Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.
Identifieur interne : 002914 ( PubMed/Checkpoint ); précédent : 002913; suivant : 002915Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.
Auteurs : Iván Darío Soto-Calder N [Colombie] ; Nicholas Jonathan Clark [États-Unis] ; Julia Vera Halo Wildschutte [États-Unis] ; Kelly Dimattio [États-Unis] ; Michael Ignatius Jensen-Seaman [États-Unis] ; Nicola Mary Anthony [États-Unis]Source :
- Molecular phylogenetics and evolution [ 1095-9513 ] ; 2014.
Descripteurs français
- KwdFr :
- ADN (génétique), ADN mitochondrial (génétique), Analyse de séquence d'ADN, Animaux, Gorilla gorilla (génétique), Génome, Génétique des populations, Marqueurs génétiques, Noyau de la cellule (génétique), Pan troglodytes (génétique), Phylogénie, Spécificité d'espèce, Séquence nucléotidique, Éléments transposables d'ADN.
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, DNA, Mitochondrial.
- genetics : Cell Nucleus, Gorilla gorilla, Pan troglodytes.
- Animals, Base Sequence, DNA Transposable Elements, Genetic Markers, Genetics, Population, Genome, Phylogeny, Sequence Analysis, DNA, Species Specificity.
Abstract
The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts examined, indicating their potential utility as molecular markers. Taken together, these findings demonstrate the potentially powerful insight that numts could make in uncovering population history in gorillas and other mammals.
DOI: 10.1016/j.ympev.2014.08.018
PubMed: 25194325
Affiliations:
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xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Jensen Seaman, Michael Ignatius" sort="Jensen Seaman, Michael Ignatius" uniqKey="Jensen Seaman M" first="Michael Ignatius" last="Jensen-Seaman">Michael Ignatius Jensen-Seaman</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Anthony, Nicola Mary" sort="Anthony, Nicola Mary" uniqKey="Anthony N" first="Nicola Mary" last="Anthony">Nicola Mary Anthony</name><affiliation wicri:level="2"><nlm:affiliation>Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148</wicri:regionArea><placeName><region type="state">Louisiane</region></placeName></affiliation></author></analytic><series><title level="j">Molecular phylogenetics and evolution</title><idno type="eISSN">1095-9513</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>Cell Nucleus (genetics)</term><term>DNA (genetics)</term><term>DNA Transposable Elements</term><term>DNA, Mitochondrial (genetics)</term><term>Genetic Markers</term><term>Genetics, Population</term><term>Genome</term><term>Gorilla gorilla (genetics)</term><term>Pan troglodytes (genetics)</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (génétique)</term><term>ADN mitochondrial (génétique)</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Gorilla gorilla (génétique)</term><term>Génome</term><term>Génétique des populations</term><term>Marqueurs génétiques</term><term>Noyau de la cellule (génétique)</term><term>Pan troglodytes (génétique)</term><term>Phylogénie</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term><term>Éléments transposables d'ADN</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term><term>DNA, Mitochondrial</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Nucleus</term><term>Gorilla gorilla</term><term>Pan troglodytes</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN</term><term>ADN mitochondrial</term><term>Gorilla gorilla</term><term>Noyau de la cellule</term><term>Pan troglodytes</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Base Sequence</term><term>DNA Transposable Elements</term><term>Genetic Markers</term><term>Genetics, Population</term><term>Genome</term><term>Phylogeny</term><term>Sequence Analysis, DNA</term><term>Species Specificity</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Génome</term><term>Génétique des populations</term><term>Marqueurs génétiques</term><term>Phylogénie</term><term>Spécificité d'espèce</term><term>Séquence nucléotidique</term><term>Éléments transposables d'ADN</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts examined, indicating their potential utility as molecular markers. Taken together, these findings demonstrate the potentially powerful insight that numts could make in uncovering population history in gorillas and other mammals.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25194325</PMID><DateCreated><Year>2014</Year><Month>12</Month><Day>03</Day></DateCreated><DateCompleted><Year>2015</Year><Month>03</Month><Day>05</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1095-9513</ISSN><JournalIssue CitedMedium="Internet"><Volume>81</Volume><PubDate><Year>2014</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Molecular phylogenetics and evolution</Title><ISOAbbreviation>Mol. Phylogenet. Evol.</ISOAbbreviation></Journal><ArticleTitle>Identification of species-specific nuclear insertions of mitochondrial DNA (numts) in gorillas and their potential as population genetic markers.</ArticleTitle><Pagination><MedlinePgn>61-70</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.ympev.2014.08.018</ELocationID><ELocationID EIdType="pii" ValidYN="Y">S1055-7903(14)00303-0</ELocationID><Abstract><AbstractText>The first hyper-variable region (HV1) of the mitochondrial control region (MCR) has been widely used as a molecular tool in population genetics, but inadvertent amplification of nuclear translocated copies of mitochondrial DNA (numts) in gorillas has compromised the use of mitochondrial DNA in population genetic studies. At least three putative classes (I, II, III) of gorilla-specific HV1 MCR numts have been uncovered over the past decade. However, the number, size and location of numt loci in gorillas and other apes are completely unknown. Furthermore, little work to date has assessed the utility of numts as candidate population genetic markers. In the present study, we screened Bacterial Artificial Chromosome (BAC) genomic libraries in the chimpanzee and gorilla to compare patterns of mitochondrial-wide insertion in both taxa. We conducted an intensive BLAST search for numts in the gorilla genome and compared the prevalence of numt loci originating from the MCR with other great ape taxa. Additional gorilla-specific