Characterization of a divergent chromosome region in the willow warbler Phylloscopus trochilus using avian genomic resources.
Identifieur interne : 001596 ( Main/Exploration ); précédent : 001595; suivant : 001597Characterization 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
Affiliations:
Links toward previous steps (curation, corpus...)
Le document en format XML
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<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>
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<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>
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<term>Genotype</term>
<term>Geography</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Population Dynamics</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term>
<term>Analyse de séquence d'ADN</term>
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<term>Génomique</term>
<term>Génotype</term>
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<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>
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