1.2. BASES TEÓRICAS
1.2.13. TECNOLOGIA DE LA COMPOTA
B. saida 80 kbp 50 0 50 100 150 200 kbp AFGP cluster I 100 50 150 200 230 kbp 0 0 50 80 kbp
AFGP cluster II AFGP cluster III
100 50 150 200 kbp 0 Gm_AFGP1 0 7 6 5 2 Mt_AFGP1 2 3 4 Bs_AFGP1 2 3 4 56 7 4 3 9 8 10 12 13 14 16 15 11
Figure 3.13 AFGP gene family expansion history in gadid lineage
AFGP genes are represented by the red arrows. Orthologous AFGP genes are connected by red lines. Grey shaded areas indicate regions of high nucleotide identities (85%-99%) between the AFGP locus of G. morhua and M. tomcod, and B. saida AFGP cluster I. The phylogenetic relationship of the three species is indicated by the lines on the left of the species names.
Table 3.1 Characteristics of all AFGP genes and pseudogenes in three gadids AFGP gene or pseudogene Length (bp) Signal peptide C-terminus non-tripeptide residues Polyprotein cleavage sites 27-nt repeats R K RAAR 5’ 3’ Bs AFGP1ψ ~1.7k Yes RVCVCVCV* 4 2 0 2 0
Bs AFGP2 766 Yes AAVL* 3 0 0 2 2
Bs AFGP3 603 Yes AAVL* 1 1 0 2 2
Bs AFGP4 1791 Yes AAVF* 2 4 0 2 2
Bs AFGP5 ~2k Yes AAVF* 0 4 0 1 2
Bs AFGP6ψ ~800 No AAVF* 1 3 0 0 2
Bs AFGP7ψ 959 Yes AAVS* 1 3 0 5 2
Bs AFGP8 2256 Yes AVF* 5 0 9 2 2
Bs AFGP9 2085 Yes AVF* 2 0 9 2 2
Bs AFGP10 ~2.7k Yes AVF* 1 0 5 2 2
Bs AFGP11 1254 Yes AVF* 5 0 4 2 2
Bs AFGP12 1737 Yes AVF* 5 0 7 2 2
Bs AFGP13 2052 Yes AVF* 5 0 8 2 2
Bs AFGP14ψ 1288 No AVF* 5 0 4 2 2
Bs AFGP15 1563 Yes AVF* 6 0 5 2 2
Bs AFGP16 ~1.2k Yes In gap 1 0 1 2 2
Gm AFGP1ψ ~2.6k Yes RVCVCVCV* 4 2 0 2 0
Gm AFGP2 529 Yes AAVL* 2 1 0 2 2
Gm AFGP3 595 Yes AAVL* 1 0 0 2 2
Gm AFGP4 637 Yes AAVL* 1 1 0 2 2
Gm AFGP5 1566 Yes AAVL* 4 0 0 2 2
Gm AFGP6 ~2.8k Yes AAVF* 0 8 0 2 2
Gm AFGP7ψ 698 Yes AAVS* 0 0 0 5 2
Mt AFGP1 796 Yes AVF* 0 1 0 1.5 2
Mt AFGP2 ~2.2k Yes AAVF* 0 1 0 2 2
Mt AFGP3 ~4.5k Yes KL* 0 0 50 5 0
Mt AFGP4ψ 723 No AAVS* 1 0 0 3 2
Notes: Pseudogenes are denoted by ‘ψ’ at the end of the gene name. The lengths of the complete genes are accurate to base pair (bp), and the estimated lengths of the incomplete genes (have gap in assembly) are indicated by ~. The symbol ‘*’ in the column ‘C-terminus non-tripeptide residues’ indicates the stop codon. Amino acid is represented by single letter. The numbers in the last five columns represent the copy number of each type of polyprotein cleavage sites and that of 27-nt repeats.
Table 3.2 Comparison of amino acid composition (%) in mature AFGPs and AFGP gene (conceptual translation) in B. saida
Size isoforms
Thr Pro Ala Arg Lys
Mature AFGPs* AFGP1-5 29.8 1.2 67.0 1.2 0 AFGP6 26.1 12.3 61.0 0.6 0 AFGP7,8 26.6 14.1 58.6 0.7 0 AFGP genes 30.0 10.1 56.6 3.0 0.3
* Notes: amino acid composition in mature AFGPs were reported by Chen et al 1997 (Chen, DeVries et al. 1997b).
