Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes
BACKGROUND: The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), occurs in...
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2015
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ftleibnizopen:oai:oai.leibnizopen.de:4SaKVYsBBwLIz6xGSVV3 2023-11-12T04:10:27+01:00 Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes Kumar, Vikas Kutschera, Verena Esther Nilsson Janke, Maria Janke, Axel 2015 https://repository.publisso.de/resource/frl:6407961 https://doi.org/10.1186/s12864-015-1724-9 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528681/ https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1724-9#Declarations eng eng http:/creativecommons.org/licenses/by/4.0/ BMC genomics, 16:585 Vulpes lagopus Arctic adaptation Positive selection Transcriptome Arctic fox Red fox Vulpes vulpes 2015 ftleibnizopen https://doi.org/10.1186/s12864-015-1724-9 2023-10-22T23:10:16Z BACKGROUND: The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), 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. RESULTS: The de novo 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. CONCLUSIONS: 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 ... Other/Unknown Material Arctic Fox Arctic Subarctic Vulpes lagopus Unknown Arctic BMC Genomics 16 1 |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
ftleibnizopen |
language |
English |
topic |
Vulpes lagopus Arctic adaptation Positive selection Transcriptome Arctic fox Red fox Vulpes vulpes |
spellingShingle |
Vulpes lagopus Arctic adaptation Positive selection Transcriptome Arctic fox Red fox Vulpes vulpes Kumar, Vikas Kutschera, Verena Esther Nilsson Janke, Maria Janke, Axel Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
topic_facet |
Vulpes lagopus Arctic adaptation Positive selection Transcriptome Arctic fox Red fox Vulpes vulpes |
description |
BACKGROUND: The genus Vulpes (true foxes) comprises numerous species that inhabit a wide range of habitats and climatic conditions, including one species, the Arctic fox (Vulpes lagopus) which is adapted to the arctic region. A close relative to the Arctic fox, the red fox (Vulpes vulpes), 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. RESULTS: The de novo 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. CONCLUSIONS: 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 ... |
author |
Kumar, Vikas Kutschera, Verena Esther Nilsson Janke, Maria Janke, Axel |
author_facet |
Kumar, Vikas Kutschera, Verena Esther Nilsson Janke, Maria Janke, Axel |
author_sort |
Kumar, Vikas |
title |
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
title_short |
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
title_full |
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
title_fullStr |
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
title_full_unstemmed |
Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
title_sort |
genetic signatures of adaptation revealed from transcriptome sequencing of arctic and red foxes |
publishDate |
2015 |
url |
https://repository.publisso.de/resource/frl:6407961 https://doi.org/10.1186/s12864-015-1724-9 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528681/ https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-015-1724-9#Declarations |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Fox Arctic Subarctic Vulpes lagopus |
genre_facet |
Arctic Fox Arctic Subarctic Vulpes lagopus |
op_source |
BMC genomics, 16:585 |
op_rights |
http:/creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1186/s12864-015-1724-9 |
container_title |
BMC Genomics |
container_volume |
16 |
container_issue |
1 |
_version_ |
1782329912188731392 |