Multiple linked β and α globin genes in Atlantic cod: A PCR based strategy of genomic exploration

Marine Genomics

Volumn 2, Issue 3-4, 2009, Pages 169-181

  Halldórsdóttir, Katrín ^a   Árnason, Einar ^a  

^a UNIVERSITY OF ICELAND   (Iceland)

Author keywords

globin genes; Genomic exploration; Hemoglobin; Hemoglobin variability; Linkage disequilibrium; PCR errors

Indexed keywords

GADUS MORHUA;

EID: 71649088312     PISSN: 18747787     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.margen.2009.10.001     Document Type: Article

References (42)

1. Andersen O., Wetten O., De Rosa M., Andre C., Alinovi C., Colafranceschi M., Brix O., and Colosimo A. Haemoglobin polymorphisms affect the oxygen-binding properties in Atlantic cod populations. Proc. R. Soc. B 276 (2009) 833-841
2. Árnason E. Mitochondrial cytochrome b DNA variation in the high fecundity Atlantic cod: trans-Atlantic clines and shallow gene-genealogy. Genetics 166 (2004) 1871-1885
3. Berenbrink M., Koldkjær P., Kepp O., and Cossins A.R. Evolution of oxygen secretion in fishes and the emergence of a complex physiological system. Science 307 (2005) 1752-1757
4. Binotti I., Giovenco S., Giardina B., Antonini E., Brunori M., and Wyman J. Studies on the functional properties of fish hemoglobins. II. The oxygen equilibrium of the isolated hemoglobin components from trout blood. Arch. Biochem. Biophys. 142 (1971) 74-80
5. Bracho M.A., Moya A., and Barrio E. Contribution of taq polymerase-induced errors to the estimation of RNA virus diversity. J. Gen. Virol. 79 (1998) 2921-2928
6. Brennan S., Owen M., Chan T., and Rukova A. Novel hemoglobin α chain elongation resulting from a 15-residue insertion and tandem duplication of the F helix. Clin. Biochem. 41 (2008) 1156-1161
7. Brittain T. Root effect hemoglobins. J. Inorg. Biochem. 99 (2005) 120-129
8. Brix O., Thorkildsen S., and Colosimo A. Temperature acclimation modulates the oxygen binding properties of the Atlantic cod (Gadus morhua L.) genotypes HbI*1/1, HbI*1/2, and HbI*2/2-by changing the concentrations of their major hemoglobin components (results from growth studies at different temperatures). Comp. Biochem. Physiol., Part A Mol. Integr. Physiol. 138 (2004) 241-251
9. Brownlie A., Hersey C., Oates A.C., Paw B.H., Falick A.M., Witkowska H.E., Flint J., Higgs D., Jessen J., Bahary N., Zhu H., Lin S., and Zon L. Characterization of embryonic globin genes of the zebrafish. Dev. Biol. 255 (2003) 48-61
10. Burge C., and Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 (1997) 78-94
11. Chan F., Robinson J., Brownlie A., Shivdasani R.A., Donovan A., Brugnara C., Kim J., Lau B., Witkowska H.E., and Zon L.I. Characterization of adult α- and β-globin genes in the zebrafish. Blood 89 (1997) 688-700
12. Decker H., and Nadja H. Negative cooperativity in Root-effect hemoglobins: role of heterogeneity. Integr. Comp. Biol. 47 4 (2006) 656-661
13. Ewing B., and Green P. Basecalling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8 (1998) 186-194
14. Ewing B., Hillier L., Wendl M., and Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 (1998) 175-185
15. Felsenstein J. PHYLIP (phylogeny inference package) version 3.6a3 (2002), Department of Genome Sciences, University of Washington, Seattle Distributed by the author
16. Frydenberg O., Møller D., Nævdal G., and Sick K. Haemoglobin polymorphism in Norwegian cod populations. Hereditas 136 (1965) 257-271
17. Fyhn U.E., Brix O., Nævdal G., and Johansen T. New variants of the haemoglobins of Atlantic cod: a tool for discriminating between coastal and Arctic cod. ICES Mar. Sci. Symp. 198 (1994) 666-670
18. Giordano D., Vergara A., Lee H., Peisach J., Balestrieri M., Mazzarella L., Parisi E., diPrisco G., and Verde C. Hemoglobin structure/function and globin-gene evolution in the Arctic fish Liparis tunicatus. Gene 406 (2007) 58-68
