Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes
Abstract 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), o...
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ftdatacite:10.6084/m9.figshare.c.3606521 2023-05-15T14:31:08+02:00 Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes Kumar, Vikas Kutschera, Verena Nilsson, Maria Janke, Axel 2015 https://dx.doi.org/10.6084/m9.figshare.c.3606521 https://figshare.com/collections/Genetic_signatures_of_adaptation_revealed_from_transcriptome_sequencing_of_Arctic_and_red_foxes/3606521 unknown Figshare https://dx.doi.org/10.1186/s12864-015-1724-9 CC BY 4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Inorganic Chemistry FOS Chemical sciences Computational Biology Collection article 2015 ftdatacite https://doi.org/10.6084/m9.figshare.c.3606521 https://doi.org/10.1186/s12864-015-1724-9 2021-11-05T12:55:41Z Abstract 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 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. Article in Journal/Newspaper Arctic Fox Arctic Subarctic Vulpes lagopus DataCite Metadata Store (German National Library of Science and Technology) Arctic |
institution |
Open Polar |
collection |
DataCite Metadata Store (German National Library of Science and Technology) |
op_collection_id |
ftdatacite |
language |
unknown |
topic |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Inorganic Chemistry FOS Chemical sciences Computational Biology |
spellingShingle |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Inorganic Chemistry FOS Chemical sciences Computational Biology Kumar, Vikas Kutschera, Verena Nilsson, Maria Janke, Axel Genetic signatures of adaptation revealed from transcriptome sequencing of Arctic and red foxes |
topic_facet |
Genetics FOS Biological sciences Evolutionary Biology 59999 Environmental Sciences not elsewhere classified FOS Earth and related environmental sciences Ecology 69999 Biological Sciences not elsewhere classified Marine Biology Inorganic Chemistry FOS Chemical sciences Computational Biology |
description |
Abstract 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 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. |
format |
Article in Journal/Newspaper |
author |
Kumar, Vikas Kutschera, Verena Nilsson, Maria Janke, Axel |
author_facet |
Kumar, Vikas Kutschera, Verena Nilsson, 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 |
publisher |
Figshare |
publishDate |
2015 |
url |
https://dx.doi.org/10.6084/m9.figshare.c.3606521 https://figshare.com/collections/Genetic_signatures_of_adaptation_revealed_from_transcriptome_sequencing_of_Arctic_and_red_foxes/3606521 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Fox Arctic Subarctic Vulpes lagopus |
genre_facet |
Arctic Fox Arctic Subarctic Vulpes lagopus |
op_relation |
https://dx.doi.org/10.1186/s12864-015-1724-9 |
op_rights |
CC BY 4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.6084/m9.figshare.c.3606521 https://doi.org/10.1186/s12864-015-1724-9 |
_version_ |
1766304842684301312 |