Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.
Identifieur interne : 001574 ( Main/Curation ); précédent : 001573; suivant : 001575Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.
Auteurs : M. Lundberg [Suède] ; S. Akesson ; S. BenschSource :
- Journal of evolutionary biology [ 1420-9101 ] ; 2011.
Descripteurs français
- KwdFr :
- Alignement de séquences (MeSH), Analyse de séquence d'ADN (MeSH), Animaux (MeSH), Chromosomes (génétique), Dynamique des populations (MeSH), Génomique (MeSH), Génotype (MeSH), Géographie (MeSH), Marqueurs génétiques (MeSH), Oiseaux chanteurs (génétique), Ordre des gènes (MeSH), Polymorphisme de nucléotide simple (MeSH), Théorème de Bayes (MeSH).
- MESH :
English descriptors
- KwdEn :
- Animals (MeSH), Bayes Theorem (MeSH), Chromosomes (genetics), Gene Order (MeSH), Genetic Markers (MeSH), Genomics (MeSH), Genotype (MeSH), Geography (MeSH), Polymorphism, Single Nucleotide (MeSH), Population Dynamics (MeSH), Sequence Alignment (MeSH), Sequence Analysis, DNA (MeSH), Songbirds (genetics).
- MESH :
- chemical : Genetic Markers.
- genetics : Chromosomes, Songbirds.
- Animals, Bayes Theorem, Gene Order, Genomics, Genotype, Geography, Polymorphism, Single Nucleotide, Population Dynamics, Sequence Alignment, Sequence Analysis, DNA.
Abstract
Genome scans have made it possible to find outlier markers thought to have been influenced by divergent selection in almost any wild population. However, the lack of genomic information in nonmodel species often makes it difficult to associate these markers with certain genes or chromosome regions. Furthermore, the extent of linkage disequilibrium (LD) in the genome will determine the density of markers required to identify the genes under selection. In this study, we investigated a chromosome region in the willow warbler Phylloscopus trochilus surrounding a single marker previously identified in a genome scan. We first located the marker in the assembled genome of another species, the zebra finch Taeniopygia guttata, and amplified surrounding sequences in Fennoscandian willow warblers. Within an investigated chromosome region of 7.3 Mb as mapped to the zebra finch genome, we observed elevated genetic differentiation between a southern and a northern population across a 2.5-Mb interval comprising numerous coding genes. Within the southern and northern populations, higher values of LD were mostly found between SNPs within the same locus, but extended across distantly situated loci when the analyses were restricted to sampling sites showing intermediate allele frequencies of southern and northern alleles. Our study shows that cross-species genome information is a useful resource to obtain candidate sequences adjacent to outlier markers in nonmodel species.
DOI: 10.1111/j.1420-9101.2011.02259.x
PubMed: 21418120
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Lundberg</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biology, Ecology Building, Lund University, Lund, Sweden.</nlm:affiliation><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Biology, Ecology Building, Lund University, Lund</wicri:regionArea></affiliation></author><author><name sortKey="Akesson, S" sort="Akesson, S" uniqKey="Akesson S" first="S" last="Akesson">S. Akesson</name></author><author><name sortKey="Bensch, S" sort="Bensch, S" uniqKey="Bensch S" first="S" last="Bensch">S. Bensch</name></author></analytic><series><title level="j">Journal of evolutionary biology</title><idno type="eISSN">1420-9101</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term><term>Bayes Theorem (MeSH)</term><term>Chromosomes (genetics)</term><term>Gene Order (MeSH)</term><term>Genetic Markers (MeSH)</term><term>Genomics (MeSH)</term><term>Genotype (MeSH)</term><term>Geography (MeSH)</term><term>Polymorphism, Single Nucleotide (MeSH)</term><term>Population Dynamics (MeSH)</term><term>Sequence Alignment (MeSH)</term><term>Sequence Analysis, DNA (MeSH)</term><term>Songbirds (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences (MeSH)</term><term>Analyse de séquence d'ADN (MeSH)</term><term>Animaux (MeSH)</term><term>Chromosomes (génétique)</term><term>Dynamique des populations (MeSH)</term><term>Génomique (MeSH)</term><term>Génotype (MeSH)</term><term>Géographie (MeSH)</term><term>Marqueurs génétiques (MeSH)</term><term>Oiseaux chanteurs (génétique)</term><term>Ordre des gènes (MeSH)</term><term>Polymorphisme de nucléotide simple (MeSH)</term><term>Théorème de Bayes (MeSH)</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Genetic Markers</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Chromosomes</term><term>Songbirds</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Chromosomes</term><term>Oiseaux chanteurs</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Bayes Theorem</term><term>Gene Order</term><term>Genomics</term><term>Genotype</term><term>Geography</term><term>Polymorphism, Single Nucleotide</term><term>Population Dynamics</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Animaux</term><term>Dynamique des populations</term><term>Génomique</term><term>Génotype</term><term>Géographie</term><term>Marqueurs génétiques</term><term>Ordre des gènes</term><term>Polymorphisme de nucléotide simple</term><term>Théorème de Bayes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Genome scans have made it possible to find outlier markers thought to have been influenced by divergent selection in almost any wild population. However, the