The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.
De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Figures





Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“These genes were not properly assembled in the first version of the Atlantic cod genome (66), but were in the second version created with PacBio reads (62,109).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [109]
In the citing paper
“Indeed, the automated annotation of the Atlantic cod genome masked these genes as repeats and they would not have been properly characterized without careful investigation using BLAST (109).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [109]
In the citing paper
“The repeated nature of these gene families requires manual annotation, and this was performed in a comparative survey of AFGPs in notothenioid fishes and codfishes (109).”
From Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases (2019) · cites this paper as [109]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
The evolutionary origin of orphan genes
Tautz, D., & Domazet-Lošo, T. (2011) · Nature Reviews Genetics · doi:10.1038/nrg3053 · Cited by 764
Assessing the gene space in draft genomes
Parra, G., Bradnam, K., Ning, Z., Keane, T., & Korf, I. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn916 · Cited by 395 · cited 2×
“…Celera assembler (Miller et al. 2008) was used to assemble the genomes, with contig N50 ranging from 5 to 9.6 kb with an average of 6.3 kb. CEGMA (Parra et al. 2009) and BUSCO (Sim~ao et al. 2015) were used to evaluate gene completeness; CEGMA gave, on average, complete or partial hits for 69%…”
MethodInfluentialDe Novo Origin of Human Protein-Coding Genes
Wu, D.-D., Irwin, D. M., & Zhang, Y.-P. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002379 · Cited by 183
Research works printed but not linked: 59
- Albà, 2007, On homology searches by protein Blast and the characterization of the age of genes, BMC Evol Biol., 7, 53, 10.1186/1471-2148-7-53 · DOI
- Altschul, 1990, Basic local alignment search tool, J Mol Biol, 215, 403, 10.1016/S0022-2836(05)80360-2 · DOI · Paper page
- Bao, 2015, Repbase update, a database of repetitive elements in eukaryotic genomes, Mob DNA, 6, 462, 10.1186/s13100-015-0041-9 · DOI
- Bildanova, 2013, Main properties and evolutionary features of antifreeze proteins, Russ J Genet Appl Res., 3, 66, 10.1134/S207905971301005X · DOI
- Cao, 2016, Neofunctionalization of zona pellucida proteins enhances freeze-prevention in the eggs of Antarctic notothenioids, Nat Comms., 7, 10.1038/ncomms12987 · DOI
- Carvunis, 2012, Proto-genes and de novo gene birth, Nature, 487, 370, 10.1038/nature11184 · DOI · Paper page
- Cheng, 1999, Evolution of an antifreeze glycoprotein, Nature, 401, 443, 10.1038/46721 · DOI
- Cheng, 1998, Evolution of the diverse antifreeze proteins, Curr Opin Genet Dev., 8, 715, 10.1016/S0959-437X(98)80042-7 · DOI
- Cheng, 2003, Functional antifreeze glycoprotein genes in temperate-water New Zealand Nototheniid fish infer an antarctic evolutionary origin, Mol Biol Evol., 20, 1897, 10.1093/molbev/msg208 · DOI
- Cheng, 2006, Nonhepatic origin of notothenioid antifreeze reveals pancreatic synthesis as common mechanism in polar fish freezing avoidance, Proc Natl Acad Sci U S A, 103, 10491, 10.1073/pnas.0603796103 · DOI
- Chen, 1997, Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish, Proc Natl Acad Sci U S A, 94, 3811, 10.1073/pnas.94.8.3811 · DOI · Paper page
- Chen, 1997, Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod, Proc Natl Acad Sci U S A, 94, 3817, 10.1073/pnas.94.8.3817 · DOI · Paper page
- Colombo, 2015, Diversity and disparity through time in the adaptive radiation of Antarctic notothenioid fishes, J Evol Biol., 28, 376, 10.1111/jeb.12570 · DOI
- Cziko, 2014, Antifreeze protein-induced superheating of ice inside Antarctic notothenioid fishes inhibits melting during summer warming, Proc Natl Acad Sci U S A, 111, 14583, 10.1073/pnas.1410256111 · DOI
