Assembly of the antifreeze glycoprotein/trypsinogen-like protease genomic locus in the Antarctic toothfish Dissostichus mawsoni (Norman)

Genomics

Volumn 98, Issue 3, 2011, Pages 194-201

  Nicodemus Johnson, Jessie ^a   Silic, Stephen ^b   Ghigliotti, Laura ^c   Pisano, Eva ^c   Cheng, C H Christina ^b  

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

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

^c UNIVERSITY OF GENOA   (Italy)

Author keywords

AFGP; Antarctic notothenioids; BAC library; Chimeric gene; Dissostichus mawsoni; Gene family evolution; Repetitive sequence assembly

Indexed keywords

ANTIFREEZE GLYCOPROTEIN; GLYCOPROTEIN; PROTEINASE; TRYPSINOGEN LIKE PROTEASE; UNCLASSIFIED DRUG;

AFPG GENE; ANTARCTIC TOOTHFISH; ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CHROMOSOMAL LOCALIZATION; FISH; GENE; GENE DOSAGE; GENE ISOLATION; GENE LOCUS; GENE SEQUENCE; HAPLOTYPE; MOLECULAR CLONING; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; TLP GENE;

ANIMALS; ANTARCTIC REGIONS; ANTIFREEZE PROTEINS; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CLONING, MOLECULAR; GENE DOSAGE; GENETIC LOCI; HAPLOTYPES; MOLECULAR SEQUENCE DATA; PERCIFORMES; PHENOTYPE; PHYLOGENY; SEQUENCE ALIGNMENT; TRYPSINOGEN;

BACTERIA (MICROORGANISMS); DISSOSTICHUS MAWSONI;

EID: 80052155511     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.06.002     Document Type: Article

References (32)