Table 3.3 Codon usage frequencies of three residue positions in the tripeptide repeats of all AFGPs in three gadid
Tripeptide 1st residue (%) Tripeptide 2nd residue (%) Tripeptide 3rd residue (%)
Thr Thr Thr Thr Arg Lys Ala Ala Ala Ala Ala Pro Pro Pro Ala Ala Ala Ala
ACA ACT ACC ACG AGA AAA GCT GCA GCT GCC GCG CCA CCT CCG GCA GCT GCC GCG
Bs_AFGP2 39.6 25.0 31.3 0.0 4.2 0.0 0.0 16.7 0.0 56.3 12.5 8.3 0.0 6.3 14.6 2.1 81.3 2.1 Bs_AFGP3 32.3 41.9 19.4 0.0 3.2 3.2 0.0 39.3 0.0 7.1 21.4 17.9 0.0 14.3 17.2 0.0 82.8 0.0 Bs_AFGP4 51.2 27.7 15.1 0.6 1.2 2.4 1.8 32.5 0.6 31.3 27.1 4.8 0.0 3.6 20.5 4.2 75.3 0.0 Bs_AFGP5 31.3 46.9 0.0 0.0 0.0 9.4 12.5 45.5 0.0 3.0 0.0 48.5 3.0 0.0 28.1 0.0 71.9 0.0 Bs_AFGP6 22.9 54.3 2.9 0.0 2.9 8.6 8.6 47.2 0.0 0.0 0.0 52.8 0.0 0.0 25.7 2.9 71.4 0.0 Bs_AFGP8 40.7 40.7 4.2 0.0 13.6 0.0 0.9 39.0 0.0 10.3 22.1 11.7 0.0 16.9 48.6 9.5 41.9 0.0 Bs_AFGP9 45.6 39.0 4.6 0.0 9.7 0.0 1.0 41.2 0.0 13.4 22.2 10.8 0.0 12.4 41.5 10.4 48.2 0.0 Bs_AFGP10 45.2 38.5 4.8 0.0 10.6 0.0 1.0 39.0 0.0 15.2 21.0 11.4 0.0 13.3 41.7 11.5 46.9 0.0 Bs_AFGP11 36.4 44.4 5.1 0.0 13.1 0.0 1.0 30.6 0.0 14.3 22.4 18.4 0.0 14.3 57.3 5.2 37.5 0.0 Bs_AFGP12 41.7 42.3 3.2 0.6 12.2 0.0 0.0 35.5 0.0 9.2 23.7 15.8 0.0 15.8 48.7 11.3 40.0 0.0 Bs_AFGP13 42.4 40.0 4.0 0.0 12.8 0.8 0.0 38.7 0.0 8.9 21.8 13.7 0.0 16.9 40.8 12.0 47.2 0.0 Bs_AFGP14 39.2 40.8 7.5 0.0 10.0 0.8 1.7 38.7 0.8 13.4 16.8 13.4 1.7 15.1 44.2 7.5 47.5 0.8 Bs_AFGP15 37.5 41.2 7.4 0.0 11.0 1.5 1.5 40.6 0.0 13.3 17.2 10.2 1.6 17.2 41.4 10.5 48.1 0.0 Bs_AFGP16 48.6 37.8 5.4 0.0 5.4 2.7 0.0 33.3 0.0 8.3 33.3 16.7 0.0 8.3 45.9 13.5 40.5 0.0 Bs Average 39.6 40.0 8.2 0.1 7.8 2.1 2.1 37.0 0.1 14.6 18.7 18.2 0.4 11.0 36.9 7.2 55.7 0.2 Gm_AFGP2 42.9 28.6 9.5 0.0 9.5 4.8 4.8 30.0 5.0 25.0 15.0 20.0 0.0 5.0 19.0 0.0 81.0 0.0 Gm_AFGP3 40.0 26.7 30.0 0.0 3.3 0.0 0.0 36.7 3.3 30.0 16.7 6.7 3.3 3.3 20.0 0.0 80.0 0.0 Gm_AFGP4 37.5 34.4 21.9 0.0 3.1 3.1 0.0 30.0 0.0 23.3 20.0 16.7 0.0 10.0 16.1 0.0 80.6 3.2 Gm_AFGP5 44.9 31.9 18.1 0.0 2.9 0.0 2.2 25.4 1.4 35.5 24.6 5.1 0.0 8.0 21.7 0.0 78.3 0.0 Gm_AFGP6 29.9 48.9 1.5 0.7 0.0 5.8 13.1 49.3 0.0 0.7 0.0 49.3 0.7 0.0 28.8 5.5 64.4 1.4 Gm Average 38.6 36.7 13.5 0.1 3.1 4.6 3.3 37.6 1.6 19.1 12.7 23.9 0.7 4.4 22.0 1.6 74.2 2.2 Mt_AFGP1 36.9 31.3 29.5 0.0 0.0 1.8 0.6 16.4 1.8 0.0 71.0 7.3 0.0 3.6 23.6 0.0 63.7 12.7 Mt_AFGP2 32.3 41.3 24.6 0.6 0.0 0.6 0.6 32.7 0.0 0.0 57.1 10.2 0.0 0.0 13.1 1.3 79.1 6.6 Mt_AFGP3 26.8 40.0 1.0 0.0 32.2 0.0 0.0 61.8 8.7 0.0 0.0 27.6 1.9 0.0 47.8 7.7 42.0 2.4 Mt Average 32.0 37.5 18.3 0.2 10.7 0.8 0.4 36.9 3.5 0.0 42.7 15.0 0.6 1.2 28.2 3.0 61.6 7.2
