Draft macronucleus genome of Euplotes crassus ciliate
Identifieur interne : 000989 ( Istex/Corpus ); précédent : 000988; suivant : 000990Draft macronucleus genome of Euplotes crassus ciliate
Auteurs : D. V. Vinogradov ; O. V. Tsoi ; A. V. Zaika ; A. V. Lobanov ; A. A. Turanov ; V. N. Gladishev ; M. S. Gel AndSource :
- Molecular Biology [ 0026-8933 ] ; 2012-04-01.
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Abstract
Abstract: Basic bioinformatics analysis has been performed on the draft macronucleus genome and transcriptome of the Euplotes crassus ciliate. More than a quarter of E. crassus genes contain several exons. Among introns, a large fraction of tiny introns was revealed with the length of 20–30 nucleotides. We determined 63 cases of alternative splicing and found 14 introns with nonstandard splicing sites. About 2000 of hypothesized genes in E. crassus have no homologues with other ciliates but in the majority of them a considerable similarity is observed with bacterial genes that can be due to contamination while ciliate sample preparation. Comparison of the genomes of E. crassus and other ciliates evidences the expansion of the same gene families, which are responsible for the vitality of free-living heterotrophic organisms.
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DOI: 10.1134/S0026893312020197
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ISTEX:9D2BA8B2915E47E9FA4ABD58DF8EF490A48D3B0ELe document en format XML
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More than a quarter of E. crassus genes contain several exons. Among introns, a large fraction of tiny introns was revealed with the length of 20–30 nucleotides. We determined 63 cases of alternative splicing and found 14 introns with nonstandard splicing sites. About 2000 of hypothesized genes in E. crassus have no homologues with other ciliates but in the majority of them a considerable similarity is observed with bacterial genes that can be due to contamination while ciliate sample preparation. Comparison of the genomes of E. crassus and other ciliates evidences the expansion of the same gene families, which are responsible for the vitality of free-living heterotrophic organisms.</div></front></TEI><istex><corpusName>springer-journals</corpusName><author><json:item><name>D. V. 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More than a quarter of E. crassus genes contain several exons. Among introns, a large fraction of tiny introns was revealed with the length of 20–30 nucleotides. We determined 63 cases of alternative splicing and found 14 introns with nonstandard splicing sites. About 2000 of hypothesized genes in E. crassus have no homologues with other ciliates but in the majority of them a considerable similarity is observed with bacterial genes that can be due to contamination while ciliate sample preparation. Comparison of the genomes of E. crassus and other ciliates evidences the expansion of the same gene families, which are responsible for the vitality of free-living heterotrophic organisms.</abstract><qualityIndicators><refBibsNative>false</refBibsNative><abstractWordCount>127</abstractWordCount><abstractCharCount>834</abstractCharCount><keywordCount>7</keywordCount><score>6.362</score><pdfWordCount>2838</pdfWordCount><pdfCharCount>17916</pdfCharCount><pdfVersion>1.3</pdfVersion><pdfPageCount>6</pdfPageCount><pdfPageSize>612 x 792 pts (letter)</pdfPageSize></qualityIndicators><title>Draft macronucleus genome of Euplotes crassus ciliate</title><genre><json:string>research-article</json:string></genre><host><title>Molecular 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More than a quarter of E. crassus genes contain several exons. Among introns, a large fraction of tiny introns was revealed with the length of 20–30 nucleotides. We determined 63 cases of alternative splicing and found 14 introns with nonstandard splicing sites. About 2000 of hypothesized genes in E. crassus have no homologues with other ciliates but in the majority of them a considerable similarity is observed with bacterial genes that can be due to contamination while ciliate sample preparation. Comparison of the genomes of E. crassus and other ciliates evidences the expansion of the same gene families, which are responsible for the vitality of free-living heterotrophic organisms.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Keywords</head><item><term>genome analysis</term></item><item><term>ciliate</term></item><item><term>genome</term></item><item><term>bioinformatics</term></item></list></keywords></textClass><textClass><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>EST</term><term>expressed sequence tags</term></item><item><term>EIC</term><term>exon-intron contigs</term></item><item><term>nt</term><term>nucleotide</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>Life Sciences</head><item><term>Biochemistry, general</term></item><item><term>Human Genetics</term></item><item><term>Life Sciences, 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ciliate</ArticleTitle><ArticleCategory>Bioinformatics</ArticleCategory><ArticleFirstPage>328</ArticleFirstPage><ArticleLastPage>333</ArticleLastPage><ArticleHistory><RegistrationDate><Year>2012</Year><Month>4</Month><Day>17</Day></RegistrationDate><Received><Year>2011</Year><Month>6</Month><Day>6</Day></Received><Accepted><Year>2011</Year><Month>9</Month><Day>28</Day></Accepted><OnlineDate><Year>2012</Year><Month>4</Month><Day>18</Day></OnlineDate></ArticleHistory><ArticleCopyright><CopyrightHolderName>Pleiades Publishing, Ltd.