Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina.
Identifieur interne : 000037 ( Main/Exploration ); précédent : 000036; suivant : 000038Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina.
Auteurs : Min Chen [République populaire de Chine] ; Zhimin Cao [République populaire de Chine]Source :
- BMC genomics [ 1471-2164 ] ; 2015.
Descripteurs français
- KwdFr :
- ARN messager (génétique), Analyse de profil d'expression de gènes (MeSH), Basidiomycota (MeSH), Famille multigénique (MeSH), Interactions hôte-pathogène (MeSH), Interférence par ARN (MeSH), Maladies des plantes (génétique), Maladies des plantes (microbiologie), Populus (génétique), Populus (microbiologie), Populus (métabolisme), Régulation de l'expression des gènes végétaux (MeSH), Réseaux de régulation génique (MeSH), Stress physiologique (génétique), Séquençage nucléotidique à haut débit (MeSH), Transduction du signal (MeSH), microARN (génétique), Étude d'association pangénomique (MeSH).
- MESH :
- génétique : ARN messager, Maladies des plantes, Populus, Stress physiologique, microARN.
- microbiologie : Maladies des plantes, Populus.
- métabolisme : Populus.
- Analyse de profil d'expression de gènes, Basidiomycota, Famille multigénique, Interactions hôte-pathogène, Interférence par ARN, Régulation de l'expression des gènes végétaux, Réseaux de régulation génique, Séquençage nucléotidique à haut débit, Transduction du signal, Étude d'association pangénomique.
English descriptors
- KwdEn :
- Basidiomycota (MeSH), Gene Expression Profiling (MeSH), Gene Expression Regulation, Plant (MeSH), Gene Regulatory Networks (MeSH), Genome-Wide Association Study (MeSH), High-Throughput Nucleotide Sequencing (MeSH), Host-Pathogen Interactions (MeSH), MicroRNAs (genetics), Multigene Family (MeSH), Plant Diseases (genetics), Plant Diseases (microbiology), Populus (genetics), Populus (metabolism), Populus (microbiology), RNA Interference (MeSH), RNA, Messenger (genetics), Signal Transduction (MeSH), Stress, Physiological (genetics).
- MESH :
- chemical , genetics : MicroRNAs, RNA, Messenger.
- genetics : Plant Diseases, Populus, Stress, Physiological.
- metabolism : Populus.
- microbiology : Plant Diseases, Populus.
- Basidiomycota, Gene Expression Profiling, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genome-Wide Association Study, High-Throughput Nucleotide Sequencing, Host-Pathogen Interactions, Multigene Family, RNA Interference, Signal Transduction.
Abstract
BACKGROUND
MicroRNAs (miRNAs) are small non-coding RNAs that regulate the gene expression of target mRNAs involved in plant growth, development, and abiotic stress and pathogen responses. Previous studies have reported miRNAs in Populus that respond to abiotic stresses, such as cold, heat, drought, flooding, high salt and mechanical stress. However, little is known about the regulatory roles of these molecules in the Populus response to the stress of foliar rust fungal infection. Here, we identified the miRNA profiles of Populus after inoculation with Melampsora larici-populina using high-throughput sequencing and bioinformatics analysis. Quantitative real-time PCR (qRT-PCR) was used to validate the expression levels of 10 miRNAs.
RESULTS
A total of 90 known miRNAs belonging to 42 families and 378 novel miRNAs were identified from three small-RNA libraries of Populus szechuanica infected with M. larici-populina isolates Sb052 and Th053 and a control. Comparative analysis revealed that the expression of 38 known miRNAs and 92 novel miRNAs in P. szechuanica after infection with different rust fungus isolates showed significant differences, and more miRNAs were suppressed during rust infection. Among the differentially expressed miRNAs, 7 known and 20 novel miRNAs were relevant to the rust fungus infection, and according to KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis, these miRNAs primarily regulate genes encoding disease-resistance proteins, serine/threonine protein kinases, transcription factors, and related proteins. QRT-PCR analysis indicated that most miRNAs were up-regulated in the Sb052 library and down-regulated in the Th053 library at 48 h post-inoculation (hpi).
