Microbe-ID: an open source toolbox for microbial genotyping and species identification.
Identifieur interne : 000B80 ( Main/Exploration ); précédent : 000B79; suivant : 000B81Microbe-ID: an open source toolbox for microbial genotyping and species identification.
Auteurs : Javier F. Tabima [États-Unis] ; Sydney E. Everhart [États-Unis] ; Meredith M. Larsen [États-Unis] ; Alexandra J. Weisberg [États-Unis] ; Zhian N. Kamvar [États-Unis] ; Matthew A. Tancos [États-Unis] ; Christine D. Smart [États-Unis] ; Jeff H. Chang [États-Unis] ; Niklaus J. Grünwald [États-Unis]Source :
- PeerJ [ 2167-8359 ] ; 2016.
Abstract
Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.
DOI: 10.7717/peerj.2279
PubMed: 27602267
PubMed Central: PMC4994078
Affiliations:
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Tabima</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR </wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Everhart, Sydney E" sort="Everhart, Sydney E" uniqKey="Everhart S" first="Sydney E" last="Everhart">Sydney E. Everhart</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Current affiliation: Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Current affiliation: Department of Plant Pathology, University of Nebraska, Lincoln, NE</wicri:regionArea><placeName><region type="state">Nebraska</region></placeName></affiliation></author><author><name sortKey="Larsen, Meredith M" sort="Larsen, Meredith M" uniqKey="Larsen M" first="Meredith M" last="Larsen">Meredith M. Larsen</name><affiliation wicri:level="2"><nlm:affiliation>Horticultural Crops Research Laboratory, USDA Agricultural Research Service , Corvallis , OR , United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Horticultural Crops Research Laboratory, USDA Agricultural Research Service , Corvallis , OR </wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Weisberg, Alexandra J" sort="Weisberg, Alexandra J" uniqKey="Weisberg A" first="Alexandra J" last="Weisberg">Alexandra J. Weisberg</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR </wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Kamvar, Zhian N" sort="Kamvar, Zhian N" uniqKey="Kamvar Z" first="Zhian N" last="Kamvar">Zhian N. Kamvar</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR </wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Tancos, Matthew A" sort="Tancos, Matthew A" uniqKey="Tancos M" first="Matthew A" last="Tancos">Matthew A. Tancos</name><affiliation wicri:level="2"><nlm:affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY , United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY </wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name><affiliation wicri:level="2"><nlm:affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY , United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY </wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Chang, Jeff H" sort="Chang, Jeff H" uniqKey="Chang J" first="Jeff H" last="Chang">Jeff H. Chang</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author><author><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name><affiliation wicri:level="2"><nlm:affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR</wicri:regionArea><placeName><region type="state">Oregon</region></placeName></affiliation></author></analytic><series><title level="j">PeerJ</title><idno type="ISSN">2167-8359</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">Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. </div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">27602267</PMID><DateCompleted><Year>2016</Year><Month>09</Month><Day>07</Day></DateCompleted><DateRevised><Year>2020</Year><Month>09</Month><Day>29</Day></DateRevised><Article PubModel="Electronic-eCollection"><Journal><ISSN IssnType="Print">2167-8359</ISSN><JournalIssue CitedMedium="Print"><Volume>4</Volume><PubDate><Year>2016</Year></PubDate></JournalIssue><Title>PeerJ</Title><ISOAbbreviation>PeerJ</ISOAbbreviation></Journal><ArticleTitle>Microbe-ID: an open source toolbox for microbial genotyping and species identification.</ArticleTitle><Pagination><MedlinePgn>e2279</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.7717/peerj.2279</ELocationID><Abstract><AbstractText>Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (microbe-id.org) and provided a working implementation for the genus Phytophthora (phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID. </AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Tabima</LastName><ForeName>Javier F</ForeName><Initials>JF</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Everhart</LastName><ForeName>Sydney E</ForeName><Initials>SE</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Current affiliation: Department of Plant Pathology, University of Nebraska, Lincoln, NE, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Larsen</LastName><ForeName>Meredith M</ForeName><Initials>MM</Initials><AffiliationInfo><Affiliation>Horticultural Crops Research Laboratory, USDA Agricultural Research Service , Corvallis , OR , United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weisberg</LastName><ForeName>Alexandra J</ForeName><Initials>AJ</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kamvar</LastName><ForeName>Zhian N</ForeName><Initials>ZN</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tancos</LastName><ForeName>Matthew A</ForeName><Initials>MA</Initials><AffiliationInfo><Affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY , United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Smart</LastName><ForeName>Christine D</ForeName><Initials>CD</Initials><AffiliationInfo><Affiliation>Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University , Geneva , NY , United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chang</LastName><ForeName>Jeff H</ForeName><Initials>JH</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Grünwald</LastName><ForeName>Niklaus J</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States; Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR, United States; Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Geneva, NY, United States; Molecular and Cellular Biology Graduate Program and Center for Genome Biology and Biocomputing, Oregon State University, Corvallis, OR, United States.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>08</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>PeerJ</MedlineTA><NlmUniqueID>101603425</NlmUniqueID><ISSNLinking>2167-8359</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Genotyping</Keyword><Keyword MajorTopicYN="N">Identification</Keyword><Keyword MajorTopicYN="N">Molecular diagnostics</Keyword><Keyword MajorTopicYN="N">Pathogen</Keyword><Keyword MajorTopicYN="N">Phytophthora</Keyword><Keyword MajorTopicYN="N">Taxonomy</Keyword></KeywordList><CoiStatement>Niklaus Grünwald and Jeff Chang are Academic Editors for PeerJ.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2016</Year><Month>04</Month><Day>29</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2016</Year><Month>07</Month><Day>02</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>9</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>9</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>9</Month><Day>8</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27602267</ArticleId><ArticleId IdType="doi">10.7717/peerj.2279</ArticleId><ArticleId 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York</li></region></list><tree><country name="États-Unis"><region name="Oregon"><name sortKey="Tabima, Javier F" sort="Tabima, Javier F" uniqKey="Tabima J" first="Javier F" last="Tabima">Javier F. Tabima</name></region><name sortKey="Chang, Jeff H" sort="Chang, Jeff H" uniqKey="Chang J" first="Jeff H" last="Chang">Jeff H. Chang</name><name sortKey="Everhart, Sydney E" sort="Everhart, Sydney E" uniqKey="Everhart S" first="Sydney E" last="Everhart">Sydney E. Everhart</name><name sortKey="Grunwald, Niklaus J" sort="Grunwald, Niklaus J" uniqKey="Grunwald N" first="Niklaus J" last="Grünwald">Niklaus J. Grünwald</name><name sortKey="Kamvar, Zhian N" sort="Kamvar, Zhian N" uniqKey="Kamvar Z" first="Zhian N" last="Kamvar">Zhian N. Kamvar</name><name sortKey="Larsen, Meredith M" sort="Larsen, Meredith M" uniqKey="Larsen M" first="Meredith M" last="Larsen">Meredith M. Larsen</name><name sortKey="Smart, Christine D" sort="Smart, Christine D" uniqKey="Smart C" first="Christine D" last="Smart">Christine D. Smart</name><name sortKey="Tancos, Matthew A" sort="Tancos, Matthew A" uniqKey="Tancos M" first="Matthew A" last="Tancos">Matthew A. Tancos</name><name sortKey="Weisberg, Alexandra J" sort="Weisberg, Alexandra J" uniqKey="Weisberg A" first="Alexandra J" last="Weisberg">Alexandra J. Weisberg</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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