Comparative genomic analysis of the mouse and rat amylase multigene family

FEBS Letters

Volumn 581, Issue 3, 2007, Pages 355-360

  Sugino, Hidehiko ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

Amylase; Evolution; Genome; Rodent

Indexed keywords

AMYLASE; SYNTAXIN; SYNTAXIN BINDING PROTEIN 3; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; EVOLUTION; GENE CLUSTER; GENE DUPLICATION; GENOME; MOUSE; MULTIGENE FAMILY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PSEUDOGENE; RAT; RODENT;

AMYLASES; ANIMALS; CHROMOSOME MAPPING; EVOLUTION, MOLECULAR; EXONS; GENE DUPLICATION; GENOMICS; MICE; MULTIGENE FAMILY; PHYLOGENY; PSEUDOGENES; RATS; SPECIES SPECIFICITY;

MAMMALIA; RATTUS; RODENTIA;

EID: 33846434844     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2006.12.039     Document Type: Article

References (53)

1. Liebhaber S.A., Goossens M., and Kan Y.W. Homology and concerted evolution at the 1 and 2 loci of human-globin. Nature 290 (1981) 26-29
2. Brown A.J.L., and Ish-Horowicz D. Evolution of the 87A and 87C heat-shock loci in Drosophila. Nature 290 (1981) 677-682
3. Ohta T. Simulating evolution by gene duplication. Genetics 115 (1987) 207-213
4. Hibner B.L., Burke W.D., and Eickbush T.H. Sequence identity in an early chorion multigene family is the result of localized gene conversion. Genetics 128 (1991) 595-606
5. Clark A. Invasion and maintenance of a gene duplication. Proc. Natl. Acad. Sci. USA 91 (1994) 2950-2954
6. Walsh J.B. How often do duplicated genes evolve new functions?. Genetics 139 (1995) 421-428
7. Lynch M., and Conery J.S. The evolutionary fate and consequences of duplicate genes. Science 290 (2000) 1151-1155
8. Rooney A.P., Piontkivska H., and Nei M. Molecular evolution of the histone 3 multigene family. Mol. Biol. Evol. 19 (2002) 68-75
9. Smith G.P. Unequal crossover and the evolution of multigene families. Cold Spring Harbor Symp. Quant. Biol. (1974) 38507-38513
10. Arnheim N. Concerted evolution of multigene families. In: Nei M., and Koehn R.K. (Eds). Evolution of Genes and Proteins (1983), Sinauer Associates, Sunderland, MA
11. Liao D. Concerted evolution: molecular mechanism and biological implications. Am. J. Hum. Genet. 64 (1999) 24-30
12. Nei M., and Hughes A.L. Balanced polymorphism and evolution by the birth-and-death process in the MHC loci. In: Tsuji K., Aizawa M., and Sasazuki T. (Eds). 11th Histocompatibility Workshop and Conference (1992), Oxford University Press, Oxford, UK
13. Nei M., Gu X., and Sitnikova T. Evolution by the birth-and-death process in multigene families of the vertebrate immune system. Proc. Natl. Acad. Sci. USA 94 (1997) 7799-7806
14. Nei M., Rogozin I.B., and Piontkivska H. Purifying selection and birth-and-death evolution in the ubiquitin gene family. Proc. Natl. Acad. Sci. USA 97 (2000) 10866-10871
15. Hardison R., and Miller W. Use of long sequence alignments to study the evolution and regulation of mammalian globin gene clusters. Mol. Biol. Evol. 10 (1993) 73-102
16. Lemons D., and McGinnis W. Genomic evolution of Hox gene clusters. Science 313 (2006) 1918-1922
17. Niimura Y., and Nei M. Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates. J. Hum. Genet. 51 (2006) 505-517
18. Quignon P., Giraud M., Rimbault M., Lavigne P., Tacher S., Morin E., Retout E., Valin A.S., Lindblad-Toh K., Nicolas J., and Galibert F. The dog and rat olfactory receptor repertoires. Genome Biol. 6 (2005) R83
19. Niimura Y., and Nei M. Comparative evolutionary analysis of olfactory receptor gene clusters between humans and mice. Gene 346 (2005) 13-21
20. Niimura Y., and Nei M. Evolution of olfactory receptor genes in the human genome. Proc. Natl. Acad. Sci. USA 100 (2003) 12235-12240
21. Niimura Y., and Nei M. Evolutionary dynamics of olfactory receptor genes in fishes and tetrapods. Proc. Natl. Acad. Sci. USA 102 (2005) 6039-6044
22. Nelson G., Hoon M.A., Chandrashekar J., Zhang Y., Ryba N.J., and Zuker C.S. Mammalian sweet taste receptors. Cell 106 (2001) 381-390
23. Nelson G., Chandrashekar J., Hoon M.A., Feng L., Zhao G., Ryba N.J., and Zuker C.S. An amino-acid taste receptor. Nature 416 (2002) 199-202
24. Shi P., and Zhang J. Contrasting modes of evolution between vertebrate sweet/umami receptor genes and bitter receptor genes. Mol. Biol. Evol. 23 (2006) 292-300
25. Forsyth I.A., and Wallis M. Growth hormone and prolactin-molecular and functional evolution. J. Mammary. Gland Biol. Neoplasia 7 (2002) 291-312
26. Wallis O.C., and Wallis M. Evolution of growth hormone in primates: the GH gene clusters of the New World monkeys marmoset (Callithrix jacchus) and white-fronted capuchin (Cebus albifrons). J. Mol. Evol. 26 (2006) 1
27. Doane W.W., Gemmill R.M., Schwartz P.E., Hawley S.A., and Norman R. Structural organization of alpha-amylase gene locus in Drosophila melanogaster and Drosophila miranda. Isozymes Curr. Top. Biol. Med. Res. 14 (1987) 229-266
