Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki
Background: Among the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of the Southern Ocean. Because P. borchgrevinki is a frequent model for investi...
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ftmontclairstuni:oai:digitalcommons.montclair.edu:biology-facpubs-1481 2024-09-30T14:24:24+00:00 Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki Bilyk, Kevin T. Cheng, C. H.Christina 2013-09-21T07:00:00Z https://digitalcommons.montclair.edu/biology-facpubs/482 https://doi.org/10.1186/1471-2164-14-634 unknown Montclair State University Digital Commons https://digitalcommons.montclair.edu/biology-facpubs/482 doi:10.1186/1471-2164-14-634 Department of Biology Faculty Scholarship and Creative Works Antarctic fish Cold adaptation Cold specialization Heat tolerance Notothenioidei Transcriptome text 2013 ftmontclairstuni https://doi.org/10.1186/1471-2164-14-634 2024-09-12T23:39:01Z Background: Among the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of the Southern Ocean. Because P. borchgrevinki is a frequent model for investigating notothenioid cold-adaptation and specialization, it is imperative that " omic" tools be developed for this species. In the absence of a sequenced genome, a well annotated reference transcriptome of the bald notothen will serve as a model of gene expression in the coldest and harshest of all polar marine environments, useful for future comparative studies of cold adaptation and thermal responses in polar teleosts and ectotherms.Results: We sequenced and annotated a reference transcriptome for P. borchgrevinki, with added attention to capturing the transcriptional responses to acute and chronic heat exposures. We sequenced by Roche 454 a normalized cDNA library constructed from pooled mRNA encompassing multiple tissues taken from environmental, warm acclimating, and acute heat stressed specimens. The resulting reads were assembled into 42,620 contigs, 17,951 of which could be annotated. We utilized this annotated portion of the reference transcriptome to map short Illumina reads sequenced from the gill and liver of environmental specimens, and also compared the gene expression profiles of these two tissue transcriptomes with those from the temperate model fish Danio rerio. From this, we identified a conserved group of 58 GO terms, in which terms related to transcription and its regulation, ubiquitin-protein ligase activity, protein ubiquitination, and protein binding among others are more prevalent in the bald notothen, suggesting the pertinent genes play essential roles in cold temperature functioning.Conclusion: We sequenced multiple tissue transcriptomes from native and heat-exposed experimental specimens of the high Antarctic, cryopelagic notothenioid P. borchgrevinki to construct a reference transcriptome. ... Text Antarc* Antarctic Southern Ocean Montclair State University Digital Commons Antarctic Southern Ocean BMC Genomics 14 1 634 |
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Open Polar |
collection |
Montclair State University Digital Commons |
op_collection_id |
ftmontclairstuni |
language |
unknown |
topic |
Antarctic fish Cold adaptation Cold specialization Heat tolerance Notothenioidei Transcriptome |
spellingShingle |
Antarctic fish Cold adaptation Cold specialization Heat tolerance Notothenioidei Transcriptome Bilyk, Kevin T. Cheng, C. H.Christina Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki |
topic_facet |
Antarctic fish Cold adaptation Cold specialization Heat tolerance Notothenioidei Transcriptome |
description |
Background: Among the cold-adapted Antarctic notothenioid fishes, the high-latitude bald notothen Pagothenia borchgrevinki is particularly notable as the sole cryopelagic species, exploiting the coldest and iciest waters of the Southern Ocean. Because P. borchgrevinki is a frequent model for investigating notothenioid cold-adaptation and specialization, it is imperative that " omic" tools be developed for this species. In the absence of a sequenced genome, a well annotated reference transcriptome of the bald notothen will serve as a model of gene expression in the coldest and harshest of all polar marine environments, useful for future comparative studies of cold adaptation and thermal responses in polar teleosts and ectotherms.Results: We sequenced and annotated a reference transcriptome for P. borchgrevinki, with added attention to capturing the transcriptional responses to acute and chronic heat exposures. We sequenced by Roche 454 a normalized cDNA library constructed from pooled mRNA encompassing multiple tissues taken from environmental, warm acclimating, and acute heat stressed specimens. The resulting reads were assembled into 42,620 contigs, 17,951 of which could be annotated. We utilized this annotated portion of the reference transcriptome to map short Illumina reads sequenced from the gill and liver of environmental specimens, and also compared the gene expression profiles of these two tissue transcriptomes with those from the temperate model fish Danio rerio. From this, we identified a conserved group of 58 GO terms, in which terms related to transcription and its regulation, ubiquitin-protein ligase activity, protein ubiquitination, and protein binding among others are more prevalent in the bald notothen, suggesting the pertinent genes play essential roles in cold temperature functioning.Conclusion: We sequenced multiple tissue transcriptomes from native and heat-exposed experimental specimens of the high Antarctic, cryopelagic notothenioid P. borchgrevinki to construct a reference transcriptome. ... |
format |
Text |
author |
Bilyk, Kevin T. Cheng, C. H.Christina |
author_facet |
Bilyk, Kevin T. Cheng, C. H.Christina |
author_sort |
Bilyk, Kevin T. |
title |
Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki |
title_short |
Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki |
title_full |
Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki |
title_fullStr |
Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki |
title_full_unstemmed |
Model of gene expression in extreme cold - reference transcriptome for the high-Antarctic cryopelagic notothenioid fish Pagothenia borchgrevinki |
title_sort |
model of gene expression in extreme cold - reference transcriptome for the high-antarctic cryopelagic notothenioid fish pagothenia borchgrevinki |
publisher |
Montclair State University Digital Commons |
publishDate |
2013 |
url |
https://digitalcommons.montclair.edu/biology-facpubs/482 https://doi.org/10.1186/1471-2164-14-634 |
geographic |
Antarctic Southern Ocean |
geographic_facet |
Antarctic Southern Ocean |
genre |
Antarc* Antarctic Southern Ocean |
genre_facet |
Antarc* Antarctic Southern Ocean |
op_source |
Department of Biology Faculty Scholarship and Creative Works |
op_relation |
https://digitalcommons.montclair.edu/biology-facpubs/482 doi:10.1186/1471-2164-14-634 |
op_doi |
https://doi.org/10.1186/1471-2164-14-634 |
container_title |
BMC Genomics |
container_volume |
14 |
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1 |
container_start_page |
634 |
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1811640846982840320 |