Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation).
Identifieur interne : 000120 ( Main/Exploration ); précédent : 000119; suivant : 000121Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation).
Auteurs : Erik A. Visser [Afrique du Sud] ; Jill L. Wegrzyn [États-Unis] ; Alexander A. Myburg [Afrique du Sud] ; Sanushka Naidoo [Afrique du Sud]Source :
- BMC genomics [ 1471-2164 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Maladies des plantes, Pinus.
- microbiologie : Maladies des plantes, Pinus.
- normes : Analyse de profil d'expression de gènes.
- physiologie : Fusarium.
- Annotation de séquence moléculaire, Normes de référence.
English descriptors
- KwdEn :
- MESH :
- genetics : Pinus, Plant Diseases.
- microbiology : Pinus, Plant Diseases.
- physiology : Fusarium.
- standards : Gene Expression Profiling.
- Molecular Sequence Annotation, Reference Standards.
Abstract
BACKGROUND
Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular mechanisms involved in the host-pathogen interaction between F. circinatum and pine species. Pinus tecunumanii and Pinus patula are two closely related tropical pine species that differ widely in their resistance to F. circinatum challenge, being resistant and susceptible respectively, providing the potential for a useful pathosystem to investigate the molecular responses underlying resistance to F. circinatum. However, no genomic resources are available for P. tecunumanii. Pathogenesis-related proteins are classes of proteins that play important roles in plant-microbe interactions, e.g. chitinases; proteins that break down the major structural component of fungal cell walls. Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine-F. circinatum interaction.
RESULTS
Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula. Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species.
CONCLUSIONS
The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum. This study also constitutes, to our knowledge, the largest index of gymnosperm PR-genes to date.
DOI: 10.1186/s12864-018-5015-0
PubMed: 30139335
PubMed Central: PMC6108113
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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Myburg</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028</wicri:regionArea><wicri:noRegion>0028</wicri:noRegion></affiliation></author><author><name sortKey="Naidoo, Sanushka" sort="Naidoo, Sanushka" uniqKey="Naidoo S" first="Sanushka" last="Naidoo">Sanushka Naidoo</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa. sanushka.naidoo@fabi.up.ac.za.</nlm:affiliation><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028</wicri:regionArea><wicri:noRegion>0028</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Fusarium (physiology)</term><term>Gene Expression Profiling (standards)</term><term>Molecular Sequence Annotation (MeSH)</term><term>Pinus (genetics)</term><term>Pinus (microbiology)</term><term>Plant Diseases (genetics)</term><term>Plant Diseases (microbiology)</term><term>Reference Standards (MeSH)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de profil d'expression de gènes (normes)</term><term>Annotation de séquence moléculaire (MeSH)</term><term>Fusarium (physiologie)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (microbiologie)</term><term>Normes de référence (MeSH)</term><term>Pinus (génétique)</term><term>Pinus (microbiologie)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Pinus</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Maladies des plantes</term><term>Pinus</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Pinus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Pinus</term><term>Plant Diseases</term></keywords><keywords scheme="MESH" qualifier="normes" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term></keywords><keywords scheme="MESH" qualifier="physiologie" xml:lang="fr"><term>Fusarium</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Fusarium</term></keywords><keywords scheme="MESH" qualifier="standards" xml:lang="en"><term>Gene Expression Profiling</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Molecular Sequence Annotation</term><term>Reference Standards</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Annotation de séquence moléculaire</term><term>Normes de référence</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular mechanisms involved in the host-pathogen interaction between F. circinatum and pine species. Pinus tecunumanii and Pinus patula are two closely related tropical pine species that differ widely in their resistance to F. circinatum challenge, being resistant and susceptible respectively, providing the potential for a useful pathosystem to investigate the molecular responses underlying resistance to F. circinatum. However, no genomic resources are available for P. tecunumanii. Pathogenesis-related proteins are classes of proteins that play important roles in plant-microbe interactions, e.g. chitinases; proteins that break down the major structural component of fungal cell walls. Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine-F. circinatum interaction.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula. Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species.</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum. This study also constitutes, to our knowledge, the largest index of gymnosperm PR-genes to date.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">30139335</PMID><DateCompleted><Year>2018</Year><Month>11</Month><Day>05</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>14</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>19</Volume><Issue>1</Issue><PubDate><Year>2018</Year><Month>Aug</Month><Day>23</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Defence transcriptome assembly and pathogenesis related gene family analysis in Pinus tecunumanii (low elevation).