Phylogenies of developmentally important proteins do not support the hypothesis of two rounds of genome duplication early in vertebrate history

Journal of Molecular Evolution

Volumn 48, Issue 5, 1999, Pages 565-576

  Hughes, Austin L ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

Evolution of development; Gene duplication; Genome duplication; Protein phylogeny; Vertebrates

Indexed keywords

BONE MORPHOGENETIC PROTEIN; DNA BINDING PROTEIN; HOMEODOMAIN PROTEIN; ZINC FINGER PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; DEVELOPMENTAL GENETICS; GENE DUPLICATION; GENOME; MOLECULAR EVOLUTION; NONHUMAN; PHYLOGENY; PROTEIN ANALYSIS; UNINDEXED SEQUENCE; VERTEBRATE;

ANIMALS; BONE MORPHOGENETIC PROTEINS; DNA-BINDING PROTEINS; EVOLUTION, MOLECULAR; FETAL PROTEINS; GENE DUPLICATION; HOMEODOMAIN PROTEINS; MEMBRANE PROTEINS; MODELS, GENETIC; MYOD PROTEIN; PHYLOGENY; POLYPLOIDY; PROTEINS; RECEPTORS, NOTCH; T-BOX DOMAIN PROTEINS; TRANSCRIPTION FACTORS; VERTEBRATES;

VERTEBRATA;

EID: 0032957497     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/PL00006499     Document Type: Article

References (46)

