Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora.
Identifieur interne : 000C69 ( Main/Exploration ); précédent : 000C68; suivant : 000C70Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora.
Auteurs : Stephanie R. Bollmann [États-Unis] ; Yufeng Fang [États-Unis] ; Caroline M. Press [États-Unis] ; Brett M. Tyler [États-Unis] ; Niklaus J. Grünwald [États-Unis]Source :
- Frontiers in plant science [ 1664-462X ] ; 2016.
Abstract
Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed.
DOI: 10.3389/fpls.2016.00284
PubMed: 27014308
PubMed Central: PMC4791657
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Grünwald</name><affiliation wicri:level="2"><nlm:affiliation>Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA; Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA; Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author></analytic><series><title level="j">Frontiers in plant science</title><idno type="ISSN">1664-462X</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27014308</PMID><DateCompleted><Year>2016</Year><Month>03</Month><Day>25</Day></DateCompleted><DateRevised><Year>2020</Year><Month>10</Month><Day>01</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-462X</ISSN><JournalIssue CitedMedium="Print"><Volume>7</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>Frontiers in plant science</Title><ISOAbbreviation>Front Plant Sci</ISOAbbreviation></Journal><ArticleTitle>Diverse Evolutionary Trajectories for Small RNA Biogenesis Genes in the Oomycete Genus Phytophthora.</ArticleTitle><Pagination><MedlinePgn>284</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fpls.2016.00284</ELocationID><Abstract><AbstractText>Gene regulation by small RNA pathways is ubiquitous among eukaryotes, but little is known about small RNA pathways in the Stramenopile kingdom. Phytophthora, a genus of filamentous oomycetes, contains many devastating plant pathogens, causing multibillion-dollar damage to crops, ornamental plants, and natural environments. The genomes of several oomycetes including Phytophthora species such as the soybean pathogen P. sojae, have been sequenced, allowing evolutionary analysis of small RNA-processing enzymes. This study examined the evolutionary origins of the oomycete small RNA-related genes Dicer-like (DCL), and RNA-dependent RNA polymerase (RDR) through broad phylogenetic analyses of the key domains. Two Dicer gene homologs, DCL1 and DCL2, and one RDR homolog were cloned and analyzed from P. sojae. Gene expression analysis revealed only minor changes in transcript levels among different life stages. Oomycete DCL1 homologs clustered with animal and plant Dicer homologs in evolutionary trees, whereas oomycete DCL2 homologs clustered basally to the tree along with Drosha homologs. Phylogenetic analysis of the RDR homologs confirmed a previous study that suggested the last common eukaryote ancestor possessed three RDR homologs, which were selectively retained or lost in later lineages. Our analysis clarifies the position of some Unikont and Chromalveolate RDR lineages within the tree, including oomycete homologs. Finally, we analyzed alterations in the domain structure of oomycete Dicer and RDR homologs, specifically focusing on the proposed domain transfer of the DEAD-box helicase domain from Dicer to RDR. Implications of the oomycete domain structure are discussed, and possible roles of the two oomycete Dicer homologs are proposed. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bollmann</LastName><ForeName>Stephanie R</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>Horticultural Crop Research Unit, USDA-Agricultural Research Service Corvallis, OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Fang</LastName><ForeName>Yufeng</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA; Interdisciplinary Ph.D. Program in Genetics, Bioinformatics and Computational Biology, Virginia TechBlacksburg, VA, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Press</LastName><ForeName>Caroline M</ForeName><Initials>CM</Initials><AffiliationInfo><Affiliation>Horticultural Crop Research Unit, USDA-Agricultural Research Service Corvallis, OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tyler</LastName><ForeName>Brett M</ForeName><Initials>BM</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State University Corvallis, OR, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grünwald</LastName><ForeName>Niklaus J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Horticultural Crop Research Unit, USDA-Agricultural Research ServiceCorvallis, OR, USA; Department of Botany and Plant Pathology and Center for Genome Biology and Biocomputing, Oregon State UniversityCorvallis, OR, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal 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IdType="pubmed">18599326</ArticleId></ArticleIdList></Reference></ReferenceList></PubmedData></pubmed><affiliations><list><country><li>États-Unis</li></country><region><li>Oregon</li><li>Virginie</li></region></list><tree><country name="États-Unis"><region name="Oregon"><name sortKey="Bollmann, Stephanie R" sort="Bollmann, Stephanie R" uniqKey="Bollmann S" first="Stephanie R" last="Bollmann">Stephanie R. Bollmann</name></region><name sortKey="Fang, Yufeng" sort="Fang, Yufeng" uniqKey="Fang Y" first="Yufeng" last="Fang">Yufeng Fang</name><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name><name sortKey="Press, Caroline M" sort="Press, Caroline M" uniqKey="Press C" first="Caroline M" last="Press">Caroline M. Press</name><name sortKey="Tyler, Brett M" sort="Tyler, Brett M" uniqKey="Tyler B" first="Brett M" last="Tyler">Brett M. Tyler</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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