19. Gonzalez J.M., Zimmermann J., and Saiz-Jimenez C. Evaluating putative chimeric sequences from PCR-amplified products. Bioinformatics 21 (2005) 333-337
20. Gordon D., Abajian C., and Green P. Consed: a graphical tool for sequence finishing. Genome Res. 8 (1998) 195-202
21. Halldórsdóttir K., and Árnason E. Organization of a β and α globin gene set in the teleost atlantic cod, Gadus morhua. Biochem. Genet. (2009). http://doi:10.1007/s10528-009-9280-0 published online ahead of print. doi:10.1007/s10528-009-9280-0
22. Johnson R.M., Prychitko T., Gumucio D., Wildman D.E., Uddin M., and Goodman M. Phylogenetic comparisons suggest that distance from the locus control region guides developmental expression of primate β-type globin genes. Proc. Natl. Acad. Sci. U. S. A. 103 (2005) 3186-3191
23. Karlsson S., and Nienhuis A.W. Developmental regulation of human globin genes. Ann. Rev. Biochem. 54 (1985) 1071-1108
24. Karpov A.K., and Novikov G.G. Hemoglobin alloforms in cod Gadus morhua (Gadiformes, Gadidae), their functional characteristics and occurrence in populations. J. Ichthyol. 6 (1980) 45-49
25. Kumar S., Tamura K., and Nei M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5 (2004) 150-163
26. Lewontin R.C., and Kojima K. The evolutionary dynamics of complex polymorphisms. Evolution 14 (1960) 458-472
27. Li Y.C., Korol A.B., Fahima T., and Nevo E. Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 21 (2004) 991-1007
28. Mazzarella L., Bonomi G., Lubrano M., Merlino A., Riccio A., Vergara A., Vitagliano L., Verde C., and Prisco G. Minimal structural requirements for Root effect: crystal structure of the cathodic hemoglobin isolated from the Antarctic fish Trematomus newnesi. Proteins 62 (2006) 316-321
29. McMorrow T., Wagner A., Harte T., and Gannon F. Sequence analysis and tissue expression of a non-Bohr beta-globin cDNA from Atlantic salmon. Gene 189 (1997) 183-188
30. Mylvaganam S., Bonaventura C., Bonaventura J., and Getzoff E. Structural basis for the Root effect in haemoglobin. Nat. Struct. Mol. Biol. 3 (1996) 275-283
31. Pelster B., and Decker H. The Root effect-a physiological perspective. Micron 35 (2004) 73-74
32. Perutz M., and Brunori M. Stereochemistry of cooperative effects in fish and amphibian haemoglobins. Nature 229 (1982) 421-426
33. Petersen M.F., and Steffensen J.F. Preferred temperature of juvenile Atlantic cod Gadus morhua with different haemoglobin genotypes at normoxia and moderate hypoxia. J. Exp. Biol. 206 (2003) 359-364
34. Pusch C.M., and Bachmann L. Spiking of contemporary human template DNA with ancient DNA extracts induces mutations under PCR and generates nonauthentic mitochondrial sequences. Mol. Biol. Evol. 21 (2004) 957-964
35. Rice J.A. Mathematical Statistics and Data Analysis. 2nd edition (1995), Duxbury Press, Belmont, California
36. Rice P., Longden I., and Bleasby A. EMBOSS: the European Molecular Biology open software suite. Trends Genet. 16 (2000) 276-277
37. Root R.W. The respiratory function of the blood of marine fishes. Biol. Bull. 61 (1931) 427-456
38. Rozas J., Sánchez-DelBarrio J.C., Messeguer X., and Rozas R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
39. Sick K. Hemoglobin polymorphisms of cod in the Baltic and the Danish Belt sea. Hereditas 54 (1965) 19-48
40. Sjakste N.I., and Sjakste T.G. Structure of globin gene domains in mammals and birds. Russ. J. Genet. 38 (2002) 1343-1358
41. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
42. Verde C., Balestrieri M., de Pascale D., Pagnozzi D., Lecointre G., and di Prisco G. The oxygen transport system in three species of the Boreal fish family Gadidae. J. Biol. Chem. 281 (2006) 22073-22084