BIBLIOGRAPHY
Alkan, C., S. Sajjadian, et al. (2011). "Limitations of next-generation genome sequence assembly." Nature Methods 8: 61-65.
Begun, D. J., H. A. Lindfors, et al. (2007). "Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade." Genetics 176(2): 1131-1137.
Bendtsen, J. D., H. Nielsen, et al. (2004). "Improved prediction of signal peptides: SignalP 3.0." Journal of Molecular Biology 340(4): 783-795.
Cai, J., R. Zhao, et al. (2008). "De novo origination of a new protein-coding gene in Saccharomyces cerevisiae." Genetics 179(1): 487.
Cardoso-Moreira, M. and M. Long (2012). The origin and evolution of new genes. Evolutionary Genomics, Springer: 161-186.
Carr, S. M., D. S. Kivlichan, et al. (1999). "Molecular systematics of gadid fishes: implications for the biogeographic origins of Pacific species." Canadian Journal of Zoology 77(1): 19-26.
Chen, L. (1996). "Antifreeze glycoproteins of Antarctic notothenioids and northern cods - gene structure, organization and evolution." Ph.D. Thesis. University of Illinois at Urbana-Champaign, Urbana, IL. Chen, L., A. L. DeVries, et al. (1997). "Convergent evolution of antifreeze glycoproteins in Antarctic
notothenioid fish and Arctic cod." Proceedings of the National Academy of Sciences 94: 3817- 3822.
Chen, S.-T., H.-C. Cheng, et al. (2007). "Evolution of hydra, a recently evolved testis-expressed gene with nine alternative first exons in Drosophila melanogaster." PLoS genetics 3(7): 1131-1143.
Cheng, C.-H. C. (1998a). "Evolution of the diverse antifreeze proteins." Current opinion in genetics & development 8: 715-720.
Cheng, C.-H. C. (1998b). "Origin and mechanism of evolution of antifreeze glycoproteins in polar fishes." Fishes of Antarctica. A biological overview: 311-328.
Cheng, C.-H. C., P. A. Cziko, et al. (2006). "Nonhepatic origin of notothenioid antifreeze reveals pancreatic synthesis as common mechanism in polar fish freezing avoidance." Proceedings of the National Academy of Sciences 103(27): 10491-10496.
Cheng, C. -H. C. (1998). "Evolution of the diverse antifreeze proteins." Current opinion in genetics & development 8(6): 715-720.
Cheng, C. -H. C. and L. Chen (1999). "Evolution of an antifreeze glycoprotein." Nature 401(6752): 443- 444.
Chung, M.-y., L. P. Ranum, et al. (1993). "Evidence for a mechanism predisposing to intergenerational CAG repeat instability in spinocerebellar ataxia type I." Nature genetics 5(3): 254-258.
Clamp, M., B. Fry, et al. (2007). "Distinguishing protein-coding and noncoding genes in the human genome." Proceedings of the National Academy of Sciences 104(49): 19428-19433.
