Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod.
Abstract Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mec...
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Online Access: | https://www.openaccessrepository.it/record/86427 https://doi.org/10.1016/j.margen.2018.02.003 |
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ftopenaccessrep:oai:zenodo.org:86427 2023-10-25T01:35:12+02:00 Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. Laura Ghigliotti Katherine R. Murphy Xuan Zhuang C.-H. Christina Cheng Eva Pisano 2018-02-06 https://www.openaccessrepository.it/record/86427 https://doi.org/10.1016/j.margen.2018.02.003 eng eng url:https://www.openaccessrepository.it/communities/itmirror https://www.openaccessrepository.it/record/86427 doi:10.1016/j.margen.2018.02.003 info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-nd/4.0/ Genetics Aquatic Science info:eu-repo/semantics/article publication-article 2018 ftopenaccessrep https://doi.org/10.1016/j.margen.2018.02.003 2023-09-26T22:18:06Z Abstract Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mechanism of evolution of this novel life-saving adaptive genetic trait remained to be definitively determined. To this end, we constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries for two AFGP-bearing gadids, the high-Arctic polar cod Boreogadus saida and the cold-temperate Atlantic tomcod Microgadus tomcod, to isolate and sequence their AFGP genomic regions for fine resolution evolutionary analyses. The BAC library construction encountered poor cloning efficiency initially, which we resolved by pretreating the agarose-embedded erythrocyte DNA with a cationic detergent, a method that may be of general use to BAC cloning for teleost species and/or where erythrocytes are the source of input DNA. The polar cod BAC library encompassed 92,160 clones with an average insert size of 94.7 kbp, and the Atlantic tomcod library contained 73,728 clones with an average insert size of 89.6 kbp. The genome sizes of B. saida and M. tomcod were estimated by cell flow cytometry to be 836 Mbp and 645 Mbp respectively, thus their BAC libraries have approximately 10- and 9.7-fold genome coverage respectively. The inclusiveness and depth of coverage were empirically confirmed by screening the libraries with three housekeeping genes. The BAC clones that mapped to the AFGP genomic loci of the two gadids were then isolated by screening the BAC libraries with gadid AFGP gene probes. Eight minimal tiling path (MTP) clones were identified for B. saida, sequenced, and assembled. The B. saida AFGP locus reconstruction produced both haplotypes, and the locus comprises three distinct AFGP gene clusters, containing a total of 16 AFGP genes and spanning a combined distance of 512 kbp. The M. tomcod AFGP locus is much ... Article in Journal/Newspaper Arctic Boreogadus saida polar cod Istituto Nazionale di Fisica Nucleare (INFN): Open Access Repository Arctic Marine Genomics 39 73 84 |
institution |
Open Polar |
collection |
Istituto Nazionale di Fisica Nucleare (INFN): Open Access Repository |
op_collection_id |
ftopenaccessrep |
language |
English |
topic |
Genetics Aquatic Science |
spellingShingle |
Genetics Aquatic Science Laura Ghigliotti Katherine R. Murphy Xuan Zhuang C.-H. Christina Cheng Eva Pisano Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. |
topic_facet |
Genetics Aquatic Science |
description |
Abstract Antifreeze glycoproteins (AFGPs) are a novel evolutionary innovation in members of the northern cod fish family (Gadidae), crucial in preventing death from inoculative freezing by environmental ice in their frigid Arctic and sub-Arctic habitats. However, the genomic origin and molecular mechanism of evolution of this novel life-saving adaptive genetic trait remained to be definitively determined. To this end, we constructed large insert genomic DNA BAC (bacterial artificial chromosome) libraries for two AFGP-bearing gadids, the high-Arctic polar cod Boreogadus saida and the cold-temperate Atlantic tomcod Microgadus tomcod, to isolate and sequence their AFGP genomic regions for fine resolution evolutionary analyses. The BAC library construction encountered poor cloning efficiency initially, which we resolved by pretreating the agarose-embedded erythrocyte DNA with a cationic detergent, a method that may be of general use to BAC cloning for teleost species and/or where erythrocytes are the source of input DNA. The polar cod BAC library encompassed 92,160 clones with an average insert size of 94.7 kbp, and the Atlantic tomcod library contained 73,728 clones with an average insert size of 89.6 kbp. The genome sizes of B. saida and M. tomcod were estimated by cell flow cytometry to be 836 Mbp and 645 Mbp respectively, thus their BAC libraries have approximately 10- and 9.7-fold genome coverage respectively. The inclusiveness and depth of coverage were empirically confirmed by screening the libraries with three housekeeping genes. The BAC clones that mapped to the AFGP genomic loci of the two gadids were then isolated by screening the BAC libraries with gadid AFGP gene probes. Eight minimal tiling path (MTP) clones were identified for B. saida, sequenced, and assembled. The B. saida AFGP locus reconstruction produced both haplotypes, and the locus comprises three distinct AFGP gene clusters, containing a total of 16 AFGP genes and spanning a combined distance of 512 kbp. The M. tomcod AFGP locus is much ... |
format |
Article in Journal/Newspaper |
author |
Laura Ghigliotti Katherine R. Murphy Xuan Zhuang C.-H. Christina Cheng Eva Pisano |
author_facet |
Laura Ghigliotti Katherine R. Murphy Xuan Zhuang C.-H. Christina Cheng Eva Pisano |
author_sort |
Laura Ghigliotti |
title |
Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. |
title_short |
Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. |
title_full |
Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. |
title_fullStr |
Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. |
title_full_unstemmed |
Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod. |
title_sort |
reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids boreogadus saida and microgadus tomcod. |
publishDate |
2018 |
url |
https://www.openaccessrepository.it/record/86427 https://doi.org/10.1016/j.margen.2018.02.003 |
geographic |
Arctic |
geographic_facet |
Arctic |
genre |
Arctic Boreogadus saida polar cod |
genre_facet |
Arctic Boreogadus saida polar cod |
op_relation |
url:https://www.openaccessrepository.it/communities/itmirror https://www.openaccessrepository.it/record/86427 doi:10.1016/j.margen.2018.02.003 |
op_rights |
info:eu-repo/semantics/openAccess https://creativecommons.org/licenses/by-nc-nd/4.0/ |
op_doi |
https://doi.org/10.1016/j.margen.2018.02.003 |
container_title |
Marine Genomics |
container_volume |
39 |
container_start_page |
73 |
op_container_end_page |
84 |
_version_ |
1780730356763197440 |