Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes
Identifieur interne : 000075 ( Main/Exploration ); précédent : 000074; suivant : 000076Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes
Auteurs : Vikas Kumar [Allemagne] ; Verena E. Kutschera [Allemagne, Suède] ; Maria A. Nilsson [Allemagne] ; Axel Janke [Allemagne]Source :
- BMC Genomics [ 1471-2164 ] ; 2015.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Adenosine Triphosphate.
- genetics : Foxes, Transcriptome.
- methods : Sequence Analysis, DNA.
- Animals, Biological Evolution, Humans, Molecular Sequence Data, Phylogeny, Species Specificity.
Abstract
The genus
The
Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.
The online version of this article (doi:10.1186/s12864-015-1724-9) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s12864-015-1724-9
PubMed: 26250829
PubMed Central: 4528681
Affiliations:
- Allemagne, Suède
- District de Darmstadt, East Middle Sweden, Hesse (Land), Svealand
- Francfort-sur-le-Main, Uppsala
- Université Johann Wolfgang Goethe de Francfort-sur-le-Main, Université d'Uppsala
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Le document en format XML
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Kutschera</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Darmstadt</region><settlement type="city">Francfort-sur-le-Main</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="Aff2">Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-75236 Uppsala</wicri:regionArea><orgName type="university">Université d'Uppsala</orgName><placeName><settlement type="city">Uppsala</settlement><region nuts="1">Svealand</region><region nuts="1">East Middle Sweden</region></placeName></affiliation></author><author><name sortKey="Nilsson, Maria A" sort="Nilsson, Maria A" uniqKey="Nilsson M" first="Maria A." last="Nilsson">Maria A. Nilsson</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Darmstadt</region><settlement type="city">Francfort-sur-le-Main</settlement></placeName></affiliation></author><author><name sortKey="Janke, Axel" sort="Janke, Axel" uniqKey="Janke A" first="Axel" last="Janke">Axel Janke</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Senckenberg Biodiversity and Climate Research Center, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Darmstadt</region><settlement type="city">Francfort-sur-le-Main</settlement></placeName></affiliation><affiliation wicri:level="4"><nlm:aff id="Aff3">Evolution & Diversity, Goethe University Frankfurt, Institute for Ecology, Biologicum, Max-von-Laue-Str.13, D-60439 Frankfurt am Main, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Evolution & Diversity, Goethe University Frankfurt, Institute for Ecology, Biologicum, Max-von-Laue-Str.13, D-60439 Frankfurt am Main</wicri:regionArea><placeName><region type="land" nuts="1">Hesse (Land)</region><region type="district" nuts="2">District de Darmstadt</region><settlement type="city">Francfort-sur-le-Main</settlement></placeName><orgName type="university">Université Johann Wolfgang Goethe de Francfort-sur-le-Main</orgName></affiliation></author></analytic><series><title level="j">BMC Genomics</title><idno type="eISSN">1471-2164</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Adenosine Triphosphate (genetics)</term><term>Animals</term><term>Biological Evolution</term><term>Foxes (genetics)</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Sequence Analysis, DNA (methods)</term><term>Species Specificity</term><term>Transcriptome (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Adenosine Triphosphate</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Foxes</term><term>Transcriptome</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Biological Evolution</term><term>Humans</term><term>Molecular Sequence Data</term><term>Phylogeny</term><term>Species Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>The genus <italic>Vulpes</italic> (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (<italic>Vulpes lagopus</italic>) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (<italic>Vulpes vulpes</italic>), occurs in subarctic to subtropical habitats. To study the genetic basis of their adaptations to different environments, transcriptome sequences from two Arctic foxes and one red fox individual were generated and analyzed for signatures of positive selection. In addition, the data allowed for a phylogenetic analysis and divergence time estimate between the two fox species.