28. Brown C.J., Aquadro C.F., and Anderson W.W. DNA sequence evolution of the amylase multigene family in Drosophila pseudoobscura. Genetics 126 (1990) 131-138
29. Shibata H., and Yamazaki T. Molecular evolution of the duplicated Amy locus in Drosophila melanogaster species subgroup: concerted evolution only in coding region and excess of nonsynonymous substitutions in speciation. Genetics 141 (1995) 223-236
30. Popadic A., Morman R.A., Doane W.W., and Anderson W.W. The evolutionary history of the amylase multigene family in Drosophila pseudoobscura. Mol. Biol. Evol. 13 (1996) 883-888
31. Steinemann S., and Steinemann M. The amylase gene cluster on the evolving sex chromosomes of Drosophila miranda. Genetics (1999) 151151-151161
32. Da Lage J.-L., Maczkowiak F., and Cariou M.-L. Molecular characterization and evolution of the amylase multigene family of Drosophila ananassae. J. Mol. Evol. 51 (2000) 391-403
33. Inomata N., and Yamazaki T. Evolution of nucleotide substitutions and gene regulation in the amylase multigenes in Drosophila kikkawai and its sibling species. Mol. Biol. Evol. 17 (2000) 601-615
34. Zang Z., Inomata N., Yamazaki T., and Kishino H. Evolutionary history and mode of the amylase multigene family in Drosophila. J Mol Evolut (2003) 57702-57709
35. Benkel B.F., Nguyen T., Uno Y., Ponce de Leon P.F., and Hickey D.A. Structural organization and chromosomal location of the chicken alpha-amylase gene family. Gene 362 (2005) 117-124
36. Tricoli J.V., and Shows T.B. Regional assignment of human amylase (AMY) to p22-p21 of chromosome 1. Somat. Cell Mol. Genet. 10 (1984) 205-210
37. Wiebauer K., Gumucio D.L., Jones J.M., Caldwell R.M., Hartle H.T., and Meisler M.H. A 78-kilobase region of mouse chromosome 3 contains salivary and pancreatic amylase genes and a pseudogene. Proc. Natl. Acad. Sci. USA 82 (1985) 5446-5449
38. Nishide T., Nakamura Y., Emi M., Yamamoto T., Ogawa M., Mori T., and Matsubara K. Primary structure of human salivary alpha-amylase gene. Gene 4 (1986) 299-304
39. Horii A., Emi M., Tomita N., Nishide T., Ogawa M., Mori T., and Matsubara K. Primary structure of human pancreatic alpha-amylase gene: its comparison with human salivary alpha-amylase gene. Gene 60 (1987) 57-64
40. Gumucio D.L., Wiebauer K., Caldwell R.M., Samuelson L.C., and Meisler M.H. Concerted evolution of human amylase genes. Mol. Cell. Biol. 8 (1988) 1197-1205
41. Samuelson L.C., Wiebauer K., Snow C.M., and Meisler M.H. Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution. Mol. Cell. Biol. 10 (1990) 2513-2520
42. Ting C.N., Rosenberg M.P., Snow C.M., Samuelson L.C., and Meisler M.H. Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene. Genes Dev. 6 (1992) 1457-1465
43. Mouse genome sequencing consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420 (2002) 520-562
44. Rat genome sequencing project consortium. Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428 (2004) 493-521
45. Cheung J., Wilson M.D., Zhang J., Khaja R., MacDonald J.R., Heng H.H., Koop B.F., and Scherer S.W. Recent segmental and gene duplications in the mouse genome. Genome Biol. 4 (2003) R47
46. Kent W.J., and Haussler D. Assembly of the working draft of the human genome with GigAssembler. Genome Res. 11 (2001) 1541-1548
47. Schwartz S., Zhang Z., Frazer K.A., Smit A., Riemer C., Bouck J., Gibbs R., Hardison R., and Miller W. PipMaker - a web server for aligning two genomic DNA sequences. Genome Res. 10 (2000) 577-586
48. Crerar M.M., Swain W.F., Pictet R.L., Nikovits W., and Rutter W.J. Isolation and characterization of a rat amylase gene family. J. Biol. Chem. 258 (1983) 1311-1317
49. Groot P.C., Bleeker M.J., Pronk J.C., Arwert F., Mager W.H., Planta R.J., Eriksson A.W., and Frants R.R. The human alpha-amylase multigene family consists of haplotypes with variable numbers of genes. Genomics 5 (1989) 29-42
50. Groot P.C., Mager W.H., Henriquez N.V., Pronk J.C., Arwert F., Planta R.J., Eriksson A.W., and Frants R.R. Evolution of the human alpha-amylase multigene family through unequal, homologous, and inter- and intrachromosomal crossovers. Genomics 8 (1990) 97-105
51. Groot P.C., Mager W.H., and Frants R.R. Interpretation of polymorphic DNA patterns in the human alpha-amylase multigene family. Genomics 10 (1991) 779-785
52. Iafrate A.J., Feuk L., Rivera M.N., Listewnik M.L., Donahoe P.K., Qi Y., Scherer S.W., and Lee C. Detection of large-scale variation in the human genome. Nat. Genet. 36 (2004) 949-951
53. Gumucio D.L., Wiebauer K., Dranginis A., Samuelson L.C., Treisman L.O., Caldwell R.M., Antonucci T.K., and Meisler M.H. Evolution of the amylase multigene family. YBR/Ki mice express a pancreatic amylase gene which is silent in other strains. J. Biol. Chem. 260 (1985) 13483-13489