The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex
Identifieur interne : 000250 ( Main/Exploration ); précédent : 000249; suivant : 000251The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive Bemisia tabaci (Hemiptera: Aleyrodidae) Cryptic Species Complex
Auteurs : Wee Tek Tay [Australie] ; Samia Elfekih [Australie] ; Leon N. Court [Australie] ; Karl H. J. Gordon [Australie] ; Hélène Delatte [France] ; Paul J. De Barro [Australie]Source :
- Genome Biology and Evolution [ 1759-6653 ] ; 2017.
Abstract
Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly
Url:
DOI: 10.1093/gbe/evx173
PubMed: 28985301
PubMed Central: 5647793
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive <italic>Bemisia tabaci</italic> (Hemiptera: Aleyrodidae) Cryptic Species Complex</title><author><name sortKey="Tay, Wee Tek" sort="Tay, Wee Tek" uniqKey="Tay W" first="Wee Tek" last="Tay">Wee Tek Tay</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Elfekih, Samia" sort="Elfekih, Samia" uniqKey="Elfekih S" first="Samia" last="Elfekih">Samia Elfekih</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Court, Leon N" sort="Court, Leon N" uniqKey="Court L" first="Leon N." last="Court">Leon N. Court</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Gordon, Karl H J" sort="Gordon, Karl H J" uniqKey="Gordon K" first="Karl H. J." last="Gordon">Karl H. J. Gordon</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Delatte, Helene" sort="Delatte, Helene" uniqKey="Delatte H" first="Hélène" last="Delatte">Hélène Delatte</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff2">CIRAD, UMR PVBMT, La Réunion, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR PVBMT, La Réunion</wicri:regionArea><wicri:noRegion>La Réunion</wicri:noRegion><wicri:noRegion>La Réunion</wicri:noRegion></affiliation></author><author><name sortKey="De Barro, Paul J" sort="De Barro, Paul J" uniqKey="De Barro P" first="Paul J." last="De Barro">Paul J. De Barro</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff3">CSIRO, Ecosciences Precinct, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Ecosciences Precinct, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">28985301</idno><idno type="pmc">5647793</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5647793</idno><idno type="RBID">PMC:5647793</idno><idno type="doi">10.1093/gbe/evx173</idno><date when="2017">2017</date><idno type="wicri:Area/Pmc/Corpus">001319</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001319</idno><idno type="wicri:Area/Pmc/Curation">001179</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001179</idno><idno type="wicri:Area/Pmc/Checkpoint">000057</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000057</idno><idno type="wicri:source">PubMed</idno><idno type="wicri:Area/PubMed/Corpus">000391</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000391</idno><idno type="wicri:Area/PubMed/Curation">000389</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000389</idno><idno type="wicri:Area/PubMed/Checkpoint">000389</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000389</idno><idno type="wicri:Area/Ncbi/Merge">004F93</idno><idno type="wicri:Area/Ncbi/Curation">004F93</idno><idno type="wicri:Area/Ncbi/Checkpoint">004F93</idno><idno type="wicri:Area/Main/Merge">000245</idno><idno type="wicri:Area/Main/Curation">000250</idno><idno type="wicri:Area/Main/Exploration">000250</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Trouble with MEAM2: Implications of Pseudogenes on Species Delimitation in the Globally Invasive <italic>Bemisia tabaci</italic> (Hemiptera: Aleyrodidae) Cryptic Species Complex</title><author><name sortKey="Tay, Wee Tek" sort="Tay, Wee Tek" uniqKey="Tay W" first="Wee Tek" last="Tay">Wee Tek Tay</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Elfekih, Samia" sort="Elfekih, Samia" uniqKey="Elfekih S" first="Samia" last="Elfekih">Samia Elfekih</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Court, Leon N" sort="Court, Leon N" uniqKey="Court L" first="Leon N." last="Court">Leon N. Court</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Gordon, Karl H J" sort="Gordon, Karl H J" uniqKey="Gordon K" first="Karl H. J." last="Gordon">Karl H. J. Gordon</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff1">CSIRO, Black Mountain Science and Innovation Park, Acton, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Black