- Denstad, 1987, Thermal hysteresis antifreeze agents in fishes from Spitsbergen waters, Pol Res., 5, 1, 10.3402/polar.v5i2.6874 · DOI
- Derome, 2002, Phylogeny of Antarctic dragonfishes (Bathydraconidae, Notothenioidei, Teleostei) and related families based on their anatomy and two mitochondrial genes, Mol Phyl Evol, 24, 139, 10.1016/S1055-7903(02)00223-3 · DOI
- DeVries, 1971, Glycoproteins as biological antifreeze agents in Antarctic fishes, Science, 172, 1152, 10.1126/science.172.3988.1152 · DOI
- Dosztanyi, 2005, IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content, Bioinformatics, 21, 3433, 10.1093/bioinformatics/bti541 · DOI
- Eastman, 1997, Comparison of the Antarctic and Arctic fish faunas, Cybium, 21, 335
- Echols, 2002, Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes, Nucleic Acids Res., 30, 2515, 10.1093/nar/30.11.2515 · DOI
- Elhaik, 2005, The “Inverse Relationship Between Evolutionary Rate and Age of Mammalian Genes” is an artifact of increased genetic distance with rate of evolution and time of divergence, Mol Biol Evol., 23, 1, 10.1093/molbev/msj006 · DOI
- Ewart, 2000, Freeze susceptibility in haddock (Melanogrammus aeglefinus), Aquaculture, 188, 91, 10.1016/S0044-8486(00)00325-2 · DOI
- Ewart, 1999, Structure, function and evolution of antifreeze proteins, Cell Mol Life Sci., 55, 271, 10.1007/s000180050289 · DOI
- Fields, 2015, Variation in blood serum antifreeze activity of Antarctic Trematomus fishes across habitat temperature and depth, Comp Biochem Physiol, Part A Mol. Integr Physiol., 185, 43, 10.1016/j.cbpa.2015.03.006 · DOI
- Frazer, 2004, VISTA: computational tools for comparative genomics, Nucleic Acids Res., 32, W273, 10.1093/nar/gkh458 · DOI
- Goodwin, 2016, Coming of age: ten years of next-generation sequencing technologies, Nat Rev Genet., 17, 333, 10.1038/nrg.2016.49 · DOI · Paper page
- Graham, 2013, Helical antifreeze proteins have independently evolved in fishes on four occasions, PLoS ONE, 8, e81285., 10.1371/journal.pone.0081285 · DOI
- Gupta, 2014, Antifreeze proteins enable plants to survive in freezing conditions, J Biosci., 39, 931, 10.1007/s12038-014-9468-2 · DOI
- Harding, 2003, “Antifreeze” glycoproteins from polar fish, Eur J Biochem., 270, 1381, 10.1046/j.1432-1033.2003.03488.x · DOI
- Hew, 1981, Antifreeze glycoproteins in the plasma of Newfoundland Atlantic cod (Gadus morhua), Can J Zool, 59, 2186, 10.1139/z81-296 · DOI
- Kennett, 1977, Cenozoic evolution of antarctic glaciation, circum-antarctic ocean, and their impact on global paleoceanography, J Geophys Res Oceans, 82, 3843, 10.1029/JC082i027p03843 · DOI
- Khalturin, 2009, More than just orphans: are taxonomically-restricted genes important in evolution?, Trends Genet., 25, 404, 10.1016/j.tig.2009.07.006 · DOI
- Kristiansen, 2005, The mechanism by which fish antifreeze proteins cause thermal hysteresis, Cryobiology, 51, 262, 10.1016/j.cryobiol.2005.07.007 · DOI
- Kumar, 2016, MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets, Mol Biol Evol., 33, 1870, 10.1093/molbev/msw054 · DOI
- Liu, 2007, Structure and evolutionary origin of Ca2+-dependent herring Type II antifreeze protein, PLoS ONE, 2, e548, 10.1371/journal.pone.0000548 · DOI
- Malmstrøm, 2017, Whole genome sequencing data and de novo draft assemblies for 66 teleost species, Sci Data, 4, 1–13., 10.1038/sdata.2016.132 · DOI
- Malmstrøm, 2016, Evolution of the immune system influences speciation rates in teleost fishes, Nat Genet., 48, 1204, 10.1038/ng.3645 · DOI
- Masel, 2006, Cryptic genetic variation is enriched for potential adaptations, Genetics, 172, 1985, 10.1534/genetics.105.051649 · DOI
- McLysaght, 2015, New genes from non-coding sequence: the role of de novo protein-coding genes in eukaryotic evolutionary innovation, Philos Trans R Soc Lond B Biol Sci., 370, 20140332, 10.1098/rstb.2014.0332 · DOI
- McLysaght, 2016, Open questions in the study of de novo genes: what, how and why, Nat Rev Genet., 17, 579, 10.1038/nrg.2016.78 · DOI
