Estimation of ancestral gene set of bilaterian animals and its implication to dynamic change of gene content in bilaterian evolution

Gene

Volumn 345, Issue 1 SPEC. ISS., 2005, Pages 65-71

  Ogura, Atsushi ^a   Ikeo, Kazuho ^a   Gojobori, Takashi ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Deuterostomes; Diversification; Gene gain; Gene loss; Genome; Protostomes

Indexed keywords

ARTICLE; FLY; GENE CLUSTER; GENE LOSS; HUMAN; NEMATODE; NONHUMAN; PLANT AND FUNGAL MORPHOLOGY; PLANT ANIMAL INTERACTION; PRIORITY JOURNAL; SPECIES DIVERSITY;

EID: 13444282380     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gene.2004.11.036     Document Type: Article

References (31)

1. M.D. Adams The genome sequence of Drosophila melanogaster Science 287 2000 2185 2195
2. A.M. Aguinaldo Evidence for a clade of nematodes, arthropods and other moulting animals Nature 387 1997 489 493
3. V.N. Babenko, and D.M. Krylov Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved Nucleic Acids Res. 32 17 2004 5029 5035
4. E.F. Ball, D.C. Hayward, R. Saint, and D.J. Miller A simple plan - cnidarians and the origins of developmental mechanisms Nat. Rev., Genet. 5 2004 567 577
5. J.E. Blair, K. Ikeo, T. Gojobori, and S.B. Hedges The evolutionary position of nematodes BMC Evol. Biol. 2 2002 7
6. S.A. Bowring, J.P. Grotzinger, C.E. Isachsen, A.H. Knoll, S.M. Pelechaty, and P. Kolosov Calibrating rates of early Cambrian evolution Science 261 1993 1293 1298
7. M.O. Dayhoff Computer analysis of protein evolution Sci. Am. 221 1969 86 95
8. D.H. Erwin, and E.H. Davidson The last common bilaterian ancestor Development 129 2002 3021 3032
9. J.R. Finnerty The origin of axial patterning in the metazoan: how old is bilateral symmetry? Int. J. Dev. Biol. 47 2003 412 529
10. H. Glenner, A.J. Hansen, M.V. Sorensen, F. Ronquist, J.P. Huelsenbeck, and E. Willerslev Bayesian inference of the metazoan phylogeny: a combined molecular and morphological approach Curr. Biol. 14 2004 1644 1649
11. E.V. Koonin A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes Genome Biol. 5 2 2004 R7
12. R.D. Kortschak, G. Samuel, R. Saint, and D.J. Miller EST analysis of the cnidarian Acropora millepora reveals extensive gene loss and rapid sequence divergence in the model invertebrates Curr. Biol. 13 2003 2190 2195
13. V. Lamour, S. Quevillon, S. Diriong, V.C. N'Guyen, M. Lipinski, and M. Mirande Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer Proc. Natl. Acad. Sci. 91 1994 8670 8674
14. E.S. Lander Initial sequencing and analysis of the human genome Nature 409 2001 6822
15. O. Lespinet, Y.I. Wolf, E.V. Koonin, and L. Aravind The role of lineage-specific gene family expansion in the evolution of eukaryotes Genome Res. 12 2002 1048 1059
16. M.Q. Martindale, K. Pang, and J.R. Finnerty Investigating the origins of triploblasty: 'mesodermal' gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum Cnidaria; class, Anthozoa Development 131 10 2004 2463 2474
17. T. Miyata, and H. Suga Divergence pattern of animal gene families and relationship with the Cambrian explosion BioEssays 23 2001 1018 1027
18. N. Nikoh, N. Hayase, N. Iwabe, K. Kuma, and T. Miyata Phylogenetic relationship of the kingdoms Animalia, Plantae, and Fungi, inferred from 23 different protein species Mol. Biol. Evol. 11 1994 762 768
19. A. Ogura, K. Ikeo, and T. Gojobori Comparative analysis of gene expression for convergent evolution of camera eye between octopus and human Genome Res. 14 2004 1555 1561
20. S. Ohno Evolution by gene duplication 1970 Springer Verlag
21. K.J. Peterson, J.B. Lyons, K.S. Nowak, C.M. Takacs, M.J. Wargo, and M.A. McPeek Estimating metazoan divergence times with a molecular clock Proc. Natl. Acad. Sci. 101 2004 6536 6541
22. F.H. Ruddle, K.L. Bentley, M.T. Murtha, and N. Risch Gene loss and gain in the evolution of the vertebrates Dev., Suppl. 1994 155 161
23. A. Stechmann, and T. Cavalier-Smith Rooting the eukaryote tree by using a derived gene fusion Science 297 2002 88 91
24. The C. elegans Sequencing Consortium Genome sequence of the nematode C. elegans: a platform for investigating biology Science 282 1998 2012 2018
25. J.S. Venter The sequence of the human genome Science 291 2001 1304 1351
26. A. Veraksa, M. Del Campo, and W. McGinnis Developmental patterning genes and their conserved functions: from model organisms to humans Mol. Genet. Metab. 69 2000 85 100
27. H. Watanabe, H. Mori, T. Itoh, and T. Gojobori Genome plasticity as a paradigm of eubacteria evolution J. Mol. Evol. 44 Suppl. 1 1997 S57 S64
28. R.H. Waterston Initial sequencing and comparative analysis of the mouse genome Nature 420 2002 520 562
29. R.L. Watts, and D.C. Watts The implications for molecular evolution of possible mechanisms of primary gene duplication J. Theor. Biol. 20 1968 227 244
30. Y.I. Wolf, I.B. Rogozin, and E.V. Koonin Coelomata and not ecdysozoa: evidence from genome-wide phylogenetic analysis Genome Res. 14 2004 29 36
31. K.I. Wolska Horizontal DNA transfer between bacteria in the environment Acta Microbiol. Pol. 52 2003 233 243