</p></sec><sec><title>Results</title><p>The <italic>de novo</italic> assembly of reads resulted in more than 160,000 contigs/transcripts per individual. Approximately 17,000 homologous genes were identified using human and the non-redundant databases. Positive selection analyses revealed several genes involved in various metabolic and molecular processes such as energy metabolism, cardiac gene regulation, apoptosis and blood coagulation to be under positive selection in foxes. Branch site tests identified four genes to be under positive selection in the Arctic fox transcriptome, two of which are fat metabolism genes. In the red fox transcriptome eight genes are under positive selection, including molecular process genes, notably genes involved in ATP metabolism. Analysis of the three transcriptomes and five Sanger re-sequenced genes in additional individuals identified a lower genetic variability within Arctic foxes compared to red foxes, which is consistent with distribution range differences and demographic responses to past climatic fluctuations. A phylogenomic analysis estimated that the Arctic and red fox lineages diverged about three million years ago.</p></sec><sec><title>Conclusions</title><p>Transcriptome data are an economic way to generate genomic resources for evolutionary studies. Despite not representing an entire genome, this transcriptome analysis identified numerous genes that are relevant to arctic adaptation in foxes. Similar to polar bears, fat metabolism seems to play a central role in adaptation of Arctic foxes to the cold climate, as has been identified in the polar bear, another arctic specialist.</p></sec><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s12864-015-1724-9) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Wozencraft, Wc" uniqKey="Wozencraft W">WC Wozencraft</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Audet, Am" uniqKey="Audet A">AM Audet</name></author><author><name sortKey="Robbins, Cb" uniqKey="Robbins C">CB Robbins</name></author><author><name sortKey="Lariviere, S" uniqKey="Lariviere S">S Larivière</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Perini, Fa" uniqKey="Perini F">FA Perini</name></author><author><name 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uniqKey="Mikhail A">A Mikhail</name></author><author><name sortKey="Kawana, M" uniqKey="Kawana M">M Kawana</name></author><author><name sortKey="Quertermous, Ee" uniqKey="Quertermous E">EE Quertermous</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Schurpf, T" uniqKey="Schurpf T">T Schürpf</name></author><author><name sortKey="Chen, Q" uniqKey="Chen Q">Q Chen</name></author><author><name sortKey="Liu, J" uniqKey="Liu J">J Liu</name></author><author><name sortKey="Wang, R" uniqKey="Wang R">R Wang</name></author><author><name sortKey="Springer, Ta" uniqKey="Springer T">TA Springer</name></author><author><name sortKey="Wang, J" uniqKey="Wang J">J Wang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Enari, M" uniqKey="Enari M">M Enari</name></author><author><name sortKey="Sakahira, H" uniqKey="Sakahira H">H Sakahira</name></author><author><name sortKey="Yokoyama, H" uniqKey="Yokoyama H">H Yokoyama</name></author><author><name sortKey="Okawa, K" uniqKey="Okawa K">K Okawa</name></author><author><name sortKey="Iwamatsu, A" uniqKey="Iwamatsu A">A Iwamatsu</name></author><author><name sortKey="Nagata, S" uniqKey="Nagata S">S Nagata</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name></author><author><name sortKey="Zou, H" uniqKey="Zou H">H Zou</name></author><author><name sortKey="Slaughter, C" uniqKey="Slaughter C">C Slaughter</name></author><author><name sortKey="Wang, X" uniqKey="Wang X">X Wang</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>Suède</li></country><region><li>District de Darmstadt</li><li>East Middle Sweden</li><li>Hesse (Land)</li><li>Svealand</li></region><settlement><li>Francfort-sur-le-Main</li><li>Uppsala</li></settlement><orgName><li>Université Johann Wolfgang Goethe de Francfort-sur-le-Main</li><li>Université d'Uppsala</li></orgName></list><tree><country name="Allemagne"><region name="Hesse (Land)"><name sortKey="Kumar, Vikas" sort="Kumar, Vikas" uniqKey="Kumar V" first="Vikas" last="Kumar">Vikas Kumar</name></region><name sortKey="Janke, Axel" sort="Janke, Axel" uniqKey="Janke A" first="Axel" last="Janke">Axel Janke</name><name sortKey="Janke, Axel" sort="Janke, Axel" uniqKey="Janke A" first="Axel" last="Janke">Axel Janke</name><name sortKey="Kutschera, Verena E" sort="Kutschera, Verena E" uniqKey="Kutschera V" first="Verena E." last="Kutschera">Verena E. Kutschera</name><name sortKey="Nilsson, Maria A" sort="Nilsson, Maria A" uniqKey="Nilsson M" first="Maria A." last="Nilsson">Maria A. Nilsson</name></country><country name="Suède"><region name="Svealand"><name sortKey="Kutschera, Verena E" sort="Kutschera, Verena E" uniqKey="Kutschera V" first="Verena E." last="Kutschera">Verena E. Kutschera</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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