High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome (original) (raw)
Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of spontaneous mutation. Genetics148, 1667–1686 (1998) CASPubMedPubMed Central Google Scholar
Nachman, M. W. & Crowell, S. L. Estimate of the mutation rate per nucleotide in humans. Genetics156, 297–304 (2000) CASPubMedPubMed Central Google Scholar
Robertson, H. M. The large srh family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses. Genome Res.10, 192–203 (2000) ArticleCASPubMed Google Scholar
Witherspoon, D. J. & Robertson, H. M. Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae. J. Mol. Evol.56, 751–769 (2003) ArticleADSCASPubMed Google Scholar
Vassilieva, L. L., Hook, A. M. & Lynch, M. The fitness effects of spontaneous mutations in Caenorhabditis elegans. Evolution54, 1234–1246 (2000) ArticleCASPubMed Google Scholar
Denver, D. R., Morris, K. & Thomas, W. K. Phylogenetics in Caenorhabditis elegans: an analysis of divergence and outcrossing. Mol. Biol. Evol.20, 393–400 (2003) ArticleCASPubMed Google Scholar
Denver, D. R., Morris, K., Lynch, M., Vassilieva, L. L. & Thomas, W. K. High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans. Science289, 2342–2344 (2000) ArticleADSCASPubMed Google Scholar
Ochman, H. Neutral mutations and neutral substitutions in bacterial genomes. Mol. Biol. Evol.20, 2091–2096 (2003) ArticleCASPubMed Google Scholar
Petrov, D. A., Lozovskaya, E. R. & Hartl, D. L. High intrinsic rate of DNA loss in Drosophila. Nature384, 346–349 (1996) ArticleADSCASPubMed Google Scholar
Petrov, D. A. & Hartl, D. L. Pseudogene evolution and natural selection for a compact genome. J. Hered.91, 221–227 (2000) ArticleCASPubMed Google Scholar
Hirotsune, S. et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature423, 91–96 (2003) ArticleADSCASPubMed Google Scholar
Yamada, K. et al. Empirical analysis of transcriptional activity in the Arabidopsis genome. Science302, 842–846 (2003) ArticleADSCASPubMed Google Scholar
Balakirev, E. S. & Ayala, F. J. Pseudogenes: are they ‘junk’ or functional DNA? Annu. Rev. Genet.37, 123–151 (2003) ArticleCASPubMed Google Scholar
Marais, G., Mouchiroud, D. & Duret, L. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proc. Natl Acad. Sci. USA98, 5688–5692 (2001) ArticleADSCASPubMedPubMed Central Google Scholar
Hahn, M. W., Stajich, J. E. & Wray, G. A. The effects of selection against spurious transcription factor binding sites. Mol. Biol. Evol.20, 901–906 (2003) ArticleCASPubMed Google Scholar
Langley, C. H. & Ito, K. Spontaneous mutability in Drosophila melanogaster, in natural and laboratory environments. Mutat. Res.36, 385–386 (1976) ArticleCASPubMed Google Scholar
Gunsalus, K. C., Yueh, W. C., MacMenamin, P. & Piano, F. RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects. Nucleic Acids Res.32, D406–D410 (2004) ArticleCASPubMedPubMed Central Google Scholar
Naclerio, G. et al. Molecular and genomic organization of clusters of repetitive DNA sequences in Caenorhabditis elegans. J. Mol. Biol.226, 159–168 (1992) ArticleCASPubMed Google Scholar
Keightley, P. D. & Ohnishi, O. EMS-induced polygenic mutation rates for nine quantitative characters in Drosophila melanogaster. Genetics148, 753–766 (1998) CASPubMedPubMed Central Google Scholar
Davies, E. K., Peters, A. D. & Keightley, P. D. High frequency of cryptic deleterious mutations in Caenorhabditis elegans. Science285, 1748–1751 (1999) ArticleCASPubMed Google Scholar
Stein, L. D. et al. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol.1, 166–192 (2003) ArticleCAS Google Scholar
Kondrashov, A. S. & Houle, D. Genotype–environment interactions and the estimation of the genomic mutation rate in Drosophila melanogaster. Proc. R. Soc. Lond. B258, 221–227 (1994) ArticleADSCAS Google Scholar
Higgins, D. G., Thompson, J. D. & Gibson, T. J. Using CLUSTAL for multiple sequence alignments. Methods Enzymol.266, 383–402 (1994) Article Google Scholar
Denver, D. R. et al. Abundance, distribution, and mutation rates of homopolymeric nucleotide runs in the genome of Caenorhabditis elegans. J. Mol. Evol.58, 584–595 (2004) ArticleADSCASPubMed Google Scholar