Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes
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 prote...
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ftawi:oai:epic.awi.de:31280 2023-05-15T13:46:52+02:00 Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes Windisch, Heidrun Lucassen, Magnus Frickenhaus, Stephan 2012-10-11 https://epic.awi.de/id/eprint/31280/ http://www.biomedcentral.com/1471-2164/13/549 https://hdl.handle.net/10013/epic.40081 unknown BIOMED CENTRAL LTD Windisch, H. , Lucassen, M. orcid:0000-0003-4276-4781 and Frickenhaus, S. orcid:0000-0002-0356-9791 (2012) Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes , BMC Genomics, 13 (549) . doi:10.1186/1471-2164-13-549 <https://doi.org/10.1186/1471-2164-13-549> , hdl:10013/epic.40081 EPIC3BMC Genomics, BIOMED CENTRAL LTD, 13(549), ISSN: 1471-2164 Article isiRev 2012 ftawi https://doi.org/10.1186/1471-2164-13-549 2021-12-24T15:38:00Z 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 comparison of 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 only partly support the flexibility hypothesis further evolutionary forces may be effective at the global transcriptome level. Article in Journal/Newspaper Antarc* Antarctic Antarctica Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) Antarctic The Antarctic BMC Genomics 13 1 549 |
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Alfred Wegener Institute for Polar- and Marine Research (AWI): ePIC (electronic Publication Information Center) |
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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 comparison of 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 only partly support the flexibility hypothesis further evolutionary forces may be effective at the global transcriptome level. |
format |
Article in Journal/Newspaper |
author |
Windisch, Heidrun Lucassen, Magnus Frickenhaus, Stephan |
spellingShingle |
Windisch, Heidrun Lucassen, Magnus Frickenhaus, Stephan Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes |
author_facet |
Windisch, Heidrun Lucassen, Magnus Frickenhaus, Stephan |
author_sort |
Windisch, Heidrun |
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 |
BIOMED CENTRAL LTD |
publishDate |
2012 |
url |
https://epic.awi.de/id/eprint/31280/ http://www.biomedcentral.com/1471-2164/13/549 https://hdl.handle.net/10013/epic.40081 |
geographic |
Antarctic The Antarctic |
geographic_facet |
Antarctic The Antarctic |
genre |
Antarc* Antarctic Antarctica |
genre_facet |
Antarc* Antarctic Antarctica |
op_source |
EPIC3BMC Genomics, BIOMED CENTRAL LTD, 13(549), ISSN: 1471-2164 |
op_relation |
Windisch, H. , Lucassen, M. orcid:0000-0003-4276-4781 and Frickenhaus, S. orcid:0000-0002-0356-9791 (2012) Evolutionary force in confamiliar marine vertebrates of different temperature realms: adaptive trends in zoarcid fish transcriptomes , BMC Genomics, 13 (549) . doi:10.1186/1471-2164-13-549 <https://doi.org/10.1186/1471-2164-13-549> , hdl:10013/epic.40081 |
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 |
container_start_page |
549 |
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1766245478089883648 |