Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation
Identifieur interne : 000E92 ( Main/Exploration ); précédent : 000E91; suivant : 000E93Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation
Auteurs : Juerg E. Frey [Suisse] ; Larissa Guillén [Mexique] ; Beatrice Frey [Suisse] ; Joerg Samietz [Suisse] ; Juan Rull [Mexique] ; Martín Aluja [Mexique]Source :
- BMC Evolutionary Biology [ 1471-2148 ] ; 2013.
Abstract
Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5′end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.
In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established “near-minimal” sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively.
We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence represent an important resource for developing taxon-specific diagnostic assays. For selected cases, possible explanations that may cause composite OTUs are discussed.
Url:
DOI: 10.1186/1471-2148-13-106
PubMed: 23718854
PubMed Central: 3682933
Affiliations:
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Frey</name><affiliation wicri:level="1"><nlm:aff id="I1">Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820</wicri:regionArea><wicri:noRegion>8820</wicri:noRegion></affiliation></author><author><name sortKey="Guillen, Larissa" sort="Guillen, Larissa" uniqKey="Guillen L" first="Larissa" last="Guillén">Larissa Guillén</name><affiliation wicri:level="1"><nlm:aff id="I2">Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México</nlm:aff><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000</wicri:regionArea><wicri:noRegion>91000</wicri:noRegion></affiliation></author><author><name sortKey="Frey, Beatrice" sort="Frey, Beatrice" uniqKey="Frey B" first="Beatrice" last="Frey">Beatrice Frey</name><affiliation wicri:level="1"><nlm:aff id="I1">Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820</wicri:regionArea><wicri:noRegion>8820</wicri:noRegion></affiliation></author><author><name sortKey="Samietz, Joerg" sort="Samietz, Joerg" uniqKey="Samietz J" first="Joerg" last="Samietz">Joerg Samietz</name><affiliation wicri:level="1"><nlm:aff id="I1">Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820</wicri:regionArea><wicri:noRegion>8820</wicri:noRegion></affiliation></author><author><name sortKey="Rull, Juan" sort="Rull, Juan" uniqKey="Rull J" first="Juan" last="Rull">Juan Rull</name><affiliation wicri:level="1"><nlm:aff id="I2">Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México</nlm:aff><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000</wicri:regionArea><wicri:noRegion>91000</wicri:noRegion></affiliation></author><author><name sortKey="Aluja, Martin" sort="Aluja, Martin" uniqKey="Aluja M" first="Martín" last="Aluja">Martín Aluja</name><affiliation wicri:level="1"><nlm:aff id="I2">Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México</nlm:aff><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000</wicri:regionArea><wicri:noRegion>91000</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23718854</idno><idno type="pmc">3682933</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682933</idno><idno type="RBID">PMC:3682933</idno><idno type="doi">10.1186/1471-2148-13-106</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000B08</idno><idno type="wicri:Area/Pmc/Curation">000B07</idno><idno type="wicri:Area/Pmc/Checkpoint">000B06</idno><idno type="wicri:Area/Ncbi/Merge">001303</idno><idno type="wicri:Area/Ncbi/Curation">001303</idno><idno type="wicri:Area/Ncbi/Checkpoint">001303</idno><idno type="wicri:Area/Main/Merge">000E96</idno><idno type="wicri:Area/Main/Curation">000E92</idno><idno type="wicri:Area/Main/Exploration">000E92</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Developing diagnostic SNP panels for the identification of true fruit flies (Diptera: Tephritidae) within the limits of COI-based species delimitation</title><author><name sortKey="Frey, Juerg E" sort="Frey, Juerg E" uniqKey="Frey J" first="Juerg E" last="Frey">Juerg E. Frey</name><affiliation wicri:level="1"><nlm:aff id="I1">Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820</wicri:regionArea><wicri:noRegion>8820</wicri:noRegion></affiliation></author><author><name sortKey="Guillen, Larissa" sort="Guillen, Larissa" uniqKey="Guillen L" first="Larissa" last="Guillén">Larissa Guillén</name><affiliation wicri:level="1"><nlm:aff id="I2">Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México</nlm:aff><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000</wicri:regionArea><wicri:noRegion>91000</wicri:noRegion></affiliation></author><author><name sortKey="Frey, Beatrice" sort="Frey, Beatrice" uniqKey="Frey B" first="Beatrice" last="Frey">Beatrice Frey</name><affiliation wicri:level="1"><nlm:aff id="I1">Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820</wicri:regionArea><wicri:noRegion>8820</wicri:noRegion></affiliation></author><author><name sortKey="Samietz, Joerg" sort="Samietz, Joerg" uniqKey="Samietz J" first="Joerg" last="Samietz">Joerg Samietz</name><affiliation wicri:level="1"><nlm:aff id="I1">Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820, Switzerland</nlm:aff><country