Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes
Abstract Background Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. Although the general hypothesis of an increased molecular flexibility in the cold is widely accepted, the results of thermal adaptation are still difficult to detect...
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ftdoajarticles:oai:doaj.org/article:c18d53bcb97e467bb89762803a4745b7 2023-05-15T13:56:15+02:00 Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes Windisch Heidrun Sigrid Lucassen Magnus Frickenhaus Stephan 2012-10-01T00:00:00Z https://doi.org/10.1186/1471-2164-13-549 https://doaj.org/article/c18d53bcb97e467bb89762803a4745b7 EN eng BMC http://www.biomedcentral.com/1471-2164/13/549 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-13-549 1471-2164 https://doaj.org/article/c18d53bcb97e467bb89762803a4745b7 BMC Genomics, Vol 13, Iss 1, p 549 (2012) Biotechnology TP248.13-248.65 Genetics QH426-470 article 2012 ftdoajarticles https://doi.org/10.1186/1471-2164-13-549 2022-12-31T08:10:53Z Abstract Background Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. Although the general hypothesis of an increased molecular flexibility in the cold is widely accepted, the results of thermal adaptation are still difficult to detect at proteomic down to the genomic sequence level. Approaches towards a more detailed picture emerge with the advent of new sequencing technologies. Only small changes in primary protein structure have been shown to modify kinetic and thermal properties of enzymes, but likewise for interspecies comparisons a high genetic identity is still essential to specify common principles. The present study uses comprehensive transcriptomic sequence information to uncover general patterns of thermal adaptation on the RNA as well as protein primary structure. Results By comparing orthologous sequences of two closely related zoarcid fish inhabiting different latitudinal zones (Antarctica: Pachycara brachycephalum , temperate zone: Zoarces viviparus ) we were able to detect significant differences in the codon usage. In the cold-adapted species a lower GC content in the wobble position prevailed for preserved amino acids. We were able to estimate 40-60% coverage of the functions represented within the two compared zoarcid cDNA-libraries on the basis of a reference genome of the phylogenetically closely related fish Gasterosteus aculeatus . A distinct pattern of amino acid substitutions could be identified for the non-synonymous codon exchanges, with a remarkable surplus of serine and reduction of glutamic acid and asparagine for the Antarctic species. Conclusion Based on the differences between orthologous sequences from confamiliar species, distinguished mainly by the temperature regimes of their habitats, we hypothesize that temperature leaves a signature on the composition of biological macromolecules (RNA, proteins) with implications for the transcription and translation level. As the observed pattern of amino acid substitutions ... Article in Journal/Newspaper Antarc* Antarctic Antarctica Directory of Open Access Journals: DOAJ Articles Antarctic The Antarctic BMC Genomics 13 1 549 |
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Open Polar |
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Directory of Open Access Journals: DOAJ Articles |
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ftdoajarticles |
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English |
topic |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
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Biotechnology TP248.13-248.65 Genetics QH426-470 Windisch Heidrun Sigrid Lucassen Magnus Frickenhaus Stephan Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
topic_facet |
Biotechnology TP248.13-248.65 Genetics QH426-470 |
description |
Abstract Background Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. Although the general hypothesis of an increased molecular flexibility in the cold is widely accepted, the results of thermal adaptation are still difficult to detect at proteomic down to the genomic sequence level. Approaches towards a more detailed picture emerge with the advent of new sequencing technologies. Only small changes in primary protein structure have been shown to modify kinetic and thermal properties of enzymes, but likewise for interspecies comparisons a high genetic identity is still essential to specify common principles. The present study uses comprehensive transcriptomic sequence information to uncover general patterns of thermal adaptation on the RNA as well as protein primary structure. Results By comparing orthologous sequences of two closely related zoarcid fish inhabiting different latitudinal zones (Antarctica: Pachycara brachycephalum , temperate zone: Zoarces viviparus ) we were able to detect significant differences in the codon usage. In the cold-adapted species a lower GC content in the wobble position prevailed for preserved amino acids. We were able to estimate 40-60% coverage of the functions represented within the two compared zoarcid cDNA-libraries on the basis of a reference genome of the phylogenetically closely related fish Gasterosteus aculeatus . A distinct pattern of amino acid substitutions could be identified for the non-synonymous codon exchanges, with a remarkable surplus of serine and reduction of glutamic acid and asparagine for the Antarctic species. Conclusion Based on the differences between orthologous sequences from confamiliar species, distinguished mainly by the temperature regimes of their habitats, we hypothesize that temperature leaves a signature on the composition of biological macromolecules (RNA, proteins) with implications for the transcription and translation level. As the observed pattern of amino acid substitutions ... |
format |
Article in Journal/Newspaper |
author |
Windisch Heidrun Sigrid Lucassen Magnus Frickenhaus Stephan |
author_facet |
Windisch Heidrun Sigrid Lucassen Magnus Frickenhaus Stephan |
author_sort |
Windisch Heidrun Sigrid |
title |
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
title_short |
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
title_full |
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
title_fullStr |
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
title_full_unstemmed |
Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
title_sort |
evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
publisher |
BMC |
publishDate |
2012 |
url |
https://doi.org/10.1186/1471-2164-13-549 https://doaj.org/article/c18d53bcb97e467bb89762803a4745b7 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
BMC Genomics, Vol 13, Iss 1, p 549 (2012) |
op_relation |
http://www.biomedcentral.com/1471-2164/13/549 https://doaj.org/toc/1471-2164 doi:10.1186/1471-2164-13-549 1471-2164 https://doaj.org/article/c18d53bcb97e467bb89762803a4745b7 |
op_doi |
https://doi.org/10.1186/1471-2164-13-549 |
container_title |
BMC Genomics |
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13 |
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1 |
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549 |
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