CONCLUSIONS
These results demonstrate that the expression of miRNAs was altered in poplar under stress associated with M. larici-populina infection, and different temporal dynamics were observed in incompatible and compatible libraries. These findings suggest important roles for miRNA regulation in Populus upon infection with foliar rust fungus.
DOI: 10.1186/s12864-015-1891-8
PubMed: 26370267
PubMed Central: PMC4570220
Affiliations:
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upon infection with the foliar rust fungus Melampsora larici-populina.</title><author><name sortKey="Chen, Min" sort="Chen, Min" uniqKey="Chen M" first="Min" last="Chen">Min Chen</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China. chenmin.11070@163.com.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100</wicri:regionArea><wicri:noRegion>712100</wicri:noRegion></affiliation></author><author><name sortKey="Cao, Zhimin" sort="Cao, Zhimin" uniqKey="Cao Z" first="Zhimin" last="Cao">Zhimin Cao</name><affiliation wicri:level="1"><nlm:affiliation>College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China. zmcao@nwsuaf.edu.cn.</nlm:affiliation><country xml:lang="fr">République populaire de Chine</country><wicri:regionArea>College 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Interference (MeSH)</term><term>RNA, Messenger (genetics)</term><term>Signal Transduction (MeSH)</term><term>Stress, Physiological (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ARN messager (génétique)</term><term>Analyse de profil d'expression de gènes (MeSH)</term><term>Basidiomycota (MeSH)</term><term>Famille multigénique (MeSH)</term><term>Interactions hôte-pathogène (MeSH)</term><term>Interférence par ARN (MeSH)</term><term>Maladies des plantes (génétique)</term><term>Maladies des plantes (microbiologie)</term><term>Populus (génétique)</term><term>Populus (microbiologie)</term><term>Populus (métabolisme)</term><term>Régulation de l'expression des gènes végétaux (MeSH)</term><term>Réseaux de régulation génique (MeSH)</term><term>Stress physiologique (génétique)</term><term>Séquençage nucléotidique à haut débit (MeSH)</term><term>Transduction du signal (MeSH)</term><term>microARN (génétique)</term><term>Étude d'association pangénomique (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>MicroRNAs</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Plant Diseases</term><term>Populus</term><term>Stress, Physiological</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ARN messager</term><term>Maladies des plantes</term><term>Populus</term><term>Stress physiologique</term><term>microARN</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Populus</term></keywords><keywords scheme="MESH" qualifier="microbiologie" xml:lang="fr"><term>Maladies des plantes</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="microbiology" xml:lang="en"><term>Plant Diseases</term><term>Populus</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Populus</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Basidiomycota</term><term>Gene Expression Profiling</term><term>Gene Expression Regulation, Plant</term><term>Gene Regulatory Networks</term><term>Genome-Wide Association Study</term><term>High-Throughput Nucleotide Sequencing</term><term>Host-Pathogen Interactions</term><term>Multigene Family</term><term>RNA Interference</term><term>Signal Transduction</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de profil d'expression de gènes</term><term>Basidiomycota</term><term>Famille multigénique</term><term>Interactions hôte-pathogène</term><term>Interférence par ARN</term><term>Régulation de l'expression des gènes végétaux</term><term>Réseaux de régulation génique</term><term>Séquençage nucléotidique à haut débit</term><term>Transduction du signal</term><term>Étude d'association pangénomique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b></p><p>MicroRNAs (miRNAs) are small non-coding RNAs that regulate the gene expression of target mRNAs involved in plant growth, development, and abiotic stress and pathogen responses. Previous studies have reported miRNAs in Populus that respond to abiotic stresses, such as cold, heat, drought, flooding, high salt and mechanical stress. However, little is known about the regulatory roles of these molecules in the Populus response to the stress of foliar rust fungal infection. Here, we identified the miRNA profiles of Populus after inoculation with Melampsora larici-populina using high-throughput sequencing and bioinformatics analysis. Quantitative real-time PCR (qRT-PCR) was used to validate the expression levels of 10 miRNAs.</p></div><div type="abstract" xml:lang="en"><p><b>RESULTS</b></p><p>A total of 90 known miRNAs belonging to 42 families and 378 novel miRNAs were identified from three small-RNA libraries of Populus szechuanica infected with M. larici-populina isolates Sb052 and Th053 and a control. Comparative analysis revealed that the expression of 38 known miRNAs and 92 novel miRNAs in P. szechuanica after infection with different rust fungus isolates showed significant differences, and more miRNAs were suppressed during rust infection. Among the differentially expressed miRNAs, 7 known and 20 novel miRNAs were relevant to the rust fungus infection, and according to KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis, these miRNAs primarily regulate genes encoding disease-resistance proteins, serine/threonine protein kinases, transcription factors, and related proteins. QRT-PCR analysis indicated that most miRNAs were up-regulated in the Sb052 library and down-regulated in the Th053 library at 48 h post-inoculation (hpi).