Coad, B. W. and J. D. Reist (2004). "Annotated list of the Arctic marine fishes of Canada." Can Manuscr Rep Fish Aquat Sci 2674(112).
Cohen, D. M., T. Inada, et al. (1990). "FAO species catalogue. v. 10: Gadiform fishes of the world (Order Gadiformes)." FAO Fisheries Synopsis (FAO).
Coulson, M. W., H. D. Marshall, et al. (2006). "Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets." Genome 49(9): 1115-1130. Craig, P. C., W. B. Griffiths, et al. (1982). "Ecological Studies of Arctic Cod (Boreogadus saida) in Beaufort Sea Coastal Waters, Alaska." Canadian Journal of Fisheries and Aquatic Sciences 39(3): 395-406. Cronin, T. M., S. A. Smith, et al. (2008). "Quaternary paleoceanography of the central arctic based on
Integrated Ocean Drilling Program Arctic Coring Expedition 302 foraminiferal assemblages." Paleoceanography 23(1): PA1S18.
Danzmann, R., M. W. Coulson, et al. (2006). "Mitochondrial genomics of gadine fishes: implications for taxonomy and biogeographic origins from whole-genome data sets." Genome 49(9): 1115-1130. Deng, C., C.-H. C. Cheng, et al. (2010). "Evolution of an antifreeze protein by neofunctionalization under
escape from adaptive conflict." Proceedings of the National Academy of Sciences 107(50): 21593-21598.
Deng, G., D. W. Andrews, et al. (1997). "Amino acid sequence of a new type of antifreeze protein, from the longhorn sculpin Myoxocephalus octodecimspinosis." FEBS letters 402(1): 17-20.
DeVries, A. L. (1971). "Glycoproteins as biological antifreeze agents in Antarctic fishes." Science
172(3988): 1152-1155.
DeVries, A. L. (1983). "Antifreeze peptides and glycopeptides in cold-water fishes." Annual Review of Physiology 45(1): 245-260.
DeVries, A. L. and C.-H. C. Cheng (2005). Antifreeze proteins and organismal freezing avoidance in polar fishes. The physiology of polar fishes. A. P. Farrell and J. F. Steffensen. San Diego, Elsevier Academic Press. 22: 155-201.
Dolezel, J., J. Bartos, et al. (2003). "Nuclear DNA content and genome size of trout and human." Cytometry. Part A: The Journal of the International Society for Analytical Cytology 51(2): 127. Douglass, J., O. Civelli, et al. (1984). "Polyprotein gene expression: generation of diversity of
neuroendocrine peptides." Annual review of biochemistry 53(1): 665-715.
Drummond, A. J. and A. Rambaut (2007). "BEAST: Bayesian evolutionary analysis by sampling trees." BMC evolutionary biology 7(1): 214.
Duman, J. G. and A. L. DeVries (1976). "Isolation, characterization, and physical properties of protein antifreezes from the winter flounder, Pseudopleuronectes americanus." Comparative Biochemistry and Physiology Part B: Comparative Biochemistry 54(3): 375-380.
Dunton, K. (1992). "Arctic biogeography: the paradox of the marine benthic fauna and flora." Trends in Ecology & Evolution 7(6): 183-189.
Eastman, J. T. (2005). "The nature of the diversity of Antarctic fishes." Polar Biology 28(2): 93-107. Eckert, R. L. and H. Green (1986). "Structure and evolution of the human involucrin gene." Cell 46: 583-
589.
Eichler, E. E., J. J. Holden, et al. (1994). "Length of uninterrupted CGG repeats determines instability in the FMR1 gene." Nature genetics 8(1): 88-94.
Ewart, K. and G. Fletcher (1993). "Herring antifreeze protein: primary structure and evidence for a C- type lectin evolutionary origin." Molecular marine biology and biotechnology 2(1): 20-27. Ewart, K. V., B. Blanchard, et al. (2000). "Freeze susceptibility in haddock (Melanogrammus aeglefinus)."
Aquaculture 188(1): 91-101.
Finotello, F., E. Lavezzo, et al. (2011). "Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data." Briefings in bioinformatics.
Fletcher, G. L., C. L. Hew, et al. (2001). "Antifreeze proteins of teleost fishes." Annual Review of Physiology 63: 359-390.
Fletcher, G. L., C. L. Hew, et al. (1982). "Isolation and characterization of antifreeze glycoproteins from the frostfish, Microgadus tomcod." Canadian Journal of Zoology 60: 348-355.
