Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon.
Identifieur interne : 001D38 ( Main/Exploration ); précédent : 001D37; suivant : 001D39Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon.
Auteurs : Kranthi K. Mandadi [États-Unis] ; Karen-Beth G. Scholthof [États-Unis]Source :
- The Plant cell [ 1532-298X ] ; 2015.
Descripteurs français
- KwdFr :
- Brachypodium (génétique), Brachypodium (virologie), Génome végétal (génétique), Oryza (génétique), Oryza (virologie), Protéines végétales (génétique), Régulation de l'expression des gènes végétaux (MeSH), Sorghum (génétique), Sorghum (virologie), Virus des plantes (pathogénicité), Épissage alternatif (génétique).
- MESH :
- génétique : Brachypodium, Génome végétal, Oryza, Protéines végétales, Sorghum, Épissage alternatif.
- pathogénicité : Virus des plantes.
- virologie : Brachypodium, Oryza, Sorghum.
- Régulation de l'expression des gènes végétaux.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Plant Proteins.
- genetics : Alternative Splicing, Brachypodium, Genome, Plant, Oryza, Sorghum.
- pathogenicity : Plant Viruses.
- virology : Brachypodium, Oryza, Sorghum.
- Gene Expression Regulation, Plant.
Abstract
In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes.
DOI: 10.1105/tpc.114.133991
PubMed: 25634987
PubMed Central: PMC4330581
Affiliations:
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The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25634987</PMID><DateCompleted><Year>2015</Year><Month>12</Month><Day>22</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1532-298X</ISSN><JournalIssue CitedMedium="Internet"><Volume>27</Volume><Issue>1</Issue><PubDate><Year>2015</Year><Month>Jan</Month></PubDate></JournalIssue><Title>The Plant cell</Title><ISOAbbreviation>Plant Cell</ISOAbbreviation></Journal><ArticleTitle>Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon.</ArticleTitle><Pagination><MedlinePgn>71-85</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1105/tpc.114.133991</ELocationID><Abstract><AbstractText>In eukaryotes, alternative splicing (AS) promotes transcriptome and proteome diversity. The extent of genome-wide AS changes occurring during a plant-microbe interaction is largely unknown. Here, using high-throughput, paired-end RNA sequencing, we generated an isoform-level spliceome map of Brachypodium distachyon infected with Panicum mosaic virus and its satellite virus. Overall, we detected ∼44,443 transcripts in B. distachyon, ∼30% more than those annotated in the reference genome. Expression of ∼28,900 transcripts was ≥2 fragments per kilobase of transcript per million mapped fragments, and ∼42% of multi-exonic genes were alternatively spliced. Comparative analysis of AS patterns in B. distachyon, rice (Oryza sativa), maize (Zea mays), sorghum (Sorghum bicolor), Arabidopsis thaliana, potato (Solanum tuberosum), Medicago truncatula, and poplar (Populus trichocarpa) revealed conserved ratios of the AS types between monocots and dicots. Virus infection quantitatively altered AS events in Brachypodium with little effect on the AS ratios. We discovered AS events for >100 immune-related genes encoding receptor-like kinases, NB-LRR resistance proteins, transcription factors, RNA silencing, and splicing-associated proteins. Cloning and molecular characterization of SCL33, a serine/arginine-rich splicing factor, identified multiple novel intron-retaining splice variants that are developmentally regulated and modulated during virus infection. B. distachyon SCL33 splicing patterns are also strikingly conserved compared with a distant Arabidopsis SCL33 ortholog. This analysis provides new insights into AS landscapes conserved among monocots and dicots and uncovered AS events in plant defense-related genes. </AbstractText><CopyrightInformation>© 2015 American Society of Plant Biologists. 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DateType="Electronic"><Year>2015</Year><Month>01</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Plant Cell</MedlineTA><NlmUniqueID>9208688</NlmUniqueID><ISSNLinking>1040-4651</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="CommentIn"><RefSource>Plant Cell. 2015 Jan;27(1):7</RefSource><PMID Version="1">25634986</PMID></CommentsCorrections></CommentsCorrectionsList><MeshHeadingList><MeshHeading><DescriptorName UI="D017398" MajorTopicYN="N">Alternative Splicing</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D058431" MajorTopicYN="N">Brachypodium</DescriptorName><QualifierName UI="Q000235" 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Mandadi</name></region><name sortKey="Scholthof, Karen Beth G" sort="Scholthof, Karen Beth G" uniqKey="Scholthof K" first="Karen-Beth G" last="Scholthof">Karen-Beth G. Scholthof</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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