</p></div><div type="abstract" xml:lang="en"><p><b>CONCLUSIONS</b></p><p>These results demonstrate that the expression of miRNAs was altered in poplar under stress associated with M. larici-populina infection, and different temporal dynamics were observed in incompatible and compatible libraries. These findings suggest important roles for miRNA regulation in Populus upon infection with foliar rust fungus.</p></div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">26370267</PMID><DateCompleted><Year>2016</Year><Month>06</Month><Day>02</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><PubDate><Year>2015</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>BMC genomics</Title><ISOAbbreviation>BMC Genomics</ISOAbbreviation></Journal><ArticleTitle>Genome-wide expression profiling of microRNAs in poplar upon infection with the foliar rust fungus Melampsora larici-populina.</ArticleTitle><Pagination><MedlinePgn>696</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-1891-8</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">MicroRNAs (miRNAs) are small non-coding RNAs that regulate the gene expression of target mRNAs involved in plant growth, development, and abiotic stress and pathogen responses. Previous studies have reported miRNAs in Populus that respond to abiotic stresses, such as cold, heat, drought, flooding, high salt and mechanical stress. However, little is known about the regulatory roles of these molecules in the Populus response to the stress of foliar rust fungal infection. Here, we identified the miRNA profiles of Populus after inoculation with Melampsora larici-populina using high-throughput sequencing and bioinformatics analysis. Quantitative real-time PCR (qRT-PCR) was used to validate the expression levels of 10 miRNAs.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">A total of 90 known miRNAs belonging to 42 families and 378 novel miRNAs were identified from three small-RNA libraries of Populus szechuanica infected with M. larici-populina isolates Sb052 and Th053 and a control. Comparative analysis revealed that the expression of 38 known miRNAs and 92 novel miRNAs in P. szechuanica after infection with different rust fungus isolates showed significant differences, and more miRNAs were suppressed during rust infection. Among the differentially expressed miRNAs, 7 known and 20 novel miRNAs were relevant to the rust fungus infection, and according to KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis, these miRNAs primarily regulate genes encoding disease-resistance proteins, serine/threonine protein kinases, transcription factors, and related proteins. QRT-PCR analysis indicated that most miRNAs were up-regulated in the Sb052 library and down-regulated in the Th053 library at 48 h post-inoculation (hpi).</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">These results demonstrate that the expression of miRNAs was altered in poplar under stress associated with M. larici-populina infection, and different temporal dynamics were observed in incompatible and compatible libraries. These findings suggest important roles for miRNA regulation in Populus upon infection with foliar rust fungus.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Chen</LastName><ForeName>Min</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China. chenmin.11070@163.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Cao</LastName><ForeName>Zhimin</ForeName><Initials>Z</Initials><AffiliationInfo><Affiliation>College of Forestry, Northwest A & F University, Yangling, Shaanxi, 712100, People's Republic of China. zmcao@nwsuaf.edu.cn.</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 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Networks</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D055106" MajorTopicYN="N">Genome-Wide Association Study</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D054884" MajorTopicYN="N">Host-Pathogen Interactions</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D035683" MajorTopicYN="N">MicroRNAs</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005810" MajorTopicYN="N">Multigene Family</DescriptorName></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="D032107" MajorTopicYN="N">Populus</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName><QualifierName UI="Q000382" MajorTopicYN="Y">microbiology</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D034622" MajorTopicYN="N">RNA Interference</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012333" MajorTopicYN="N">RNA, Messenger</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015398" MajorTopicYN="N">Signal Transduction</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013312" MajorTopicYN="N">Stress, Physiological</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate 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