Frazer, K. A., L. Pachter, et al. (2004). "VISTA: computational tools for comparative genomics." Nucleic Acids Research 32: W273-W279.
Gatesy, J., C. Hayashi, et al. (2001). "Extreme diversity, conservation, and convergence of spider silk fibroin sequences." Science 291(5513): 2603.
Goddard, S. V., M. H. Kao, et al. (1999). "Population differences in antifreeze production cycles of juvenile Atlantic cod (Gadus morhua) reflect adaptations to overwintering environment." Canadian Journal of Fisheries and Aquatic Sciences 56: 1991-1999.
Goddard, S. V., J. S. Wroblewski, et al. (1994). "Overwintering of adult northern Atlantic cod (Gadus morhua) in cold inshore waters as evidenced by plasma antifreeze glycoprotein levels." Canadian Journal of Fisheries and Aquatic Sciences 51: 2834-2842.
Gradinger, R. R. and B. A. Bluhm (2004). "In-situ observations on the distribution and behavior of amphipods and Arctic cod (Boreogadus saida) under the sea ice of the High Arctic Canada Basin." Polar Biology 27(10): 595-603.
Graham, L. A. and P. L. Davies (2005). "Glycine-rich antifreeze proteins from snow fleas." Science
310(5747): 461.
Green, P. (2002). "Whole-genome disassembly." Proceedings of the National Academy of Sciences 99(7): 4143.
Hall, T. E., N. J. Cole, et al. (2003). "Temperature and the expression of seven muscle-specific protein genes during embryogenesis in the Atlantic cod Gadus morhua." Journal of Experimental Biology
206(18): 3187.
Hardie, D. C. and P. D. N. Hebert (2003). "The nucleotypic effects of cellular DNA content in cartilaginous and ray-finned fishes." Genome 46(4): 683-706.
Haymet, A., L. G. Ward, et al. (1999). "Winter flounder “antifreeze” proteins: synthesis and ice growth inhibition of analogues that probe the relative importance of hydrophobic and hydrogen- bonding interactions." Journal of the American Chemical Society 121(5): 941-948.
Heinen, T. J., F. Staubach, et al. (2009). "Emergence of a new gene from an intergenic region." Current Biology 19(18): 1527-1531.
Hew, C. L., S. Joshi, et al. (1985). "Structures of shorthorn sculpin antifreeze polypeptides." European Journal of Biochemistry 151(1): 167-172.
Hew, C. L., D. Slaughter, et al. (1981). "Antifreeze glycoproteins in the plasma of Newfoundland Atlantic cod (Gadus morhua)." Canadian Journal of Zoology 59: 2186-2192.
Howes, G. J. (1991). "Biogeography of gadoid fishes." Journal of Biogeography 18(6): 595-622.
Hsiao, K.-C., C. Cheng, et al. (1990). "An antifreeze glycopeptide gene from the Antarctic cod Notothenia coriiceps neglecta encodes a polyprotein of high peptide copy number." Proceedings of the National Academy of Sciences 87(23): 9265-9269.
Huelsenbeck, J. P. and F. Ronquist (2001). "MRBAYES: Bayesian inference of phylogenetic trees." Bioinformatics 17(8): 754-755.
Jacob, F. (1977). "Evolution and tinkering." Science 196(4295): 1161-1166.
Johansen, S. D., D. H. Coucheron, et al. (2009). "Large-scale sequence analyses of Atlantic cod." New Biotechnology 25(5): 263-271.
Kaessmann, H. (2010). "Origins, evolution, and phenotypic impact of new genes." Genome research
20(10): 1313.
Kennett, J. P. (1977). "Cenozoic evolution of Antarctic glaciation, the circum-Antarctic Ocean, and their impact on global paleoceanography." Journal of geophysical research 82(27): 3843-3860. Kidd, J. M., N. Sampas, et al. (2010). "Characterization of missing human genome sequences and copy-
number polymorphic insertions." Nature Methods 7(5): 365-371.
Knowles, D. G. and A. McLysaght (2009). "Recent de novo origin of human protein-coding genes." Genome research 19(10): 1752.
Lacruz, R. S., R. Lakshminarayanan, et al. (2011). "Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin." PloS one 6(3): e18028.
