Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species.
Identifieur interne : 000798 ( Main/Exploration ); précédent : 000797; suivant : 000799Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying Phytophthora Species.
Auteurs : Xiao Yang [États-Unis] ; Chuanxue Hong [États-Unis]Source :
- Frontiers in microbiology [ 1664-302X ] ; 2018.
Abstract
The genus Phytophthora is agriculturally and ecologically important. As the number of Phytophthora species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named Phytophthora species. These genetic markers were the cytochrome-c oxidase 1 (cox1), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (β-tub), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and tigA gene fusion protein (tigA). As indicated by species distance, cox1 had the highest genus-wide resolution, followed by ITS, tigA, and β-tub. Resolution of these four markers also varied with (sub)clade. β-tub alone could readily identify all species in clade 1, cox1 for clade 2, and tigA for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and β-tub (96%) were easier to amplify than cox1 (75%) and tigA (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown Phytophthora isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.
DOI: 10.3389/fmicb.2018.02334
PubMed: 30337915
PubMed Central: PMC6178919
Affiliations:
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As the number of <i>Phytophthora</i> species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named <i>Phytophthora</i> species. These genetic markers were the cytochrome-<i>c</i> oxidase 1 (<i>cox1</i>), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (β<i>-tub</i>), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and <i>tigA</i> gene fusion protein (<i>tigA</i>). As indicated by species distance, <i>cox1</i> had the highest genus-wide resolution, followed by ITS, <i>tigA</i>, and β<i>-tub</i>. Resolution of these four markers also varied with (sub)clade. β<i>-tub</i> alone could readily identify all species in clade 1, <i>cox1</i> for clade 2, and <i>tigA</i> for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and β<i>-tub</i> (96%) were easier to amplify than <i>cox1</i> (75%) and <i>tigA</i> (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown <i>Phytophthora</i> isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">30337915</PMID><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">1664-302X</ISSN><JournalIssue CitedMedium="Print"><Volume>9</Volume><PubDate><Year>2018</Year></PubDate></JournalIssue><Title>Frontiers in microbiology</Title><ISOAbbreviation>Front Microbiol</ISOAbbreviation></Journal><ArticleTitle>Differential Usefulness of Nine Commonly Used Genetic Markers for Identifying <i>Phytophthora</i> Species.</ArticleTitle><Pagination><MedlinePgn>2334</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.3389/fmicb.2018.02334</ELocationID><Abstract><AbstractText>The genus <i>Phytophthora</i> is agriculturally and ecologically important. As the number of <i>Phytophthora</i> species continues to grow, identifying isolates in this genus has become increasingly challenging even by DNA sequencing. This study evaluated nine commonly used genetic markers against 154 formally described and 17 provisionally named <i>Phytophthora</i> species. These genetic markers were the cytochrome-<i>c</i> oxidase 1 (<i>cox1</i>), internal transcribed spacer region (ITS), 60S ribosomal protein L10, beta-tubulin (β<i>-tub</i>), elongation factor 1 alpha, enolase, heat shock protein 90, 28S ribosomal DNA, and <i>tigA</i> gene fusion protein (<i>tigA</i>). As indicated by species distance, <i>cox1</i> had the highest genus-wide resolution, followed by ITS, <i>tigA</i>, and β<i>-tub</i>. Resolution of these four markers also varied with (sub)clade. β<i>-tub</i> alone could readily identify all species in clade 1, <i>cox1</i> for clade 2, and <i>tigA</i> for clades 7 and 8. Two or more genetic markers were required to identify species in other clades. For PCR consistency, ITS (99% PCR success rate) and β<i>-tub</i> (96%) were easier to amplify than <i>cox1</i> (75%) and <i>tigA</i> (71%). Accordingly, it is recommended to take a two-step approach: classifying unknown <i>Phytophthora</i> isolates to clade by ITS sequences, as this marker is easy to amplify and its signature sequences are readily available, then identifying to species by one or more of the most informative markers for the respective (sub)clade.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiao</ForeName><Initials>X</Initials><AffiliationInfo><Affiliation>Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hong</LastName><ForeName>Chuanxue</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Hampton Roads Agricultural Research and Extension Center, Virginia Tech, Virginia Beach, VA, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType 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