1. Eastman J.T. Antarctic Fish Biology: Evolution in a Unique Environment 1993, Academic, San Diego.
2. Livermore R., Nankivell A., Eagles G., Morris P. Paleogene opening of Drake Passage. Earth Planet. Sci. Lett. 2005, 236:459-470.
3. Kennett J. Marine Geology 1982, Prentice-Hall, Englewood, NJ.
4. Eastman J.T. The nature of diversity of Antarctic fishes. Polar Biol. 2005, 28:93-107.
5. Chen Z., Cheng C.-H.C., Zhang J., Cao L., Chen L., Zhou L., Yudong J., Hua Y., Deng C., Dai Z., Xu Q., Sun S., Shen Y., Chen L. Transcriptomic and genomic evolution under constant cold in Antarctic notothenioid fish. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:12944-12949.
6. Detrich H.W., Parker S.K., Williams R.C.J., Nogales E., Downing K.H. Cold adaptation of microtubule assembly and dynamics. Structural interpretation of primary sequence changes present in the alpha- and beta-tubulins of antarctic fishes. J. Biol. Chem. 2000, 275:37038-37047.
7. Fields P.A., Somero G.N. Hot spots in cold adaptation: localized increases in conformational flexibility in lactate dehydrogenase A4 orthologs of Antarctic notothenioid fishes. Proc. Natl. Acad. Sci. U. S. A. 1998, 95:11476-11481.
8. Kiss A.J., Mirarefi A.Y., Ramakrishnan S., Zukoski C.F., Devries A.L., Cheng C.H. Cold-stable eye lens crystallins of the Antarctic nototheniid toothfish Dissostichus mawsoni Norman. J. Exp. Biol. 2004, 207:4633-4649.
9. DeVries A.L. Glycoproteins as biological antifreeze agents in Antarctic fishes. Science 1971, 172:1152-1155.
10. DeVries A.L., Cheng C.-H.C. Antifreeze proteins and organismal freezing avoidance in polar fishes. The Physiology of Polar Fishes 2005, 155-201. Elsevier Academic Press, San Diego. A.P. Farrell, J.F. Steffensen (Eds.).
11. Jin Y., DeVries A.L. Antifreeze glycoprotein levels in Antarctic notothenioid fishes inhabiting different thermal environments and the effect of warm acclimation. Comp. Biochem. Physiol. B 2006, 144:290-300.
12. Hsiao K.C., Cheng C.-H.C., Fernandes I.E., Detrich H.W., DeVries A.L. An antifreeze glycopeptide gene from the antarctic cod Notothenia coriiceps neglecta encodes a polyprotein of high peptide copy number. Proc. Natl. Acad. Sci. U. S. A. 1990, 87:9265-9269.
13. Chen L., DeVries A.L., Cheng C.-H.C. Evolution of antifreeze glycoprotein gene from a trypsinogen gene in Antarctic notothenioid fish. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:3811-3816.
14. Cheng C.-H.C., Chen L. Evolution of an antifreeze glycoprotein. Nature 1999, 401:443-444.
15. Cheng C.-H.C., Detrich H.W. Molecular ecophysiology of Antarctic notothenioid fishes. Phil. Trans. R. Soc. Lond. B Biol. Sci. 2007, 362:2215-2232.
16. Cheng C.-H.C., Cziko P.A., Evans C.W. Nonhepatic origin of notothenioid antifreeze reveals pancreatic synthesis as common mechanism in polar fish freezing avoidance. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:10491-10496.
17. Amemiya C.T., Powers T.P., Prohaska S.J., Grimwood J., Schmutz J., Dickson M., Miyake T., Schoenborn M.A., Myers R.M., Ruddle F.H., Stadler P.F. HOX clusters of Latimeria: complete characterization provides further evidence for slow evolution of the coelacanth genome. Proc. Natl. Acad. Sci. U. S. A. 2010, 107:3622-3627.
18. Ronaghi M. Pyrosequencing sheds light on DNA sequencing. Genome Res. 2001, 11:3-11.
19. Metzker M.L. Emerging technologies in DNA sequencing. Genome Res. 2005, 15:1767-1776.
20. Goldberg S.M., Johnson J., Busam D., Feldblyum T., Ferriera S., Friedman R., Halpern A., Khouri H., Kravitz S.A., Lauro F.M., Li K., Rogers Y.H., Strausberg R., Sutton G., Tallon L., Thomas T., Venter E., Frazier M., Venter J.C. A Sanger/pyrosequencing hybrid approach for the generation of high-quality draft assemblies of marine microbial genomes. Proc. Natl. Acad. Sci. U. S. A. 2006, 103:11240-11245.
21. Zimmermann J., Voss H., Schwager C., Stegemann J., Ansorge W. Automated Sanger dideoxy sequencing reaction protocol. FEBS Lett. 1988, 233:432-436.
22. Wicker T., Schlagenhauf E., Graner A., Close T.J., Keller B., Stein N. 454 sequencing put to the test using the complex genome of barley. BMC Genomics 2006, 7:275.
23. Soderlund C., Humphray S., Dunham A., French L. Contigs built with fingerprints, markers, and FPC V4.7. Genome Res. 2000, 10:1772-1787.
24. Soderlund C., Longden I., Mott R. FPC: a system for building contigs from restriction fingerprinted clones. Comp. Appl. Biosci. 1997, 13:523-535.
25. Smith M.J. Evolutionary genetics 1998, Oxford.
26. Detrich H.W., Stuart A., Schoenborn M., Parker S.K., Methe B.A., Amemiya C.T. Genome enablement of the notothenioidei: genome size estimates from 11 species and BAC libraries from 2 representative taxa. J. Exp. Zool. B Mol. Dev. Evol. 2010, 314:369-381.
27. Council N.R. Frontiers in Polar Biology in the Genomic Era 2003, National Academy of Sciences, Washington DC.
28. Albertson R.C., Cresko W., Detrich H.W., Postlethwait J.H. Evolutionary mutant models for human disease. Trends Genet. 2009, 25:74-81.
29. Amemiya C.T., Ota T., Litman G.W. Construction of P1 artificial chromosome (PAC) libraries from lower vertebrates. Analysis of Nonmammalian Genomes 1996, 223-256. Academic Press, San Diego, CA. E. Lai, B. Birren (Eds.).
30. Parchem R.J., Poulin F., Stuart A.B., Amemiya C.T., Patel N.H. BAC library for the amphipod crustacean, Parhyale hawaiensis. Genomics 2010, 95:261-267.
31. Ghigliotti L., Mazzei F., Ozouf-Costaz C., Bonillo C., Williams R., Cheng C.-H.C., Pisano E. The two giant sister species of the Southern Ocean, Dissostichus eleginoides and Dissostichus mawsoni, differ in karyotype and chromosomal pattern of ribosomal RNA genes. Polar Biol. 2006, 30:625-634.
32. Tamura K., Dudley J., Nei M., Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol. Biol. Evol. 2007, 24:1596-1599.