Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence.

Auteurs : Evgeny E. Akkuratov [États-Unis] ; Lorraine Walters [États-Unis] ; Arnab Saha-Mandal [États-Unis] ; Sushant Khandekar [États-Unis] ; Erin Crawford [États-Unis] ; Craig L. Zirbel [États-Unis] ; Scott Leisner [États-Unis] ; Ashwin Prakash [États-Unis] ; Larisa Fedorova [États-Unis] ; Alexei Fedorov [États-Unis]

Source :

Gene [ 1879-0038 ] ; 2014.

RBID : pubmed:25014137

Descripteurs français

KwdFr :
- ARN de transfert (génétique), ARN des plantes (composition chimique), Algorithmes (MeSH), Animaux (MeSH), Arabidopsis (croissance et développement), Arabidopsis (génétique), Bases de données génétiques (MeSH), Biologie informatique (méthodes), Bryophyta (génétique), Données de séquences moléculaires (MeSH), Fleurs (génétique), Génome végétal (MeSH), Humains (MeSH), Introns (MeSH), Magnoliopsida (génétique), Oryza (génétique), Phylogenèse (MeSH), Populus (génétique), Souris (MeSH), Séquence conservée (MeSH), Séquence nucléotidique (MeSH), Vitis (génétique).
MESH :
- composition chimique : ARN des plantes.
- croissance et développement : Arabidopsis.
- génétique : ARN de transfert, Arabidopsis, Bryophyta, Fleurs, Magnoliopsida, Oryza, Populus, Vitis.
- méthodes : Biologie informatique.
- Algorithmes, Animaux, Bases de données génétiques, Données de séquences moléculaires, Génome végétal, Humains, Introns, Phylogenèse, Souris, Séquence conservée, Séquence nucléotidique.

English descriptors

KwdEn :
- Algorithms (MeSH), Animals (MeSH), Arabidopsis (genetics), Arabidopsis (growth & development), Base Sequence (MeSH), Bryophyta (genetics), Computational Biology (methods), Conserved Sequence (MeSH), Databases, Genetic (MeSH), Flowers (genetics), Genome, Plant (MeSH), Humans (MeSH), Introns (MeSH), Magnoliopsida (genetics), Mice (MeSH), Molecular Sequence Data (MeSH), Oryza (genetics), Phylogeny (MeSH), Populus (genetics), RNA, Plant (chemistry), RNA, Transfer (genetics), Vitis (genetics).
MESH :
- chemical , chemistry : RNA, Plant.
- genetics : Arabidopsis, Bryophyta, Flowers, Magnoliopsida, Oryza, Populus, RNA, Transfer, Vitis.
- growth & development : Arabidopsis.
- methods : Computational Biology.
- Algorithms, Animals, Base Sequence, Conserved Sequence, Databases, Genetic, Genome, Plant, Humans, Introns, Mice, Molecular Sequence Data, Phylogeny.

Abstract

Orthologous introns have identical positions relative to the coding sequence in orthologous genes of different species. By analyzing the complete genomes of five plants we generated a database of 40,512 orthologous intron groups of dicotyledonous plants, 28,519 orthologous intron groups of angiosperms, and 15,726 of land plants (moss and angiosperms). Multiple sequence alignments of each orthologous intron group were obtained using the Mafft algorithm. The number of conserved regions in plant introns appeared to be hundreds of times fewer than that in mammals or vertebrates. Approximately three quarters of conserved intronic regions among angiosperms and dicots, in particular, correspond to alternatively-spliced exonic sequences. We registered only a handful of conserved intronic ncRNAs of flowering plants. However, the most evolutionarily conserved intronic region, which is ubiquitous for all plants examined in this study, including moss, possessed multiple structural features of tRNAs, which caused us to classify it as a putative tRNA-like ncRNA. Intronic sequences encoding tRNA-like structures are not unique to plants. Bioinformatics examination of the presence of tRNA inside introns revealed an unusually long-term association of four glycine tRNAs inside the Vac14 gene of fish, amniotes, and mammals.

DOI: 10.1016/j.gene.2014.07.012
PubMed: 25014137

Affiliations:

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Le document en format XML

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<term>Arabidopsis (growth & development)</term>
<term>Base Sequence (MeSH)</term>
<term>Bryophyta (genetics)</term>
<term>Computational Biology (methods)</term>
<term>Conserved Sequence (MeSH)</term>
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<term>Molecular Sequence Data (MeSH)</term>
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<term>Phylogeny (MeSH)</term>
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<term>RNA, Transfer (genetics)</term>
<term>Vitis (genetics)</term>
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<keywords scheme="KwdFr" xml:lang="fr"><term>ARN de transfert (génétique)</term>
<term>ARN des plantes (composition chimique)</term>
<term>Algorithmes (MeSH)</term>
<term>Animaux (MeSH)</term>
<term>Arabidopsis (croissance et développement)</term>
<term>Arabidopsis (génétique)</term>
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<term>Génome végétal (MeSH)</term>
<term>Humains (MeSH)</term>
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<term>Oryza (génétique)</term>
<term>Phylogenèse (MeSH)</term>
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<term>Oryza</term>
<term>Populus</term>
<term>RNA, Transfer</term>
<term>Vitis</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN de transfert</term>
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<term>Bryophyta</term>
<term>Fleurs</term>
<term>Magnoliopsida</term>
<term>Oryza</term>
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</keywords>
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<term>Base Sequence</term>
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<term>Genome, Plant</term>
<term>Humans</term>
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<term>Humains</term>
<term>Introns</term>
<term>Phylogenèse</term>
<term>Souris</term>
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<front><div type="abstract" xml:lang="en">Orthologous introns have identical positions relative to the coding sequence in orthologous genes of different species. By analyzing the complete genomes of five plants we generated a database of 40,512 orthologous intron groups of dicotyledonous plants, 28,519 orthologous intron groups of angiosperms, and 15,726 of land plants (moss and angiosperms). Multiple sequence alignments of each orthologous intron group were obtained using the Mafft algorithm. The number of conserved regions in plant introns appeared to be hundreds of times fewer than that in mammals or vertebrates. Approximately three quarters of conserved intronic regions among angiosperms and dicots, in particular, correspond to alternatively-spliced exonic sequences. We registered only a handful of conserved intronic ncRNAs of flowering plants. However, the most evolutionarily conserved intronic region, which is ubiquitous for all plants examined in this study, including moss, possessed multiple structural features of tRNAs, which caused us to classify it as a putative tRNA-like ncRNA. Intronic sequences encoding tRNA-like structures are not unique to plants. Bioinformatics examination of the presence of tRNA inside introns revealed an unusually long-term association of four glycine tRNAs inside the Vac14 gene of fish, amniotes, and mammals. </div>
</front>
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<ELocationID EIdType="doi" ValidYN="Y">10.1016/j.gene.2014.07.012</ELocationID>
<ELocationID EIdType="pii" ValidYN="Y">S0378-1119(14)00775-6</ELocationID>
<Abstract><AbstractText>Orthologous introns have identical positions relative to the coding sequence in orthologous genes of different species. By analyzing the complete genomes of five plants we generated a database of 40,512 orthologous intron groups of dicotyledonous plants, 28,519 orthologous intron groups of angiosperms, and 15,726 of land plants (moss and angiosperms). Multiple sequence alignments of each orthologous intron group were obtained using the Mafft algorithm. The number of conserved regions in plant introns appeared to be hundreds of times fewer than that in mammals or vertebrates. Approximately three quarters of conserved intronic regions among angiosperms and dicots, in particular, correspond to alternatively-spliced exonic sequences. We registered only a handful of conserved intronic ncRNAs of flowering plants. However, the most evolutionarily conserved intronic region, which is ubiquitous for all plants examined in this study, including moss, possessed multiple structural features of tRNAs, which caused us to classify it as a putative tRNA-like ncRNA. Intronic sequences encoding tRNA-like structures are not unique to plants. Bioinformatics examination of the presence of tRNA inside introns revealed an unusually long-term association of four glycine tRNAs inside the Vac14 gene of fish, amniotes, and mammals. </AbstractText>
<CopyrightInformation>Copyright © 2014 Elsevier B.V. All rights reserved.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Akkuratov</LastName>
<ForeName>Evgeny E</ForeName>
<Initials>EE</Initials>
<AffiliationInfo><Affiliation>Faculty of Biology and Soil Science, St. Petersburg State University, St. Petersburg 199034, Russia; Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: akkuratov.evgeny@gmail.com.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Walters</LastName>
<ForeName>Lorraine</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA; Department of Bioengineering, University of Toledo, Main Campus, Toledo, OH 43606, USA. Electronic address: lorraine.walters@rockets.utoledo.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Saha-Mandal</LastName>
<ForeName>Arnab</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: asahaman@ucalgary.ca.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Khandekar</LastName>
<ForeName>Sushant</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Department of Biological Sciences, University of Toledo, Main Campus, Toledo, OH 43606, USA. Electronic address: sushant43606@yahoo.com.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Crawford</LastName>
<ForeName>Erin</ForeName>
<Initials>E</Initials>
<AffiliationInfo><Affiliation>Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: erin.crawford@utoledo.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Zirbel</LastName>
