Genomic, evolutionary, and expression analyses of cee, an ancient gene involved in normal growth and development

Genomics

Volumn 91, Issue 4, 2008, Pages 315-325

  Fernandes, Jorge M O ^a,b   Macqueen, Daniel J ^b   Lee, Hung Tai ^b   Johnston, Ian A ^b  

^a NORD UNIVERSITY   (Norway)

^b UNIVERSITY OF ST ANDREWS   (United Kingdom)

Author keywords

Cee; Conserved edge expressed protein; Development; Myogenesis; Purifying selection

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; EXON; FISH GENETICS; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC SELECTION; GENOME; INTRON; INVERTEBRATE; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORGANOGENESIS; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; SALMON; TELEOST; VERTEBRATE; YEAST;

ANIMALS; BASE SEQUENCE; DNA PRIMERS; DNA, COMPLEMENTARY; EVOLUTION; GENE EXPRESSION; GENOMICS; MUSCLE DEVELOPMENT; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; TETRAODONTIFORMES;

CAENORHABDITIS ELEGANS; EUKARYOTA; INVERTEBRATA; SALMO SALAR; TELEOSTEI; TETRAODONTIDAE; TETRAPODA; UROCHORDATA; VERTEBRATA;

EID: 41049097108     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2007.10.017     Document Type: Article

References (45)