MCR numts were retrieved either through BAC library screens or using an anchored-PCR (A-PCR) amplification using genomic DNA from five unrelated gorillas. Locus-specific primers were designed to identify numt insertional polymorphisms and evaluate their potential as population genetic markers. Mitochondrial-wide surveys of chimpanzee and gorilla BACs showed that the number of numts does not differ between these two taxa. However, MCR numts are more abundant in chimpanzees than in other great apes. We identified and mapped 67 putative gorilla-specific numts, including two that contain the entire HV1 domain, cluster with sequences from two numt classes (I, IIb) and will likely co-amplify with mitochondrial sequences using most published HV1 primers. However, phylogenetic analysis coupled with post-hoc analysis of mitochondrial variation can successfully differentiate nuclear sequences. Insertional polymorphisms were evident in three out of five numts examined, indicating their potential utility as molecular markers. Taken together, these findings demonstrate the potentially powerful insight that numts could make in uncovering population history in gorillas and other mammals.</AbstractText><CopyrightInformation>Copyright © 2014 Elsevier Inc. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Soto-Calderón</LastName><ForeName>Iván Darío</ForeName><Initials>ID</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA; Genética, Mejoramiento y Modelación Animal (GaMMA), University of Antioquia, AA1226 Medellín, Colombia. Electronic address: ivandariosoto@hotmail.com.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Clark</LastName><ForeName>Nicholas Jonathan</ForeName><Initials>NJ</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Wildschutte</LastName><ForeName>Julia Vera Halo</ForeName><Initials>JV</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>DiMattio</LastName><ForeName>Kelly</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jensen-Seaman</LastName><ForeName>Michael Ignatius</ForeName><Initials>MI</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, Duquesne University, 600 Forbes Ave., Pittsburgh, PA 15282, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Anthony</LastName><ForeName>Nicola Mary</ForeName><Initials>NM</Initials><AffiliationInfo><Affiliation>Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R15 GM073682</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>R15 GM073682-01</GrantID><Acronym>GM</Acronym><Agency>NIGMS NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>09</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Mol Phylogenet Evol</MedlineTA><NlmUniqueID>9304400</NlmUniqueID><ISSNLinking>1055-7903</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004251">DNA Transposable Elements</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004272">DNA, Mitochondrial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Genome Res. 2002 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UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004251" MajorTopicYN="Y">DNA Transposable Elements</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004272" MajorTopicYN="N">DNA, Mitochondrial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="Y">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005828" MajorTopicYN="Y">Genetics, Population</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016678" MajorTopicYN="N">Genome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006071" MajorTopicYN="N">Gorilla gorilla</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D002679" MajorTopicYN="N">Pan troglodytes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013045" MajorTopicYN="N">Species Specificity</DescriptorName></MeshHeading></MeshHeadingList><OtherID Source="NLM">NIHMS627048</OtherID><OtherID Source="NLM">PMC4252773</OtherID><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">BAC screens</Keyword><Keyword MajorTopicYN="N">Gorilla</Keyword><Keyword MajorTopicYN="N">Great ape</Keyword><Keyword MajorTopicYN="N">Mitochondrial DNA</Keyword><Keyword MajorTopicYN="N">Numt</Keyword><Keyword MajorTopicYN="N">Polymorphism</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2013</Year><Month>12</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2014</Year><Month>05</Month><Day>31</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2014</Year><Month>08</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>9</Month><Day>8</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>9</Month><Day>10</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>3</Month><Day>7</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25194325</ArticleId><ArticleId IdType="pii">S1055-7903(14)00303-0</ArticleId><ArticleId IdType="doi">10.1016/j.ympev.2014.08.018</ArticleId><ArticleId IdType="pmc">PMC4252773</ArticleId><ArticleId IdType="mid">NIHMS627048</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Colombie</li><li>États-Unis</li></country><region><li>Louisiane</li><li>Pennsylvanie</li></region></list><tree><country name="Colombie"><noRegion><name sortKey="Soto Calder N, Ivan Dario" sort="Soto Calder N, Ivan Dario" uniqKey="Soto Calder N I" first="Iván Darío" last="Soto-Calder N">Iván Darío Soto-Calder N</name></noRegion></country><country name="États-Unis"><region name="Louisiane"><name sortKey="Clark, Nicholas Jonathan" sort="Clark, Nicholas Jonathan" uniqKey="Clark N" first="Nicholas Jonathan" last="Clark">Nicholas Jonathan Clark</name></region><name sortKey="Anthony, Nicola Mary" sort="Anthony, Nicola Mary" uniqKey="Anthony N" first="Nicola Mary" last="Anthony">Nicola Mary Anthony</name><name sortKey="Dimattio, Kelly" sort="Dimattio, Kelly" uniqKey="Dimattio K" first="Kelly" last="Dimattio">Kelly Dimattio</name><name sortKey="Jensen Seaman, Michael Ignatius" sort="Jensen Seaman, Michael Ignatius" uniqKey="Jensen Seaman M" first="Michael Ignatius" last="Jensen-Seaman">Michael Ignatius Jensen-Seaman</name><name sortKey="Wildschutte, Julia Vera Halo" sort="Wildschutte, Julia Vera Halo" uniqKey="Wildschutte J" first="Julia Vera Halo" last="Wildschutte">Julia Vera Halo Wildschutte</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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