Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013
Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased i...
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Data Archiving and Networked Services (DANS)
2020
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Online Access: | https://doi.org/10.5061/dryad.606j6 |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::3a8f92a3ce6feca06822d005ffc431ab 2023-05-15T15:55:08+02:00 Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 Malenfant, René M. Coltman, David L. Richardson, Evan S. Lunn, Nicholas J. Davis, Corey S. Coltman, David W. Lunn, Nick J. 2020-07-17 https://doi.org/10.5061/dryad.606j6 undefined unknown Data Archiving and Networked Services (DANS) http://dx.doi.org/10.5061/dryad.606j6 https://dx.doi.org/10.5061/dryad.606j6 lic_creative-commons oai:easy.dans.knaw.nl:easy-dataset:84299 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:84299 10.5061/dryad.606j6 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c Life sciences medicine and health care Conservation Genetics Ecological Genetics Mammals Climate Change Population Genetics - Empirical Quantitative Genetics Wapusk National Park Churchill Manitoba Canada Cenozoic Ursus maritimus Ursidae Caniformia Carnivora Eutheria Mammallia Animalia Mammalia envir demo Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2020 fttriple https://doi.org/10.5061/dryad.606j6 2023-01-22T16:53:31Z Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential evolutionary consequences, little is yet known about the adaptive genetic variation in body size or fat accumulation that would have to underlie any such change. In this study, we used high-throughput Illumina sequencing to develop SNPs from pooled blood and fat transcriptomes, using samples from five adult female polar bears and five (unrelated) dependent cubs. In total, we generated 371,258 transcripts of which 36,755 were deemed to be “full length” (i.e., covered more than 90% of their best BLAST hit), and we identified 63,020 SNPs. Since this study was conducted, we have used a subset of these SNPs to develop an Illumina BeadArray for quantitative genetics research in Western Hudson Bay. Custom Perl script for extracting SNPsPerl program used to extract SNPs. Properly accounts for REFSKIP characters (i.e., "") that result from spliced alignments and seemed to be problematic in more widely available SNP calling packages, such as samtools and varscan.getsnpsfrommpileup.plSNP VCF fileVCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were: coverage >= 10, freq. of minor allele >= 0.2, read support for minor allele >= 3, number of alleles = 2. All SNPs were also verified using the program SysCall, and were retained only if the posterior probability of being a variant was >= 0.95.pb_syscallsnps.vcf.txtContig annotation filePutative gene and gene ontology annotations for transcripts that were deemed to be "full length" (i.e., cover >= 90% of their best blastx hit in RefSeq). ... Dataset Churchill Hudson Bay polar bear Sea ice Ursus maritimus Wapusk national park Unknown Hudson Bay Canada Hudson |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
unknown |
topic |
Life sciences medicine and health care Conservation Genetics Ecological Genetics Mammals Climate Change Population Genetics - Empirical Quantitative Genetics Wapusk National Park Churchill Manitoba Canada Cenozoic Ursus maritimus Ursidae Caniformia Carnivora Eutheria Mammallia Animalia Mammalia envir demo |
spellingShingle |
Life sciences medicine and health care Conservation Genetics Ecological Genetics Mammals Climate Change Population Genetics - Empirical Quantitative Genetics Wapusk National Park Churchill Manitoba Canada Cenozoic Ursus maritimus Ursidae Caniformia Carnivora Eutheria Mammallia Animalia Mammalia envir demo Malenfant, René M. Coltman, David L. Richardson, Evan S. Lunn, Nicholas J. Davis, Corey S. Coltman, David W. Lunn, Nick J. Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 |
topic_facet |
Life sciences medicine and health care Conservation Genetics Ecological Genetics Mammals Climate Change Population Genetics - Empirical Quantitative Genetics Wapusk National Park Churchill Manitoba Canada Cenozoic Ursus maritimus Ursidae Caniformia Carnivora Eutheria Mammallia Animalia Mammalia envir demo |
description |
Polar bears (Ursus maritimus) in the Western Hudson Bay subpopulation have been declining in size and body condition for decades, as climate change causes earlier sea ice breakup, reduced hunting time on the ice, and an increasingly long fasting season. As Western Hudson Bay females have decreased in size, rates of litter production and average litter size have also decreased, while cub mortality and average time to independence have increased. Although these changes have potential evolutionary consequences, little is yet known about the adaptive genetic variation in body size or fat accumulation that would have to underlie any such change. In this study, we used high-throughput Illumina sequencing to develop SNPs from pooled blood and fat transcriptomes, using samples from five adult female polar bears and five (unrelated) dependent cubs. In total, we generated 371,258 transcripts of which 36,755 were deemed to be “full length” (i.e., covered more than 90% of their best BLAST hit), and we identified 63,020 SNPs. Since this study was conducted, we have used a subset of these SNPs to develop an Illumina BeadArray for quantitative genetics research in Western Hudson Bay. Custom Perl script for extracting SNPsPerl program used to extract SNPs. Properly accounts for REFSKIP characters (i.e., "") that result from spliced alignments and seemed to be problematic in more widely available SNP calling packages, such as samtools and varscan.getsnpsfrommpileup.plSNP VCF fileVCF file containing info for SNPs called using the getsnpsfrommpileup.pl script. Settings used were: coverage >= 10, freq. of minor allele >= 0.2, read support for minor allele >= 3, number of alleles = 2. All SNPs were also verified using the program SysCall, and were retained only if the posterior probability of being a variant was >= 0.95.pb_syscallsnps.vcf.txtContig annotation filePutative gene and gene ontology annotations for transcripts that were deemed to be "full length" (i.e., cover >= 90% of their best blastx hit in RefSeq). ... |
format |
Dataset |
author |
Malenfant, René M. Coltman, David L. Richardson, Evan S. Lunn, Nicholas J. Davis, Corey S. Coltman, David W. Lunn, Nick J. |
author_facet |
Malenfant, René M. Coltman, David L. Richardson, Evan S. Lunn, Nicholas J. Davis, Corey S. Coltman, David W. Lunn, Nick J. |
author_sort |
Malenfant, René M. |
title |
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 |
title_short |
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 |
title_full |
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 |
title_fullStr |
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 |
title_full_unstemmed |
Data from: "Polar bear (Ursus maritimus) transcriptome assembly and SNP discovery" in Genomic Resources Notes accepted 1 August 2013-30 September 2013 |
title_sort |
data from: "polar bear (ursus maritimus) transcriptome assembly and snp discovery" in genomic resources notes accepted 1 august 2013-30 september 2013 |
publisher |
Data Archiving and Networked Services (DANS) |
publishDate |
2020 |
url |
https://doi.org/10.5061/dryad.606j6 |
geographic |
Hudson Bay Canada Hudson |
geographic_facet |
Hudson Bay Canada Hudson |
genre |
Churchill Hudson Bay polar bear Sea ice Ursus maritimus Wapusk national park |
genre_facet |
Churchill Hudson Bay polar bear Sea ice Ursus maritimus Wapusk national park |
op_source |
oai:easy.dans.knaw.nl:easy-dataset:84299 oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:84299 10.5061/dryad.606j6 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 re3data_____::r3d100000044 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c |
op_relation |
http://dx.doi.org/10.5061/dryad.606j6 https://dx.doi.org/10.5061/dryad.606j6 |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.606j6 |
_version_ |
1766390476956499968 |