Sequencing and annotation of the Ophiostoma ulmi genome.
Identifieur interne : 000850 ( PubMed/Checkpoint ); précédent : 000849; suivant : 000851Sequencing and annotation of the Ophiostoma ulmi genome.
Auteurs : Shima Khoshraftar [Canada] ; Stacy Hung ; Sadia Khan ; Yunchen Gong ; Vibha Tyagi ; John Parkinson ; Mohini Sain ; Alan M. Moses ; Dinesh ChristendatSource :
- BMC genomics [ 1471-2164 ] ; 2013.
English descriptors
- KwdEn :
- Expressed Sequence Tags, Fungal Proteins (chemistry), Fungal Proteins (genetics), Fungal Proteins (metabolism), Genome, Fungal, Ophiostoma (classification), Ophiostoma (genetics), Phylogeny, RNA, Messenger (chemistry), RNA, Messenger (genetics), RNA, Messenger (metabolism), Sequence Analysis, DNA, Sequence Analysis, RNA, Virulence (genetics).
- MESH :
- chemical , chemistry : Fungal Proteins, RNA, Messenger.
- chemical , genetics : Fungal Proteins, RNA, Messenger.
- chemical , metabolism : Fungal Proteins, RNA, Messenger.
- classification : Ophiostoma.
- genetics : Ophiostoma, Virulence.
- Expressed Sequence Tags, Genome, Fungal, Phylogeny, Sequence Analysis, DNA, Sequence Analysis, RNA.
Abstract
The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics.
DOI: 10.1186/1471-2164-14-162
PubMed: 23496816
Affiliations:
Links toward previous steps (curation, corpus...)
Links to Exploration step
pubmed:23496816Le document en format XML
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Moses</name></author><author><name sortKey="Christendat, Dinesh" sort="Christendat, Dinesh" uniqKey="Christendat D" first="Dinesh" last="Christendat">Dinesh Christendat</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2013">2013</date><idno type="RBID">pubmed:23496816</idno><idno type="pmid">23496816</idno><idno type="doi">10.1186/1471-2164-14-162</idno><idno type="wicri:Area/PubMed/Corpus">000947</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000947</idno><idno type="wicri:Area/PubMed/Curation">000947</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000947</idno><idno type="wicri:Area/PubMed/Checkpoint">000947</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000947</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Sequencing and annotation of the Ophiostoma ulmi genome.</title><author><name sortKey="Khoshraftar, Shima" sort="Khoshraftar, Shima" uniqKey="Khoshraftar S" first="Shima" last="Khoshraftar">Shima Khoshraftar</name><affiliation wicri:level="4"><nlm:affiliation>Department of Cell & Systems Biology University of Toronto, Toronto, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Department of Cell & Systems Biology University of Toronto, Toronto</wicri:regionArea><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Hung, Stacy" sort="Hung, Stacy" uniqKey="Hung S" first="Stacy" last="Hung">Stacy Hung</name></author><author><name sortKey="Khan, Sadia" sort="Khan, Sadia" uniqKey="Khan S" first="Sadia" last="Khan">Sadia Khan</name></author><author><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name></author><author><name sortKey="Tyagi, Vibha" sort="Tyagi, Vibha" uniqKey="Tyagi V" first="Vibha" last="Tyagi">Vibha Tyagi</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author><author><name sortKey="Sain, Mohini" sort="Sain, Mohini" uniqKey="Sain M" first="Mohini" last="Sain">Mohini Sain</name></author><author><name sortKey="Moses, Alan M" sort="Moses, Alan M" uniqKey="Moses A" first="Alan M" last="Moses">Alan M. Moses</name></author><author><name sortKey="Christendat, Dinesh" sort="Christendat, Dinesh" uniqKey="Christendat D" first="Dinesh" last="Christendat">Dinesh Christendat</name></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2013" type="published">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Expressed Sequence Tags</term><term>Fungal Proteins (chemistry)</term><term>Fungal Proteins (genetics)</term><term>Fungal Proteins (metabolism)</term><term>Genome, Fungal</term><term>Ophiostoma (classification)</term><term>Ophiostoma (genetics)</term><term>Phylogeny</term><term>RNA, Messenger (chemistry)</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (metabolism)</term><term>Sequence Analysis, DNA</term><term>Sequence Analysis, RNA</term><term>Virulence (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Fungal Proteins</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Fungal Proteins</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Fungal Proteins</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Ophiostoma</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Ophiostoma</term><term>Virulence</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Expressed Sequence Tags</term><term>Genome, Fungal</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Sequence Analysis, RNA</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">23496816</PMID><DateCreated><Year>2013</Year><Month>04</Month><Day>09</Day></DateCreated><DateCompleted><Year>2013</Year><Month>10</Month><Day>21</Day></DateCompleted><DateRevised><Year>2017</Year><Month>02</Month><Day>20</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><PubDate><Year>2013</Year><Month>Mar</Month><Day>12</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Sequencing and annotation of the Ophiostoma ulmi genome.