<ForeName>Craig L</ForeName>
<Initials>CL</Initials>
<AffiliationInfo><Affiliation>Department of Mathematics and Statistics, Bowling Green State University, Bowling Green, OH 43403, USA. Electronic address: zirbel@bgsu.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Leisner</LastName>
<ForeName>Scott</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>Department of Biological Sciences, University of Toledo, Main Campus, Toledo, OH 43606, USA. Electronic address: scott.leisner@utoledo.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Prakash</LastName>
<ForeName>Ashwin</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: ashwin.prakash@jhmi.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Fedorova</LastName>
<ForeName>Larisa</ForeName>
<Initials>L</Initials>
<AffiliationInfo><Affiliation>Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: lvfedorova3@gmail.com.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Fedorov</LastName>
<ForeName>Alexei</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Program in Bioinformatics and Proteomics/Genomics, University of Toledo, Health Science Campus, Toledo, OH 43614, USA; Department of Medicine, University of Toledo, Health Science Campus, Toledo, OH 43614, USA. Electronic address: Alexei.fedorov@utoledo.edu.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<GrantList CompleteYN="Y"><Grant><GrantID>1R01GM085328-01A1</GrantID>
<Acronym>GM</Acronym>
<Agency>NIGMS NIH HHS</Agency>
<Country>United States</Country>
</Grant>
</GrantList>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2014</Year>
<Month>07</Month>
<Day>08</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>Netherlands</Country>
<MedlineTA>Gene</MedlineTA>
<NlmUniqueID>7706761</NlmUniqueID>
<ISSNLinking>0378-1119</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D018749">RNA, Plant</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>9014-25-9</RegistryNumber>
<NameOfSubstance UI="D012343">RNA, Transfer</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017360" MajorTopicYN="N">Arabidopsis</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000254" MajorTopicYN="N">growth & development</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D044002" MajorTopicYN="N">Bryophyta</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName>
<QualifierName UI="Q000379" MajorTopicYN="N">methods</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017124" MajorTopicYN="N">Conserved Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D030541" MajorTopicYN="N">Databases, Genetic</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D035264" MajorTopicYN="N">Flowers</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018745" MajorTopicYN="N">Genome, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D007438" MajorTopicYN="Y">Introns</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D019684" MajorTopicYN="N">Magnoliopsida</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D051379" MajorTopicYN="N">Mice</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D012275" MajorTopicYN="N">Oryza</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D018749" MajorTopicYN="Y">RNA, Plant</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
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<MeshHeading><DescriptorName UI="D012343" MajorTopicYN="N">RNA, Transfer</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D027843" MajorTopicYN="N">Vitis</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
<KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Computational biology</Keyword>
<Keyword MajorTopicYN="N">Genomics</Keyword>
<Keyword MajorTopicYN="N">MALAT1</Keyword>
<Keyword MajorTopicYN="N">mascRNA</Keyword>
</KeywordList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year>
<Month>12</Month>
<Day>29</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2014</Year>
<Month>06</Month>
<Day>26</Day>
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<PubMedPubDate PubStatus="accepted"><Year>2014</Year>
<Month>07</Month>
<Day>07</Day>
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<Day>12</Day>
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<PubMedPubDate PubStatus="medline"><Year>2014</Year>
<Month>9</Month>
<Day>30</Day>
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<PublicationStatus>ppublish</PublicationStatus>
<ArticleIdList><ArticleId IdType="pubmed">25014137</ArticleId>
<ArticleId IdType="pii">S0378-1119(14)00775-6</ArticleId>
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<affiliations><list><country><li>États-Unis</li>
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<region><li>Ohio</li>
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<tree><country name="États-Unis"><region name="Ohio"><name sortKey="Akkuratov, Evgeny E" sort="Akkuratov, Evgeny E" uniqKey="Akkuratov E" first="Evgeny E" last="Akkuratov">Evgeny E. Akkuratov</name>
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<name sortKey="Crawford, Erin" sort="Crawford, Erin" uniqKey="Crawford E" first="Erin" last="Crawford">Erin Crawford</name>
<name sortKey="Fedorov, Alexei" sort="Fedorov, Alexei" uniqKey="Fedorov A" first="Alexei" last="Fedorov">Alexei Fedorov</name>
<name sortKey="Fedorova, Larisa" sort="Fedorova, Larisa" uniqKey="Fedorova L" first="Larisa" last="Fedorova">Larisa Fedorova</name>
<name sortKey="Khandekar, Sushant" sort="Khandekar, Sushant" uniqKey="Khandekar S" first="Sushant" last="Khandekar">Sushant Khandekar</name>
<name sortKey="Leisner, Scott" sort="Leisner, Scott" uniqKey="Leisner S" first="Scott" last="Leisner">Scott Leisner</name>
<name sortKey="Prakash, Ashwin" sort="Prakash, Ashwin" uniqKey="Prakash A" first="Ashwin" last="Prakash">Ashwin Prakash</name>
<name sortKey="Saha Mandal, Arnab" sort="Saha Mandal, Arnab" uniqKey="Saha Mandal A" first="Arnab" last="Saha-Mandal">Arnab Saha-Mandal</name>
<name sortKey="Walters, Lorraine" sort="Walters, Lorraine" uniqKey="Walters L" first="Lorraine" last="Walters">Lorraine Walters</name>
<name sortKey="Zirbel, Craig L" sort="Zirbel, Craig L" uniqKey="Zirbel C" first="Craig L" last="Zirbel">Craig L. Zirbel</name>
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Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence.

Bioinformatics analysis of plant orthologous introns: identification of an intronic tRNA-like sequence.

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