1. Altringham J.D., and Johnston I.A. Modelling muscle power output in a swimming fish. J. Exp. Biol. 148 (1990) 395-402
2. Bone Q., Kicenuik J., and Jones D.R. On the roles of the different fibre types in fish myotomes at intermediate speeds. Fish Bull. 76 (1978) 691-699
3. Johnston I.A., Davison W., and Goldspink G. Energy metabolism of carp swimming muscles. J. Comp. Physiol. 114 (1977) 203-216
4. Johnston I.A., et al. Plasticity of muscle fibre number in seawater stages of Atlantic salmon in response to photoperiod manipulation. J. Exp. Biol. 206 (2003) 3425-3435
5. Weatherley A.H., Gill H.S., and Lobo A.F. Recruitment and maximal diameter of axial muscle fibres in teleosts and their relationship to somatic growth and ultimate size. J. Fish Biol. 33 (1988) 851-859
6. Rowlerson A., and Veggetti A. Cellular mechanisms of post-embryonic muscle growth in aquaculture species. In: Johnston I.A. (Ed). Muscle Development and Growth (2000), Academic Press, San Diego 103-140
7. Johnston I.A., et al. Rapid evolution of muscle fibre number in post-glacial populations of Arctic charr Salvelinus alpinus. J. Exp. Biol. 207 (2004) 4343-4360
8. van Raamsdonk W., Mos W., Smit-Onel M.J., van der Laarse W.J., and Fehres R. The development of the spinal motor column in relation to the myotomal muscle fibers in the zebrafish (Brachydanio rerio). I. Posthatching development. Anat. Embryol. (Berlin) 167 (1983) 125-139
9. Fernandes J.M., et al. A genomic approach to reveal novel genes associated with myotube formation in the model teleost, Takifugu rubripes. Physiol. Genomics 22 (2005) 327-338
10. Kamath R.S., et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421 (2003) 231-237
11. Simmer F., et al. Genome-wide RNAi of C. elegans using the hypersensitive rrf-3 strain reveals novel gene functions. PLoS Biol. 1 (2003) E12
12. Hedges S.B., et al. A genomic timescale for the origin of eukaryotes. BMC Evol. Biol. 1 (2001) 4
13. Hedges S.B. The origin and evolution of model organisms. Nat. Rev., Genet. 3 (2002) 838-849
14. Blair J.E., Shah P., and Hedges S.B. Evolutionary sequence analysis of complete eukaryote genomes. BMC Bioinformatics 6 (2005) 53
15. Huh W.K., et al. Global analysis of protein localization in budding yeast. Nature 425 (2003) 686-691
16. Fleischer T.C., Weaver C.M., McAfee K.J., Jennings J.L., and Link A.J. Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes. Genes Dev. 20 (2006) 1294-1307
17. Ito T., et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. U. S. A. 98 (2001) 4569-4574
18. Hu Z., Potthoff B., Hollenberg C.P., and Ramezani-Rad M. Mdy2, a ubiquitin-like (UBL)-domain protein, is required for efficient mating in Saccharomyces cerevisiae. J. Cell Sci. 119 (2006) 326-338
19. Schuldiner M., et al. Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile. Cell 123 (2005) 507-519
20. Shen J., Hsu C.M., Kang B.K., Rosen B.P., and Bhattacharjee H. The Saccharomyces cerevisiae Arr4p is involved in metal and heat tolerance. Biometals 16 (2003) 369-378
21. Giaever G., et al. Functional profiling of the Saccharomyces cerevisiae genome. Nature 418 (2002) 387-391
22. Delsuc F., Brinkmann H., Chourrout D., and Philippe H. Tunicates and not cephalochordates are the closest living relatives of vertebrates. Nature 439 (2006) 965-968
23. Babushok D.V., Ostertag E.M., and Kazazian Jr. H.H. Current topics in genome evolution: molecular mechanisms of new gene formation. Cell. Mol. Life Sci. 64 (2007) 542-554
24. Meyer A., and Schartl M. Gene and genome duplications in vertebrates: the one-to-four (-to-eight in fish) rule and the evolution of novel gene functions. Curr. Opin. Cell Biol. 11 (1999) 699-704
25. Evans B.J., Kelley D.B., Tinsley R.C., Melnick D.J., and Cannatella D.C. A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution. Mol. Phylogenet. Evol. 33 (2004) 197-213
26. Morin R.D., et al. Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling. Genome Res. 16 (2006) 796-803
27. Steinke D., Salzburger W., and Meyer A. Novel relationships among ten fish model species revealed based on a phylogenomic analysis using ESTs. J. Mol. Evol. 62 (2006) 772-784
28. Yang Z., and Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17 (2000) 32-43
29. Zhang J., Kumar S., and Nei M. Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol. Biol. Evol. 14 (1997) 1335-1338
30. Lang D., Powell S.K., Plummer R.S., Young K.P., and Ruggeri B.A. PAX genes: roles in development, pathophysiology, and cancer. Biochem. Pharmacol. 73 (2007) 1-14
31. Hollway G.E., et al. Whole-somite rotation generates muscle progenitor cell compartments in the developing zebrafish embryo. Dev. Cell 12 (2007) 207-219
32. Stellabotte F., Dobbs-McAuliffe B., Fernandez D.A., Feng X., and Devoto S.H. Dynamic somite cell rearrangements lead to distinct waves of myotome growth. Development 134 (2007) 1253-1257
33. Macqueen D.J., Robb D., and Johnston I.A. Temperature influences the coordinated expression of myogenic regulatory factors during embryonic myogenesis in Atlantic salmon (Salmo salar L.). J. Exp. Biol. 210 (2007) 2781-2794
34. Devoto S.H., et al. Generality of vertebrate developmental patterns: evidence for a dermomyotome in fish. Evol. Dev. 8 (2006) 101-110
35. Gertz E.M., Yu Y.K., Agarwala R., Schaffer A.A., and Altschul S.F. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 4 (2006) 41
36. Fernandes J.M., Kinghorn J.R., and Johnston I.A. Differential regulation of multiple alternatively spliced transcripts of MyoD. Gene 391 (2007) 178-185
37. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
38. Ovcharenko I., et al. Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res. 15 (2005) 184-194
39. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
40. Guindon S., Lethiec F., Duroux P., and Gascuel O. PHYML online-a Web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res. 33 (2005) W557-W559
41. Kumar S., Tamura K., Jakobsen I.B., and Nei M. MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17 (2001) 1244-1245
42. Suyama M., Torrents D., and Bork P. PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res. 34 (2006) W609-W612
43. Korber B. HIV Sequence Signatures and Similarities. In: Rodrigo A.G., and Learn G.H. (Eds). Computational and Evolutionary Analysis of HIV Molecular Sequences (2000), Kluwer Academic, Dordrecht 55-72
44. Nei M., and Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3 (1986) 418-426
45. Jowett T. Double in situ hybridization techniques in zebrafish. Methods 23 (2001) 345-358