Lemaitre, C. and M.-F. Sagot (2008). "A small trip in the untranquil world of genomes: A survey on the detection and analysis of genome rearrangement breakpoints." Theoretical computer science
395(2): 171-192.
Levine, M. T., C. D. Jones, et al. (2006). "Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression." Proceedings of the National Academy of Sciences 103(26): 9935.
Levinson, G. and G. A. Gutman (1987). "Slipped-strand mispairing: a major mechanism for DNA sequence evolution." Molecular biology and evolution 4(3): 203-221.
Li, C., G. Ortí, et al. (2007). "A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study." BMC Evolutionary Biology 7(1): 44.
Li, C.-Y., Y. Zhang, et al. (2010). "A human-specific de novo protein-coding gene associated with human brain functions." PLoS computational biology 6(3): 1-11.
Li, D., Y. Dong, et al. (2010). "A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand." Cell research 20(4): 408-420.
Liu, Y., Z. Li, et al. (2007). "Structure and evolutionary origin of Ca2+-dependent herring type II antifreeze protein." PLoS One 2(6): e548.
Livermore, R., A. Nankivell, et al. (2005). "Paleogene opening of Drake passage." Earth and Planetary Science Letters 236(1): 459-470.
Long, M., E. Betrán, et al. (2003). "The origin of new genes: glimpses from the young and old." Nature Reviews Genetics 4(11): 865-875.
MacDougall, M., D. Simmons, et al. (1997). "Dentin phosphoprotein and dentin sialoprotein are cleavage products expressed from a single transcript coded by a gene on human chromosome 4." Journal of Biological Chemistry 272(2): 835.
Matthiessen, J., J. Knies, et al. (2009). "Pliocene palaeoceanography of the Arctic Ocean and subarctic seas." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 367(1886): 21-48.
Middleton, A. J., A. M. Brown, et al. (2009). "Identification of the ice-binding face of a plant antifreeze protein." FEBS letters 583(4): 815-819.
Miyake, T. and C. T. Amemiya (2004). "BAC libraries and comparative genomics of aquatic chordate species." Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology 138(3): 233-244.
Ng, S. Y., P. Gunning, et al. (1985). "Evolution of the functional human beta-actin gene and its multi- pseudogene family: conservation of noncoding regions and chromosomal dispersion of pseudogenes." Molecular and cellular biology 5(10): 2720.
Nicodemus-Johnson, J., S. Silic, et al. (2011). "Assembly of the Antifreeze Glycoprotein/Trypsinogen-Like Protease Genomic Locus in the Antarctic fish Dissostichus mawsoni (Norman)." Genomics 98: 194-201.
Nicodemus-Johnson, J. D. (2010). "Analysis of the antifreeze glycoprotein containing genomic locus in the Antarctic notothenioid fish Dissostichus mawsoni." Ph.D. Thesis. University of Illinois at Urbana-Champaign, Urbana, IL.
O'Grady, S. M., J. D. Schrag, et al. (1982). "Comparison of antifreeze glycopeptides from Arctic and Antarctic fishes." Journal of Experimental Zoology 224(2): 177-185.
Ohno, S. (1970). Evolution by gene duplication, London: George Alien & Unwin Ltd. Berlin, Heidelberg and New York: Springer-Verlag.
Osuga, D. T. and R. E. Feeney (1978). "Antifreeze glycoproteins from Arctic fish." Journal of Biological Chemistry 253(15): 5338-5343.
Petersen, T. N., S. Brunak, et al. (2011). "SignalP 4.0: discriminating signal peptides from transmembrane regions." Nature Methods 8(10): 785-786.
Pogson, G. H. and S. E. Fevolden (2003). "Natural selection and the genetic differentiation of coastal and Arctic populations of the Atlantic cod in northern Norway: a test involving nucleotide sequence variation at the pantophysin (PanI) locus." Molecular Ecology Notes 12(1): 63-74.
Posada, D. (2008). "jModelTest: phylogenetic model averaging." Molecular biology and evolution 25(7): 1253-1256.
Raymond, J. A., Y. Lin, et al. (1975). "Glycoprotein and protein antifreezes in two Alaskan fishes." Journal of Experimental Zoology 193(1): 125-130.
Regier, J. C. (1986). "Evolution and higher-order structure of architectural proteins in silkmoth chorion." The EMBO Journal 5(8): 1981.