1. Arora K, Levine MS, O'Connor MB (1994) The screw gene encodes a ubiquitously expressed member of the TGF-β family required for specification of dorsal cell fates in the Drosophila embryo. Genes Dev 8:2588-2601
2. Bailey WJ, Kim J, Wagner GP, Ruddle FH (1997) Phylogenetic reconstruction of the vertebrate Hox cluster duplication. Mol Biol Evol 14:843-853
3. Balczarek KA, Lai Z-C, Kumar S (1997) Evolution and functional diversification of the Paired Box (Pax) DNA-binding domains. Mol Biol Evol 14:829-842
4. Celeste AJ, Jannazi JA, Taylor RC, et al. (1990) Identification of transforming growth factor β family members present in bone-inductive protein purified from bovine bone. Proc Natl Acad Sci USA 87:9843-9847
5. Coulier F, Pontarotti P, Roubin R, Hartung H, Goldfarb M, Birnbaum D (1997) Of worms and men: an evolutionary perspective on the fibroblast growth factor (FGF) and FGF receptor families. J Mol Evol 44:43-56
6. Doll U, Niessing J (1993) Continued expression of the chicken caudal homologue in endodermally derived organs. Dev Biol 156:155-163
7. Felsenstein J (1985) Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39:95-105
8. Ferris SD, Whitt GS (1977) Loss of duplicate gene expression after polyploidisation. Nature 265:258-260
9. Finston TL, Hebert PDN, Foottit RB (1995) Genome size variation in aphids. Insect Biochem Mol Biol 25:189-196
10. Higgins DG, Bleasby AJ, Fuchs R (1992) Clustal V: improved software for multiple sequence alignment. Comput Appl Biosci 8:189-191
11. Holland PWH, Garcia-Fernandez J, Williams NA, Sidow A (1994) Gene duplications and the origins of vertebrate development. Development 1994 Suppl: 125-133
12. Hopwood ND, Pluck A, Gurdon JB (1989) MyoD expression in the forming somites is an early response to mesoderm induction in Xenopu s embryos. EMBO J 8:3409-3417
13. Hu Y, Kazenwadel J, James R (1993) Isolation and characterization of the murine homeobox gene Cdx-1. J Biol Chem 268:27214-27225
14. Hughes AL, Hughes MK (1995) Small genomes for better flyers. Nature 377:391
15. Kasahara M, Hayashi M, Tanaka K, et al. (1996) Chromosomal localization of the proteasome Z subunit gene reveals an ancient chromosomal duplication involving the major histocompatibility complex. Proc Natl Acad Sci USA 93:9096-9101
16. Kingsley C, Winoto A (1992) Cloning of GT box-binding proteins: a novel Sp1 multigene family regulating T-cell receptor gene expression. Mol Cell Biol 12:4251-4261
17. Kispert A, Herrmann BG (1993) The Brachyury gene encodes a novel DNA binding protein. EMBO J 12:3211-3220
18. Kispert A, Herrmann BG, Leptin M, Reuter R (1994) Homologs of the mouse Brachyury gene are involved in the specification of posterior terminal structures in Drosophila, Tribolium, and Locusta. Genes Dev 8:2137-2150
19. Krause M, Fire A, Harrison SW, Priess J, Weintraub H (1990) Ce-MyoD accumulation defines the body wall muscle cell fate during C. elegans embryogenesis. Cell 63:907-918
20. Kumar S, Tamura K, Nei M (1993) MEGA: molecular evolutionary genetic analysis, Version 1.0. Pennsylvania State University, University Park
21. Larsson KA, Johansen KM, Xu T, Artavanis-Tsakonas (1985) The human NOTCH1, 2, and 3 genes are located at chromosome positions 9q34, 1p13-p 11 and 19p13.2-p13.1 in regions of neoplasia-associated translocation. Genomics 24:253-258
22. Li W-H (1980) Rate of gene silencing at duplicate loci: a theoretical study and interpretation of data from tetraploid fishes. Genetics 95:237-258
23. Ma W-J, Cheng S, Campbell C, Wright A, Furneaux H (1996) Cloning and characterization of HuR, a ubiquitously expressed elav-like protein. J Biol Chem 271:6144-6151
24. Miklos GLG, Rubin GM (1996) The role of the genome project in determining gene function: insight from model organisms. Cell 86:521-529
25. Milbrandt J (1987) A nerve growth factor-induced gene encodes a possible transcriptional regulatory factor. Science 238:797-799
26. Miner JH, Wold B (1990) Herculin, a fourth member of the MyoD family of myogenic regulatory genes. Proc Natl Acad Sci USA 87:1089-1093
27. Mlodik M, Gehring WJ (1987) Expression of the caudal gene in the germ line of Drosophila: formation of an RNA and protein gradient during early embryogenesis. Cell 48:465-478
28. Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
29. Oh S-H, Johnson R, Wu DK (1996) Differential expression of bone morphogenetic proteins in the developing vestibular and auditory sensory organs. J Neurosci 16:6463-6475
30. Ohno S (1970) Evolution by gene duplication. Springer Verlag, New York
31. Olmo E, Capriglione T, Odierna G (1989) Genome size evolution in vertebrates: trends and contrasts. Comp Biochem Physiol 92B:447-453
32. Ota T, Nei M (1994) Estimation of the number of amino acid substitutions per site when the substitution rate varies among sites. J Mol Evol 38:642-643
33. Padgett RW, St. Johnston RD, Gelbart WM (1987) A transcript from a Drosophila pattern gene predicts a protein homologous to the transforming growth factor-β family. Nature 325:81-84
34. Patterson BM, Walldorf U, Eldridge J, Dubendorfer A, Frasch M, Gehring WJ (1991) The Drosophila homologue of vertebrate myogenic-determination genes encodes a transiently expressed nuclear protein marking primary myogenic cells. Proc Natl Acad Sci USA 88:3782-3786
35. Penalva LOF, Sakamoto H, Navarro-Sabate A, et al. (1996) Regulation of the gene sex-lethal: a comparative analysis of Drosophila melanogaster and Drosophila subobscura. Genetics 144:1653-1664
36. Perron M, Theodore L, Wegnez M (1995) Isolation and embryonic expression of Xel-1, a nervous system-specific Xenopus gene related to the elav family. Mech Dev 51:235-249
37. Rasch EM, Barr HJ, Rasch RW (1971) The DNA content of sperm of Drosophila melanogaster. Chromosoma 33:1-18
38. Robinow S, Campos AR, Yao K-M, White K (1988) The elav gene product of Drosophila, required in neurons, has three RNP consensus motifs. Science 242:1570-1572
39. Sidow A (1996) Gen(om)e duplications in the evolution of early vertebrates. Curr Opin Genet Dev 6:715-722
40. Supp DM, Witte DP, Branford WW, Smith EP, Potter SS (1996) Sp4, a member of the Sp1-family of zinc finger transcription factors, is required for normal murine growth, viability, and male fertility. Dev Biol 176:284-299
41. Swofford DL (1990) PAUP: phylogenetic analysis using parsimony. Illinois Natural History Survey, Champaign
42. Szarski H (1970) Changes in the amount of DNA in cell nuclei during vertebrate evolution. Nature 226:651-652
43. Wharton KA, Johansen KM, Xu T, Artavanis-Tsakonas S (1985) Nucleotide sequence from the neurogenic locus notch implies a gene product that shares homology with proteins containing EGF-like repeats. Cell 43:567-581
44. Wharton KA, Thomsen GH, Gelbart WM (1991) Drosophila 60A gene, another transforming growth factor β family member, is closely related to human bone morphogenetic proteins. Proc Natl Acad Sci USA 88:9214-9218
45. Wimmer EA, Jackie H, Pfeifle C, Cohen SM (1993) A Drosophila homologue of human Sp1 is a head-specific segmentation gene. Nature 366:690-694
46. Zhang J, Nei M (1996) Evolution of antennapedia-class homeobox genes. Genetics 142:295-303