</CopyrightHolderName><CopyrightYear>2012</CopyrightYear></ArticleCopyright><ArticleGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ArticleGrants></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1" CorrespondingAffiliationID="Aff1"><AuthorName DisplayOrder="Western"><GivenName>D.</GivenName><GivenName>V.</GivenName><FamilyName>Vinogradov</FamilyName></AuthorName><Contact><Email>dimavin@bioinf.fbb.msu.ru</Email></Contact></Author><Author AffiliationIDS="Aff1 Aff2"><AuthorName DisplayOrder="Western"><GivenName>O.</GivenName><GivenName>V.</GivenName><FamilyName>Tsoi</FamilyName></AuthorName><Contact><Email>bioeng@genebee.msu.ru</Email></Contact></Author><Author AffiliationIDS="Aff1 Aff2"><AuthorName DisplayOrder="Western"><GivenName>A.</GivenName><GivenName>V.</GivenName><FamilyName>Zaika</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff3"><AuthorName DisplayOrder="Western"><GivenName>A.</GivenName><GivenName>V.</GivenName><FamilyName>Lobanov</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff3"><AuthorName DisplayOrder="Western"><GivenName>A.</GivenName><GivenName>A.</GivenName><FamilyName>Turanov</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff3"><AuthorName DisplayOrder="Western"><GivenName>V.</GivenName><GivenName>N.</GivenName><FamilyName>Gladishev</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1 Aff2"><AuthorName DisplayOrder="Western"><GivenName>M.</GivenName><GivenName>S.</GivenName><FamilyName>Gel’fand</FamilyName></AuthorName></Author><Affiliation ID="Aff1"><OrgDivision>Kharkevich Institute for Information Transmission Problems</OrgDivision><OrgName>Russian Academy of Sciences</OrgName><OrgAddress><City>Moscow</City><Postcode>127994</Postcode><Country Code="RU">Russia</Country></OrgAddress></Affiliation><Affiliation ID="Aff2"><OrgDivision>Department of Bioengineering and Bioinformatics</OrgDivision><OrgName>Moscow State University</OrgName><OrgAddress><City>Moscow</City><Postcode>119991</Postcode><Country Code="RU">Russia</Country></OrgAddress></Affiliation><Affiliation ID="Aff3"><OrgDivision>Brigham and Women’s Hospital</OrgDivision><OrgName>Harvard Medical School</OrgName><OrgAddress><City>Boston</City><State>MA</State><Postcode>02115</Postcode><Country Code="US">USA</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Abstract</Heading><Para>Basic bioinformatics analysis has been performed on the draft macronucleus genome and transcriptome of the <Emphasis Type="Italic">Euplotes crassus</Emphasis> ciliate. More than a quarter of <Emphasis Type="Italic">E. crassus</Emphasis> genes contain several exons. Among introns, a large fraction of tiny introns was revealed with the length of 20–30 nucleotides. We determined 63 cases of alternative splicing and found 14 introns with nonstandard splicing sites. About 2000 of hypothesized genes in <Emphasis Type="Italic">E. crassus</Emphasis> have no homologues with other ciliates but in the majority of them a considerable similarity is observed with bacterial genes that can be due to contamination while ciliate sample preparation. Comparison of the genomes of <Emphasis Type="Italic">E. crassus</Emphasis> and other ciliates evidences the expansion of the same gene families, which are responsible for the vitality of free-living heterotrophic organisms.</Para></Abstract><KeywordGroup Language="En"><Heading>Keywords</Heading><Keyword>genome analysis</Keyword><Keyword>ciliate</Keyword><Keyword>genome</Keyword><Keyword>bioinformatics</Keyword></KeywordGroup><AbbreviationGroup><Heading>Abbreviations</Heading><DefinitionList><DefinitionListEntry><Term>EST</Term><Description><Para>expressed sequence tags</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>EIC</Term><Description><Para>exon-intron contigs</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>nt</Term><Description><Para>nucleotide</Para></Description></DefinitionListEntry></DefinitionList></AbbreviationGroup><ArticleNote Type="Misc"><SimplePara>Original Russian Text © D.V. Vinogradov, O.V. Tsoi, A.V. Zaika, A.V. Lobanov, A.A. Turanov, V.N. Gladishev, M.S. Gel’fand, 2012, published in Molekulyarnaya Biologiya, 2012, Vol. 46, No. 2, pp. 361–367.</SimplePara></ArticleNote></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Draft macronucleus genome of Euplotes crassus ciliate</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Draft macronucleus genome of Euplotes crassus ciliate</title></titleInfo><name type="personal" displayLabel="corresp"><namePart type="given">D.</namePart><namePart type="given">V.