Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae.
Identifieur interne : 000759 ( Main/Exploration ); précédent : 000758; suivant : 000760Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae.
Auteurs : Yang Wang [République populaire de Chine] ; Wenwu Ye [République populaire de Chine] ; Yuanchao Wang [République populaire de Chine]Source :
- Molecular plant pathology [ 1364-3703 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ARN long non codant, Transcription génétique.
- pathogénicité : Oomycetes, Phytophthora.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : RNA, Long Noncoding.
- genetics : Transcription, Genetic.
- pathogenicity : Oomycetes, Phytophthora.
Abstract
Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.
DOI: 10.1111/mpp.12692
PubMed: 29665235
PubMed Central: PMC6638102
Affiliations:
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with effector gene transcription in Phytophthora sojae.</title><author><name sortKey="Wang, Yang" sort="Wang, Yang" uniqKey="Wang Y" first="Yang" last="Wang">Yang Wang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095</wicri:regionArea><wicri:noRegion>Jiangsu 210095</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095</wicri:regionArea><wicri:noRegion>Jiangsu 210095</wicri:noRegion></affiliation></author><author><name sortKey="Ye, Wenwu" sort="Ye, Wenwu" uniqKey="Ye W" first="Wenwu" last="Ye">Wenwu Ye</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095</wicri:regionArea><wicri:noRegion>Jiangsu 210095</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095</wicri:regionArea><wicri:noRegion>Jiangsu 210095</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095</wicri:regionArea><wicri:noRegion>Jiangsu 210095</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:affiliation>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095</wicri:regionArea><wicri:noRegion>Jiangsu 210095</wicri:noRegion></affiliation></author></analytic><series><title level="j">Molecular plant pathology</title><idno type="eISSN">1364-3703</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Oomycetes (pathogenicity)</term><term>Phytophthora (pathogenicity)</term><term>RNA, Long Noncoding (genetics)</term><term>Transcription, Genetic (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN long non codant (génétique)</term><term>Oomycetes (pathogénicité)</term><term>Phytophthora (pathogénicité)</term><term>Transcription génétique (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>RNA, Long Noncoding</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Transcription, Genetic</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN long non codant</term><term>Transcription génétique</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Oomycetes</term><term>Phytophthora</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Oomycetes</term><term>Phytophthora</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29665235</PMID><DateCompleted><Year>2019</Year><Month>03</Month><Day>04</Day></DateCompleted><DateRevised><Year>2020</Year><Month>02</Month><Day>25</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1364-3703</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>9</Issue><PubDate><Year>2018</Year><Month>09</Month></PubDate></JournalIssue><Title>Molecular plant pathology</Title><ISOAbbreviation>Mol Plant Pathol</ISOAbbreviation></Journal><ArticleTitle>Genome-wide identification of long non-coding RNAs suggests a potential association with effector gene transcription in Phytophthora sojae.</ArticleTitle><Pagination><MedlinePgn>2177-2186</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/mpp.12692</ELocationID><Abstract><AbstractText>Numerous long non-coding RNAs (lncRNAs) identified and characterized in mammals, plants and fungi have been found to play critical regulatory roles in biological processes. However, little is known about the role of lncRNAs in oomycete plant pathogens, which cause devastating damage to the economy and ecosystems. We used strand-specific RNA sequencing (RNA-seq) to generate a computational pipeline to identify lncRNAs in Phytophthora sojae, a model oomycete plant pathogen. In total, 940 lncRNAs with 1010 isoforms were identified from RNA-seq data obtained from four representative stages of P. sojae. The lncRNAs had shorter transcript lengths, longer exon lengths, fewer numbers of exons, lower GC content and higher minimum free energy values compared with protein-coding genes. lncRNAs in P. sojae exhibited low sequence conservation amongst oomycetes and P. sojae isolates. Transcriptional data indicated that P. sojae lncRNAs tended to be transcribed in a stage-specific manner; representative lncRNAs were validated by semi-quantitative reverse transcription-polymerase chain reaction. Phytophthora sojae lncRNAs were concentrated in gene-sparse regions, and lncRNAs were associated with secreted protein and effector coding genes. The neighbouring genes of lncRNAs encoded various effector family members, and RNA-seq data revealed a correlation between the transcription level of lncRNAs and their neighbouring genes. Our results provide the first comprehensive identification of lncRNAs in oomycetes and suggest a potential association between lncRNAs and effector genes.</AbstractText><CopyrightInformation>© 2018 BSPP and John Wiley & Sons Ltd.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yang</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ye</LastName><ForeName>Wenwu</ForeName><Initials>W</Initials><Identifier Source="ORCID">0000-0001-7347-8935</Identifier><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yuanchao</ForeName><Initials>Y</Initials><Identifier Source="ORCID">0000-0001-5803-5343</Identifier><AffiliationInfo><Affiliation>Department of Plant Pathology, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, Jiangsu 210095, China.</Affiliation></AffiliationInfo></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>2018</Year><Month>07</Month><Day>17</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Plant Pathol</MedlineTA><NlmUniqueID>100954969</NlmUniqueID><ISSNLinking>1364-3703</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D062085">RNA, Long Noncoding</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D009868" MajorTopicYN="N">Oomycetes</DescriptorName><QualifierName UI="Q000472" MajorTopicYN="N">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010838" MajorTopicYN="N">Phytophthora</DescriptorName><QualifierName UI="Q000472" MajorTopicYN="Y">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D062085" MajorTopicYN="N">RNA, Long Noncoding</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014158" MajorTopicYN="N">Transcription, Genetic</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">Phytophthora
</Keyword><Keyword MajorTopicYN="Y">RNA-seq</Keyword><Keyword MajorTopicYN="Y">effector</Keyword><Keyword MajorTopicYN="Y">long non-coding RNAs</Keyword><Keyword MajorTopicYN="Y">transcriptional regulation</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>01</Month><Day>11</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2018</Year><Month>03</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>04</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>4</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>3</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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populaire de Chine"><noRegion><name sortKey="Wang, Yang" sort="Wang, Yang" uniqKey="Wang Y" first="Yang" last="Wang">Yang Wang</name></noRegion><name sortKey="Wang, Yang" sort="Wang, Yang" uniqKey="Wang Y" first="Yang" last="Wang">Yang Wang</name><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name><name sortKey="Wang, Yuanchao" sort="Wang, Yuanchao" uniqKey="Wang Y" first="Yuanchao" last="Wang">Yuanchao Wang</name><name sortKey="Ye, Wenwu" sort="Ye, Wenwu" uniqKey="Ye W" first="Wenwu" last="Ye">Wenwu Ye</name><name sortKey="Ye, Wenwu" sort="Ye, Wenwu" uniqKey="Ye W" first="Wenwu" last="Ye">Wenwu Ye</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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