- Miller, 2008, Aggressive assembly of pyrosequencing reads with mates, Bioinformatics, 24, 2818, 10.1093/bioinformatics/btn548 · DOI
- Miya, 2016, Multiple independent reduction or loss of antifreeze trait in low Antarctic and sub-Antarctic notothenioid fishes, Antarct Sci., 28, 17, 10.1017/S0954102015000413 · DOI
- Near, 2012, Ancient climate change, antifreeze, and the evolutionary diversification of Antarctic fishes, Proc Natl Acad Sci U S A, 109, 3434, 10.1073/pnas.1115169109 · DOI
- Nicodemus-Johnson, 2011, Assembly of the antifreeze glycoprotein/trypsinogen-like protease genomic locus in the Antarctic toothfish Dissostichus mawsoni (Norman), Genomics, 98, 194, 10.1016/j.ygeno.2011.06.002 · DOI
- Praebel, 2005, Antifreeze activity in the gastrointestinal fluids of Arctogadus glacialis (Peters 1874) is dependent on food type, J Evol Biol., 208, 2609
- Romero, 1998, Thousands of proteins likely to have long disordered regions, Pac Symp Biocomput, 3, 437
- Rondeau, 2014, The genome and linkage map of the northern pike (Esox lucius): conserved synteny revealed between the Salmonid Sister Group and the Neoteleostei, PLoS ONE, 9, e102089, 10.1371/journal.pone.0102089 · DOI
- Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180 · DOI
- Schlötterer, 2015, Genes from scratch—the evolutionary fate of de novo genes, Trends Genet., 31, 215, 10.1016/j.tig.2015.02.007 · DOI
- Shin, 2014, The genome sequence of the Antarctic bullhead notothen reveals evolutionary adaptations to a cold environment, Genome Biol., 15, 468., 10.1186/s13059-014-0468-1 · DOI
- Simão, 2015, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs, Bioinformatics, 31, 3210, 10.1093/bioinformatics/btv351 · DOI · Paper page
- Star, 2011, The genome sequence of Atlantic cod reveals a unique immune system, Nature, 477, 207, 10.1038/nature10342 · DOI · Paper page
- Tørresen, 2017, An improved genome assembly uncovers prolific tandem repeats in Atlantic cod, BMC Genomics, 18, 311, 10.1186/s12864-016-3448-x · DOI · Paper page
- Wilson, 2017, Young genes are highly disordered as predicted by the preadaptation hypothesis of de novo gene birth, Nat Ecol Evol., 1, 0146–0146., 10.1038/s41559-017-0146 · DOI
- Wilson, 2011, Putatively noncoding transcripts show extensive association with ribosomes, Genome Biol Evol., 3, 1245, 10.1093/gbe/evr099 · DOI
- Wöhrmann, 1995, Antifreeze glycopeptides of the high-Antarctic silverfish Pleuragramma antarcticum (Notothenioidei), Comp Biochem Physiol C Pharmacol Toxicol Endocrinol., 111, 121, 10.1016/0742-8413(95)00007-T · DOI
- Yang, 2013, Chemical synthesis of a masked analogue of the fish antifreeze potentiating protein (AFPP), Org Biomol Chem., 11, 4935, 10.1039/c3ob41066h · DOI
- Yates, 2016, 2016. Ensembl 2016, Nucleic Acids Res., 44, D710, 10.1093/nar/gkv1157 · DOI
- Zhuang, 2012, Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome, BMC Genomics, 13, 293., 10.1186/1471-2164-13-293 · DOI · Paper page
Cited by
Sorted by citations
Tørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Self-citation
Metadata
- Authors
- Baalsrud, H. T., Tørresen, O. K., Solbakken, M. H., Salzburger, W., Hanel, R., Jakobsen, K. S., & Jentoft, S.
- Affiliations
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis (CEES), University of Oslo, Oslo, Norway
- Institute of Fisheries Ecology, Johann Heinrich von Thünen Institute, Federal Research Institute for Rural Areas, Forestry and Fisheries, Hamburg, Germany
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-12-05
- Volume
- 35
- Issue
- 3
- Pages
- 593-606
- ISSN
- 0737-4038
- 1537-1719
- PMC
- PMC5850335
- Cited by
- 116
- References
- 3
- Language
- en
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. https://app.cochat.ai/papers/10.1093/molbev/msx311
- The paper
- Baalsrud, H. T., Tørresen, O. K., Solbakken, M. H., Salzburger, W., Hanel, R., Jakobsen, K. S., & Jentoft, S. (2018). De Novo Gene Evolution of Antifreeze Glycoproteins in Codfishes Revealed by Whole Genome Sequence Data. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msx311