lack of genomic information in nonmodel species often makes it difficult to associate these markers with certain genes or chromosome regions. Furthermore, the extent of linkage disequilibrium (LD) in the genome will determine the density of markers required to identify the genes under selection. In this study, we investigated a chromosome region in the willow warbler Phylloscopus trochilus surrounding a single marker previously identified in a genome scan. We first located the marker in the assembled genome of another species, the zebra finch Taeniopygia guttata, and amplified surrounding sequences in Fennoscandian willow warblers. Within an investigated chromosome region of 7.3 Mb as mapped to the zebra finch genome, we observed elevated genetic differentiation between a southern and a northern population across a 2.5-Mb interval comprising numerous coding genes. Within the southern and northern populations, higher values of LD were mostly found between SNPs within the same locus, but extended across distantly situated loci when the analyses were restricted to sampling sites showing intermediate allele frequencies of southern and northern alleles. Our study shows that cross-species genome information is a useful resource to obtain candidate sequences adjacent to outlier markers in nonmodel species.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">21418120</PMID><DateCompleted><Year>2011</Year><Month>08</Month><Day>26</Day></DateCompleted><DateRevised><Year>2011</Year><Month>05</Month><Day>10</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1420-9101</ISSN><JournalIssue CitedMedium="Internet"><Volume>24</Volume><Issue>6</Issue><PubDate><Year>2011</Year><Month>Jun</Month></PubDate></JournalIssue><Title>Journal of evolutionary biology</Title><ISOAbbreviation>J Evol Biol</ISOAbbreviation></Journal><ArticleTitle>Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.</ArticleTitle><Pagination><MedlinePgn>1241-53</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1111/j.1420-9101.2011.02259.x</ELocationID><Abstract><AbstractText>Genome scans have made it possible to find outlier markers thought to have been influenced by divergent selection in almost any wild population. However, the lack of genomic information in nonmodel species often makes it difficult to associate these markers with certain genes or chromosome regions. Furthermore, the extent of linkage disequilibrium (LD) in the genome will determine the density of markers required to identify the genes under selection. In this study, we investigated a chromosome region in the willow warbler Phylloscopus trochilus surrounding a single marker previously identified in a genome scan. We first located the marker in the assembled genome of another species, the zebra finch Taeniopygia guttata, and amplified surrounding sequences in Fennoscandian willow warblers. Within an investigated chromosome region of 7.3 Mb as mapped to the zebra finch genome, we observed elevated genetic differentiation between a southern and a northern population across a 2.5-Mb interval comprising numerous coding genes. Within the southern and northern populations, higher values of LD were mostly found between SNPs within the same locus, but extended across distantly situated loci when the analyses were restricted to sampling sites showing intermediate allele frequencies of southern and northern alleles. Our study shows that cross-species genome information is a useful resource to obtain candidate sequences adjacent to outlier markers in nonmodel species.</AbstractText><CopyrightInformation>© 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Lundberg</LastName><ForeName>M</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Department of Biology, Ecology Building, Lund University, Lund, Sweden.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Akesson</LastName><ForeName>S</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Bensch</LastName><ForeName>S</ForeName><Initials>S</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>03</Month><Day>18</Day></ArticleDate></Article><MedlineJournalInfo><Country>Switzerland</Country><MedlineTA>J Evol Biol</MedlineTA><NlmUniqueID>8809954</NlmUniqueID><ISSNLinking>1010-061X</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D005819">Genetic Markers</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001499" MajorTopicYN="N">Bayes Theorem</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D002875" MajorTopicYN="N">Chromosomes</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023061" MajorTopicYN="N">Gene Order</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005819" MajorTopicYN="N">Genetic Markers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005843" MajorTopicYN="N">Geography</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020641" MajorTopicYN="Y">Polymorphism, Single Nucleotide</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011157" MajorTopicYN="N">Population Dynamics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020308" MajorTopicYN="N">Songbirds</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>3</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>3</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>8</Month><Day>30</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">21418120</ArticleId><ArticleId IdType="doi">10.1111/j.1420-9101.2011.02259.x</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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