Protein genes in repetitive sequence-antifreeze glycoproteins in Atlantic cod genome

BMC Genomics

Volumn 13, Issue 1, 2012, Pages

  Zhuang, Xuan ^a   Yang, Chun ^b,c   Fevolden, Svein Erik ^d   Cheng, C H C ^a  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c Currently at EMD Millipore   (United States)

^d UNIVERSITY OF TROMSØ   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIFREEZE GLYCOPROTEIN; FISH PROTEIN; GLYCOPROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; ATLANTIC COD; CODON; CONTROLLED STUDY; FISH GENETICS; GENE IDENTIFICATION; GENE LOCUS; GENE SEQUENCE; GENETIC SIMILARITY; GENOTYPE; GLYCOSYLATION; HABITAT; HOMOZYGOSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ASSEMBLY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS; SOUTHERN BLOTTING; TANDEM REPEAT;

ANIMALS; ANTIFREEZE PROTEINS; COMPUTATIONAL BIOLOGY; GADUS MORHUA; GENETIC LOCI; GENOME; GENOTYPE; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA;

BOREOGADUS; BOREOGADUS SAIDA; GADUS MORHUA; TELEOSTEI;

EID: 84863102734     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-13-293     Document Type: Article

References (27)

1. Green P. Whole-genome disassembly. Proc Natl Acad Sci USA 2002, 99(7):4143.
2. Finotello F, Lavezzo E, Fontana P, Peruzzo D, Albiero A, Barzon L, Falda M, Di Camillo B, Toppo S. Comparative analysis of algorithms for whole-genome assembly of pyrosequencing data. Brief Bioinform 2011, 13(3):269-280.
3. Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrom M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, et al. The genome sequence of Atlantic cod reveals a unique immune system. Nature 2011, 477(7363):207-210.
4. Goddard SV, Kao MH, Fletcher GL. Population differences in antifreeze production cycles of juvenile Atlantic cod (Gadus morhua) reflect adaptations to overwintering environment. Can J Fish Aquat Sci 1999, 56:1991-1999.
5. Goddard SV, Wroblewski JS, Taggart CT, Howse KA, Bailey WL, Kao MH, Fletcher GL. Overwintering of adult northern Atlantic cod (Gadus morhua) in cold inshore waters as evidenced by plasma antifreeze glycoprotein levels. Can J Fish Aquat Sci 1994, 51:2834-2842.
6. Hew CL, Slaughter D, Fletcher GL, Joshi S. Antifreeze glycoproteins in the plasma of Newfoundland Atlantic cod (Gadus morhua). Can J Zool 1981, 59:2186-2192.
7. Cheng C-HC. Evolution of the diverse antifreeze proteins. Curr Opin Genet Dev 1998, 8:715-720.
8. Fletcher GL, Hew CL, Davies PL. Antifreeze proteins of teleost fishes. Annu Rev Physiol 2001, 63:359-390.
9. Chen L, DeVries AL, Cheng C-HC. Convergent evolution of antifreeze glycoproteins in Antarctic notothenioid fish and Arctic cod. Proc Natl Acad Sci USA 1997, 94(8):3817-3822.
10. DeVries AL, Cheng C-HC. Antifreeze proteins and organismal freezing avoidance in polar fishes. The physiology of polar fishes. vol. 22 2005, 155-201. Elsevier Academic Press, San Diego, Farrell AP, Steffensen JF.
11. Pogson GH, Fevolden SE. 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. Mol Ecol 2003, 12(1):63-74.
12. Sarvas TH, Fevolden SE. Pantophysin (Pan I) locus divergence between inshore v. offshore and northern v. southern populations of Atlantic cod in the north-east Atlantic. J Fish Biol 2005, 67:444-469.
13. Johansen SD, Coucheron DH, Andreassen M, Karlsen BO, Furmanek T, Jørgensen TE, Emblem T, Breines R, Nordeide JT, Moum T. Large-scale sequence analyses of Atlantic cod. New Biotechnol 2009, 25(5):263-271.
14. Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res 2004, 32:W273-W279.
15. Nicodemus-Johnson J, Silic S, Ghigliotti L, Pisano E, Cheng CHC. Assembly of the Antifreeze Glycoprotein/Trypsinogen-Like Protease Genomic Locus in the Antarctic fish Dissostichus mawsoni (Norman). Genomics 2011, 98:194-201.
16. Scott GK, Davies PL, Kao MH, Fletcher GL. Differential amplification of antifreeze protein genes in the pleuronectinae. J Mol Evol 1988, 27(1):29-35.
17. Graham LA, Davies PL. Glycine-rich antifreeze proteins from snow fleas. Science 2005, 310(5747):461.
18. Middleton AJ, Brown AM, Davies PL, Walker VK. Identification of the ice-binding face of a plant antifreeze protein. FEBS Lett 2009, 583(4):815-819.
19. Gatesy J, Hayashi C, Motriuk D, Woods J, Lewis R. Extreme diversity, conservation, and convergence of spider silk fibroin sequences. Science 2001, 291(5513):2603.
20. Regier JC. Evolution and higher-order structure of architectural proteins in silkmoth chorion. EMBO J 1986, 5(8):1981.
21. Lacruz RS, Lakshminarayanan R, Bromley KM, Hacia JG, Bromage TG, Snead ML, Moradian-Oldak J, Paine ML. Structural analysis of a repetitive protein sequence motif in strepsirrhine primate amelogenin. PLoS One 2011, 6(3):e18028.
22. MacDougall M, Simmons D, Luan X, Nydegger J, Feng J, Gu TT. Dentin phosphoprotein and dentin sialoprotein are cleavage products expressed from a single transcript coded by a gene on human chromosome 4. J Biol Chem 1997, 272(2):835.
23. Eckert RL, Green H. Structure and evolution of the human involucrin gene. Cell 1986, 46:583-589.
24. Yamada Y, Avvedimento VE, Mudryj M, Ohkubo H, Vogeli G, Irani M, Pastan I, de Crombrugghe B. The collagen gene: evidence for its evolutionary assembly by amplification of a DNA segment containing an exon of 54 bp. Cell 1980, 22:887-892.
25. Alkan C, Sajjadian S, Eichler EE. Limitations of next-generation genome sequence assembly. Nat Methods 2011, 8:61-65.
26. Kidd JM, Sampas N, Antonacci F, Graves T, Fulton R, Hayden HS, Alkan C, Malig M, Ventura M, Giannuzzi G. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat Methods 2010, 7(5):365-371.
27. Miyake T, Amemiya CT. BAC libraries and comparative genomics of aquatic chordate species. Comp Biochem Physiol C 2004, 138:233-244.