</ArticleTitle><Pagination><MedlinePgn>632</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-018-5015-0</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular mechanisms involved in the host-pathogen interaction between F. circinatum and pine species. Pinus tecunumanii and Pinus patula are two closely related tropical pine species that differ widely in their resistance to F. circinatum challenge, being resistant and susceptible respectively, providing the potential for a useful pathosystem to investigate the molecular responses underlying resistance to F. circinatum. However, no genomic resources are available for P. tecunumanii. Pathogenesis-related proteins are classes of proteins that play important roles in plant-microbe interactions, e.g. chitinases; proteins that break down the major structural component of fungal cell walls. Generating a reference sequence for P. tecunumanii and characterizing pathogenesis related gene families in these two pine species is an important step towards unravelling the pine-F. circinatum interaction.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Eight reference based and 12 de novo assembled transcriptomes were produced, for juvenile shoot tissue from both species. EvidentialGene pipeline redundancy reduction, expression filtering, protein clustering and taxonomic filtering produced a 50 Mb shoot transcriptome consisting of 28,621 contigs for P. tecunumanii and a 72 Mb shoot transcriptome consisting of 52,735 contigs for P. patula. Predicted protein sequences encoded by the assembled transcriptomes were clustered with reference proteomes from 92 other species to identify pathogenesis related gene families in P. patula, P. tecunumanii and other pine species.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">The P. tecunumanii transcriptome is the first gene catalogue for the species, representing an important resource for studying resistance to the pitch canker pathogen, F. circinatum. This study also constitutes, to our knowledge, the largest index of gymnosperm PR-genes to date.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Visser</LastName><ForeName>Erik A</ForeName><Initials>EA</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wegrzyn</LastName><ForeName>Jill L</ForeName><Initials>JL</Initials><AffiliationInfo><Affiliation>Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Myburg</LastName><ForeName>Alexander A</ForeName><Initials>AA</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Naidoo</LastName><ForeName>Sanushka</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa. sanushka.naidoo@fabi.up.ac.za.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>97892</GrantID><Agency>National Research Foundation</Agency><Country></Country></Grant><Grant><GrantID>86936</GrantID><Agency>National Research Foundation</Agency><Country></Country></Grant><Grant><GrantID>97911</GrantID><Agency>National Research Foundation</Agency><Country></Country></Grant><Grant><GrantID>96413</GrantID><Agency>Technology and Human Resources for Industry Programme (THRIP)</Agency><Country></Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2018</Year><Month>08</Month><Day>23</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Genomics</MedlineTA><NlmUniqueID>100965258</NlmUniqueID><ISSNLinking>1471-2164</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D005670" MajorTopicYN="N">Fusarium</DescriptorName><QualifierName UI="Q000502" MajorTopicYN="N">physiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020869" MajorTopicYN="Y">Gene Expression Profiling</DescriptorName><QualifierName UI="Q000592" MajorTopicYN="N">standards</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058977" MajorTopicYN="N">Molecular Sequence Annotation</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D028223" MajorTopicYN="N">Pinus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010935" MajorTopicYN="N">Plant Diseases</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012015" MajorTopicYN="N">Reference Standards</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Disease resistance</Keyword><Keyword MajorTopicYN="N">Fusarium circinatum</Keyword><Keyword MajorTopicYN="N">PR genes</Keyword><Keyword MajorTopicYN="N">Pinus patula</Keyword><Keyword MajorTopicYN="N">Pinus tecunumanii</Keyword><Keyword MajorTopicYN="N">Transcriptome assembly</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year><Month>01</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2018</Year><Month>08</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2018</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2018</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2018</Year><Month>11</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">30139335</ArticleId><ArticleId IdType="doi">10.1186/s12864-018-5015-0</ArticleId><ArticleId 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Visser</name></noRegion><name sortKey="Myburg, Alexander A" sort="Myburg, Alexander A" uniqKey="Myburg A" first="Alexander A" last="Myburg">Alexander A. Myburg</name><name sortKey="Naidoo, Sanushka" sort="Naidoo, Sanushka" uniqKey="Naidoo S" first="Sanushka" last="Naidoo">Sanushka Naidoo</name></country><country name="États-Unis"><noRegion><name sortKey="Wegrzyn, Jill L" sort="Wegrzyn, Jill L" uniqKey="Wegrzyn J" first="Jill L" last="Wegrzyn">Jill L. Wegrzyn</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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