</ArticleTitle><Pagination><MedlinePgn>162</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2164-14-162</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">The ascomycete fungus Ophiostoma ulmi was responsible for the initial pandemic of the massively destructive Dutch elm disease in Europe and North America in early 1910. Dutch elm disease has ravaged the elm tree population globally and is a major threat to the remaining elm population. O. ulmi is also associated with valuable biomaterials applications. It was recently discovered that proteins from O. ulmi can be used for efficient transformation of amylose in the production of bioplastics.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We have sequenced the 31.5 Mb genome of O.ulmi using Illumina next generation sequencing. Applying both de novo and comparative genome annotation methods, we predict a total of 8639 gene models. The quality of the predicted genes was validated using a variety of data sources consisting of EST data, mRNA-seq data and orthologs from related fungal species. Sequence-based computational methods were used to identify candidate virulence-related genes. Metabolic pathways were reconstructed and highlight specific enzymes that may play a role in virulence.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">This genome sequence will be a useful resource for further research aimed at understanding the molecular mechanisms of pathogenicity by O. ulmi. It will also facilitate the identification of enzymes necessary for industrial biotransformation applications.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Khoshraftar</LastName><ForeName>Shima</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Cell & Systems Biology University of Toronto, Toronto, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hung</LastName><ForeName>Stacy</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Khan</LastName><ForeName>Sadia</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Gong</LastName><ForeName>Yunchen</ForeName><Initials>Y</Initials></Author><Author ValidYN="Y"><LastName>Tyagi</LastName><ForeName>Vibha</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Parkinson</LastName><ForeName>John</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Sain</LastName><ForeName>Mohini</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Moses</LastName><ForeName>Alan M</ForeName><Initials>AM</Initials></Author><Author ValidYN="Y"><LastName>Christendat</LastName><ForeName>Dinesh</ForeName><Initials>D</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2013</Year><Month>03</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005656">Fungal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012333">RNA, Messenger</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Microbiology. 2007 Aug;153(Pt 8):2781-90</RefSource><PMID Version="1">17660442</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Mol Plant Microbe Interact. 1998 Oct;11(10):1009-16</RefSource><PMID Version="1">9768518</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2012 Jan;40(Database issue):D290-301</RefSource><PMID Version="1">22127870</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>BMC Bioinformatics. 2005;6:31</RefSource><PMID Version="1">15713233</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Nucleic Acids Res. 2010 Jan;38(Database issue):D196-203</RefSource><PMID 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Fungal</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055156" MajorTopicYN="N">Ophiostoma</DescriptorName><QualifierName UI="Q000145" MajorTopicYN="N">classification</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017423" MajorTopicYN="N">Sequence Analysis, RNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D014774" 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IdType="doi">10.1186/1471-2164-14-162</ArticleId><ArticleId IdType="pmc">PMC3618308</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><noCountry><name sortKey="Christendat, Dinesh" sort="Christendat, Dinesh" uniqKey="Christendat D" first="Dinesh" last="Christendat">Dinesh Christendat</name><name sortKey="Gong, Yunchen" sort="Gong, Yunchen" uniqKey="Gong Y" first="Yunchen" last="Gong">Yunchen Gong</name><name sortKey="Hung, Stacy" sort="Hung, Stacy" uniqKey="Hung S" first="Stacy" last="Hung">Stacy Hung</name><name sortKey="Khan, Sadia" sort="Khan, Sadia" uniqKey="Khan S" first="Sadia" last="Khan">Sadia Khan</name><name sortKey="Moses, Alan M" sort="Moses, Alan M" uniqKey="Moses A" first="Alan M" last="Moses">Alan M. Moses</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Sain, Mohini" sort="Sain, Mohini" uniqKey="Sain M" first="Mohini" last="Sain">Mohini Sain</name><name sortKey="Tyagi, Vibha" sort="Tyagi, Vibha" uniqKey="Tyagi V" first="Vibha" last="Tyagi">Vibha Tyagi</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Khoshraftar, Shima" sort="Khoshraftar, Shima" uniqKey="Khoshraftar S" first="Shima" last="Khoshraftar">Shima Khoshraftar</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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