Mountain Science and Innovation Park, Acton</wicri:regionArea><wicri:noRegion>Acton</wicri:noRegion></affiliation></author><author><name sortKey="Delatte, Helene" sort="Delatte, Helene" uniqKey="Delatte H" first="Hélène" last="Delatte">Hélène Delatte</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff2">CIRAD, UMR PVBMT, La Réunion, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>CIRAD, UMR PVBMT, La Réunion</wicri:regionArea><wicri:noRegion>La Réunion</wicri:noRegion><wicri:noRegion>La Réunion</wicri:noRegion></affiliation></author><author><name sortKey="De Barro, Paul J" sort="De Barro, Paul J" uniqKey="De Barro P" first="Paul J." last="De Barro">Paul J. De Barro</name><affiliation wicri:level="1"><nlm:aff id="evx173-aff3">CSIRO, Ecosciences Precinct, Brisbane, Queensland, Australia</nlm:aff><country xml:lang="fr">Australie</country><wicri:regionArea>CSIRO, Ecosciences Precinct, Brisbane, Queensland</wicri:regionArea><wicri:noRegion>Queensland</wicri:noRegion></affiliation></author></analytic><series><title level="j">Genome Biology and Evolution</title><idno type="eISSN">1759-6653</idno><imprint><date when="2017">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Molecular species identification using suboptimal PCR primers can over-estimate species diversity due to coamplification of nuclear mitochondrial (NUMT) DNA/pseudogenes. For the agriculturally important whitefly <italic>Bemisia tabaci</italic> cryptic pest species complex, species identification depends primarily on characterization of the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene. The lack of robust PCR primers for the mtDNA COI gene can undermine correct species identification which in turn compromises management strategies. This problem is identified in the <italic>B. tabaci</italic> Africa/Middle East/Asia Minor clade which comprises the globally invasive Mediterranean (MED) and Middle East Asia Minor I (MEAM1) species, Middle East Asia Minor 2 (MEAM2), and the Indian Ocean (IO) species. Initially identified from the Indian Ocean island of Réunion, MEAM2 has since been reported from Japan, Peru, Turkey and Iraq. We identified MEAM2 individuals from a Peruvian population via Sanger sequencing of the mtDNA COI gene. In attempting to characterize the MEAM2 mitogenome, we instead characterized mitogenomes of MEAM1. We also report on the mitogenomes of MED, AUS, and IO thereby increasing genomic resources for members of this complex. Gene synteny (i.e., same gene composition and orientation) was observed with published <italic>B. tabaci</italic> cryptic species mitogenomes. Pseudogene fragments matching MEAM2 partial mtDNA COI gene exhibited low frequency single nucleotide polymorphisms that matched low copy number DNA fragments (<3%) of MEAM1 genomes, whereas presence of internal stop codons, loss of expected stop codons and poor primer annealing sites, all suggested MEAM2 as a pseudogene artifact and so not a real species.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alam, Mm" uniqKey="Alam M">MM Alam</name></author><author><name sortKey="Westfall, Km" uniqKey="Westfall K">KM Westfall</name></author><author><name sortKey="Palsson, S" uniqKey="Palsson S">S. 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Kanmiya</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Wang, H L" uniqKey="Wang H">H-L Wang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Australie</li><li>France</li></country></list><tree><country name="Australie"><noRegion><name sortKey="Tay, Wee Tek" sort="Tay, Wee Tek" uniqKey="Tay W" first="Wee Tek" last="Tay">Wee Tek Tay</name></noRegion><name sortKey="Court, Leon N" sort="Court, Leon N" uniqKey="Court L" first="Leon N." last="Court">Leon N. Court</name><name sortKey="De Barro, Paul J" sort="De Barro, Paul J" uniqKey="De Barro P" first="Paul J." last="De Barro">Paul J. De Barro</name><name sortKey="Elfekih, Samia" sort="Elfekih, Samia" uniqKey="Elfekih S" first="Samia" last="Elfekih">Samia Elfekih</name><name sortKey="Gordon, Karl H J" sort="Gordon, Karl H J" uniqKey="Gordon K" first="Karl H. J." last="Gordon">Karl H. J. Gordon</name></country><country name="France"><noRegion><name sortKey="Delatte, Helene" sort="Delatte, Helene" uniqKey="Delatte H" first="Hélène" last="Delatte">Hélène Delatte</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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