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Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod.

https://arctichealth.org/en/permalink/ahliterature290188
Source
Mar Genomics. 2018 Jun; 39:73-84
Publication Type
Journal Article
Date
Jun-2018
Author
Xuan Zhuang
Katherine R Murphy
Laura Ghigliotti
Eva Pisano
C-H Christina Cheng
Author Affiliation
Department of Animal Biology, University of Illinois at Urbana - Champaign, 515 Morrill Hall, Urbana, IL 61801, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. Electronic address: xzhuang3@uchicago.edu.
Source
Mar Genomics. 2018 Jun; 39:73-84
Date
Jun-2018
Language
English
Publication Type
Journal Article
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 smaller at approximately 80?kbp, and contains only three AFGP genes. Fluorescent in situ hybridization with an AFGP gene probe showed the AFGP locus in both species occupies a single chromosomal location. The large AFGP locus with its high gene dosage in B. saida is consistent with its chronically freezing high Arctic habitats, while the small gene family in M. tomcod correlates with its milder habitats in lower latitudes. The results from this study provided the data for fine resolution sequence analyses that would yield insight into the molecular mechanisms and history of gadid AFGP gene evolution driven by northern hemisphere glaciation.
PubMed ID
29510906 View in PubMed
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Reconstruction of the repetitive antifreeze glycoprotein genomic loci in the cold-water gadids Boreogadus saida and Microgadus tomcod.

https://arctichealth.org/en/permalink/ahliterature295167
Source
Mar Genomics. 2018 Jun; 39:73-84
Publication Type
Journal Article
Date
Jun-2018
Author
Xuan Zhuang
Katherine R Murphy
Laura Ghigliotti
Eva Pisano
C-H Christina Cheng
Author Affiliation
Department of Animal Biology, University of Illinois at Urbana - Champaign, 515 Morrill Hall, Urbana, IL 61801, USA; Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA. Electronic address: xzhuang3@uchicago.edu.
Source
Mar Genomics. 2018 Jun; 39:73-84
Date
Jun-2018
Language
English
Publication Type
Journal Article
Keywords
Animals
Antifreeze Proteins - genetics
Chromosomes, Artificial, Bacterial
Cloning, Molecular
Fish Proteins - genetics
Gadiformes - genetics
Gene Library
Genome
In Situ Hybridization, Fluorescence
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 smaller at approximately 80?kbp, and contains only three AFGP genes. Fluorescent in situ hybridization with an AFGP gene probe showed the AFGP locus in both species occupies a single chromosomal location. The large AFGP locus with its high gene dosage in B. saida is consistent with its chronically freezing high Arctic habitats, while the small gene family in M. tomcod correlates with its milder habitats in lower latitudes. The results from this study provided the data for fine resolution sequence analyses that would yield insight into the molecular mechanisms and history of gadid AFGP gene evolution driven by northern hemisphere glaciation.
PubMed ID
29510906 View in PubMed
Less detail