Reisman, H. M., G. L. Fletcher, et al. (1987). "Antifreeze proteins in the grubby sculpin, Myoxocephalus aenaeus and the tomcod, Microgadus tomcod: comparisons of seasonal cycles." Environmental biology of fishes 18(4): 295-301.
Sambrook, J. and D. W. Russell (2001). Molecular cloning: a laboratory manual, Cold spring harbor laboratory press.
Sarvas, T. H. and S. E. Fevolden (2005). "Pantophysin (Pan I) locus divergence between inshore v. offshore and northern v. southern populations of Atlantic cod in the north-east Atlantic." Journal of Fish Biology 67: 444-469.
Scott, G. K., P. L. Davies, et al. (1988). "Differential amplification of antifreeze protein genes in the pleuronectinae." Journal of Molecular Evolusion 27(1): 29-35.
Shevenell, A. E., J. P. Kennett, et al. (2004). "Middle Miocene southern ocean cooling and Antarctic cryosphere expansion." Science 305(5691): 1766-1770.
Smit, A., Hubley, R & Green, P. (1996-2010). RepeatMasker Open-3.0. http://www.repeatmasker.org. Smith, G. P. (1976). "Evolution of repeated DNA sequences by unequal crossover." Science 191(4227):
528-535.
Soderlund, C., S. Humphray, et al. (2000). "Contigs built with fingerprints, markers, and FPC V4. 7." Genome Research 10(11): 1772-1787.
Star, B., A. J. Nederbragt, et al. (2011). "The genome sequence of Atlantic cod reveals a unique immune system." Nature 477(7363): 207-210.
Stothard, P. (2000). "The sequence manipulation suite: JavaScript programs for analyzing and formatting protein and DNA sequences." Biotechniques 28(6): 1102-1104.
Stransky, C., H. Baumann, et al. (2008). "Separation of Norwegian coastal cod and Northeast Arctic cod by outer otolith shape analysis." Fisheries Research 90(1): 26-35.
Sukumaran, J. and M. T. Holder (2010). "DendroPy: a Python library for phylogenetic computing." Bioinformatics 26(12): 1569-1571.
Thompson, J. D., D. G. Higgins, et al. (1994). "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice." Nucleic acids research 22(22): 4673-4680.
Van Voorhies, W., J. Raymond, et al. (1978). "Glycoproteins as biological antifreeze agents in the cod, Gadus ogac (Richardson)." Physiological Zoology: 347-353.
Vandekerchkove, J. and K. Weber (1978). "At least six different actins are expressed in a higher mammal: an analysis based on the amino acid sequences of the amino-terminal tryptic peptide." Journal of Molecular Biology 126: 783-802.
Wassmann, P., H. Svendsen, et al. (1996). "Selected aspects of the physical oceanography and particle fluxes in fjords of northern Norway." Journal of Marine Systems 8(1): 53-71.
Wise, R. J., P. J. Barr, et al. (1990). "Expression of a human proprotein processing enzyme: correct cleavage of the von Willebrand factor precursor at a paired basic amino acid site." Proceedings of the National Academy of Sciences 87(23): 9378-9382.
Wu, D.-D., D. M. Irwin, et al. (2011). "De novo origin of human protein-coding genes." PLoS genetics
7(11): e1002379.
Xiao, W., H. Liu, et al. (2009). "A rice gene of de novo origin negatively regulates pathogen-induced defense response." PLoS One 4(2): e4603.
Yamada, Y., V. E. Avvedimento, et al. (1980). "The collagen gene: evidence for its evolutionary assembly by amplification of a DNA segment containing an exon of 54 bp." Cell 22: 887-892.
Yang, C. (2002). "Antifreeze glycoproteins in northern cods: gene family sizes, sequences, structures, organizations, and evolution." Ph.D. Thesis. University of Illinois at Urbana-Champaign, Urbana, IL.
Yang, Z. and J. Huang (2011). "De novo origin of new genes with introns in Plasmodium vivax." FEBS letters 585(4): 641-644.
Zhang, X., Y. Zhang, et al. (2010). "Construction and characterization of a bacterial artificial chromosome (BAC) library of Pacific white shrimp, Litopenaeus vannamei." Marine Biotechnology 12(2): 141- 149.
Zhou, Q., G. Zhang, et al. (2008). "On the origin of new genes in Drosophila." Genome research 18(9): 1446.
Zwickl, D. (2006). "GARLI: genetic algorithm for rapid likelihood inference." http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html.