</namePart><namePart type="family">Vinogradov</namePart><affiliation>Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia</affiliation><affiliation>E-mail: dimavin@bioinf.fbb.msu.ru</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">O.</namePart><namePart type="given">V.</namePart><namePart type="family">Tsoi</namePart><affiliation>Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia</affiliation><affiliation>Department of Bioengineering and Bioinformatics, Moscow State University, 119991, Moscow, Russia</affiliation><affiliation>E-mail: bioeng@genebee.msu.ru</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="given">V.</namePart><namePart type="family">Zaika</namePart><affiliation>Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia</affiliation><affiliation>Department of Bioengineering and Bioinformatics, Moscow State University, 119991, Moscow, Russia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="given">V.</namePart><namePart type="family">Lobanov</namePart><affiliation>Brigham and Women’s Hospital, Harvard Medical School, 02115, Boston, MA, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">A.</namePart><namePart type="given">A.</namePart><namePart type="family">Turanov</namePart><affiliation>Brigham and Women’s Hospital, Harvard Medical School, 02115, Boston, MA, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">V.</namePart><namePart type="given">N.</namePart><namePart type="family">Gladishev</namePart><affiliation>Brigham and Women’s Hospital, Harvard Medical School, 02115, Boston, MA, USA</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">M.</namePart><namePart type="given">S.</namePart><namePart type="family">Gel’fand</namePart><affiliation>Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia</affiliation><affiliation>Department of Bioengineering and Bioinformatics, Moscow State University, 119991, Moscow, Russia</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>SP MAIK Nauka/Interperiodica</publisher><place><placeTerm type="text">Dordrecht</placeTerm></place><dateCreated encoding="w3cdtf">2011-06-06</dateCreated><dateIssued encoding="w3cdtf">2012-04-01</dateIssued><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: Basic bioinformatics analysis has been performed on the draft macronucleus genome and transcriptome of the Euplotes crassus ciliate. More than a quarter of E. crassus genes contain several exons. Among introns, a large fraction of tiny introns was revealed with the length of 20–30 nucleotides. We determined 63 cases of alternative splicing and found 14 introns with nonstandard splicing sites. About 2000 of hypothesized genes in E. crassus have no homologues with other ciliates but in the majority of them a considerable similarity is observed with bacterial genes that can be due to contamination while ciliate sample preparation. Comparison of the genomes of E. crassus and other ciliates evidences the expansion of the same gene families, which are responsible for the vitality of free-living heterotrophic organisms.</abstract><note>Bioinformatics</note><subject lang="en"><genre>Keywords</genre><topic>genome analysis</topic><topic>ciliate</topic><topic>genome</topic><topic>bioinformatics</topic></subject><subject><genre>Abbreviations</genre><topic>EST : expressed sequence tags</topic><topic>EIC : exon-intron contigs</topic><topic>nt : nucleotide</topic></subject><relatedItem type="host"><titleInfo><title>Molecular Biology</title></titleInfo><titleInfo type="abbreviated"><title>Mol Biol</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">2012-04-18</dateIssued><copyrightDate encoding="w3cdtf">2012</copyrightDate></originInfo><subject><genre>Life Sciences</genre><topic>Biochemistry, general</topic><topic>Human Genetics</topic><topic>Life Sciences, general</topic></subject><identifier type="ISSN">0026-8933</identifier><identifier type="eISSN">1608-3245</identifier><identifier type="JournalID">11008</identifier><identifier type="IssueArticleCount">18</identifier><identifier type="VolumeIssueCount">6</identifier><part><date>2012</date><detail type="volume"><number>46</number><caption>vol.</caption></detail><detail type="issue"><number>2</number><caption>no.</caption></detail><extent unit="pages"><start>328</start><end>333</end></extent></part><recordInfo><recordOrigin>Pleiades Publishing, Ltd., 2012</recordOrigin></recordInfo></relatedItem><identifier type="istex">9D2BA8B2915E47E9FA4ABD58DF8EF490A48D3B0E</identifier><identifier type="ark">ark:/67375/VQC-JS0VVBS1-N</identifier><identifier type="DOI">10.1134/S0026893312020197</identifier><identifier type="ArticleID">6371</identifier><identifier type="ArticleID">S0026893312020197</identifier><accessCondition type="use and reproduction" contentType="copyright">Pleiades Publishing, Ltd., 2012</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Pleiades Publishing, Ltd., 2012</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-JS0VVBS1-N/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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