xml:lang="fr">Suisse</country><wicri:regionArea>Federal Department of Economic Affairs FDEA, Agroscope Changins-Wädenswil Research Station ACW, Department of Plant Protection, Schloss, P.O. 185, Wädenswil, 8820</wicri:regionArea><wicri:noRegion>8820</wicri:noRegion></affiliation></author><author><name sortKey="Rull, Juan" sort="Rull, Juan" uniqKey="Rull J" first="Juan" last="Rull">Juan Rull</name><affiliation wicri:level="1"><nlm:aff id="I2">Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México</nlm:aff><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000</wicri:regionArea><wicri:noRegion>91000</wicri:noRegion></affiliation></author><author><name sortKey="Aluja, Martin" sort="Aluja, Martin" uniqKey="Aluja M" first="Martín" last="Aluja">Martín Aluja</name><affiliation wicri:level="1"><nlm:aff id="I2">Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000, México</nlm:aff><country xml:lang="fr" wicri:curation="lc">Mexique</country><wicri:regionArea>Instituto de Ecología, A.C, Apartado Postal 63, Xalapa, Veracruz, 91000</wicri:regionArea><wicri:noRegion>91000</wicri:noRegion></affiliation></author></analytic><series><title level="j">BMC Evolutionary Biology</title><idno type="eISSN">1471-2148</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Rapid and reliable identification of quarantine pests is essential for plant inspection services to prevent introduction of invasive species. For insects, this may be a serious problem when dealing with morphologically similar cryptic species complexes and early developmental stages that lack distinctive characters useful for taxonomic identification. DNA based barcoding could solve many of these problems. The standard barcode fragment, an approx. 650 base pairs long sequence of the 5′end of the mitochondrial cytochrome oxidase I (COI), enables differentiation of a very wide range of arthropods. However, problems remain in some taxa, such as Tephritidae, where recent genetic differentiation among some of the described species hinders accurate molecular discrimination.</p></sec><sec><title>Results</title><p>In order to explore the full species discrimination potential of COI, we sequenced the barcoding region of the COI gene of a range of economically important Tephritid species and complemented these data with all GenBank and BOLD entries for the systematic group available as of January 2012. We explored the limits of species delimitation of this barcode fragment among 193 putative Tephritid species and established operational taxonomic units (OTUs), between which discrimination is reliably possible. Furthermore, to enable future development of rapid diagnostic assays based on this sequence information, we characterized all single nucleotide polymorphisms (SNPs) and established “near-minimal” sets of SNPs that differentiate among all included OTUs with at least three and four SNPs, respectively.</p></sec><sec><title>Conclusions</title><p>We found that although several species cannot be differentiated based on the genetic diversity observed in COI and hence form composite OTUs, 85% of all OTUs correspond to described species. Because our SNP panels are developed based on all currently available sequence information and rely on a minimal pairwise difference of three SNPs, they are highly reliable and hence represent an important resource for developing taxon-specific diagnostic assays. For selected cases, possible explanations that may cause composite OTUs are discussed.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Olden, Jd" uniqKey="Olden J">JD Olden</name></author><author><name sortKey="Leroy Poff, N" uniqKey="Leroy Poff N">N Leroy Poff</name></author><author><name sortKey="Douglas, Mr" uniqKey="Douglas M">MR Douglas</name></author><author><name sortKey="Douglas, Me" uniqKey="Douglas M">ME Douglas</name></author><author><name sortKey="Fausch, Kd" uniqKey="Fausch K">KD Fausch</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Armstrong, Kf" uniqKey="Armstrong K">KF Armstrong</name></author><author><name sortKey="Ball, Sl" uniqKey="Ball S">SL Ball</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Frezal, L" uniqKey="Frezal L">L Frézal</name></author><author><name sortKey="Leblois, R" uniqKey="Leblois R">R 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Frey</name></noRegion><name sortKey="Frey, Beatrice" sort="Frey, Beatrice" uniqKey="Frey B" first="Beatrice" last="Frey">Beatrice Frey</name><name sortKey="Samietz, Joerg" sort="Samietz, Joerg" uniqKey="Samietz J" first="Joerg" last="Samietz">Joerg Samietz</name></country><country name="Mexique"><noRegion><name sortKey="Guillen, Larissa" sort="Guillen, Larissa" uniqKey="Guillen L" first="Larissa" last="Guillén">Larissa Guillén</name></noRegion><name sortKey="Aluja, Martin" sort="Aluja, Martin" uniqKey="Aluja M" first="Martín" last="Aluja">Martín Aluja</name><name sortKey="Rull, Juan" sort="Rull, Juan" uniqKey="Rull J" first="Juan" last="Rull">Juan Rull</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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