Natural history and evolutionary principles of gene duplication in fungi (original) (raw)
Ohno, S. Evolution by Gene Duplication (Allen and Unwin, London, 1970) Book Google Scholar
Lynch, M. & Conery, J. S. The origins of genome complexity. Science302, 1401–1404 (2003) ArticleADSCAS Google Scholar
Blomme, T. et al. The gain and loss of genes during 600 million years of vertebrate evolution. Genome Biol.7, R43 (2006) Article Google Scholar
Freeling, M. & Thomas, B. C. Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity. Genome Res.16, 805–814 (2006) ArticleCAS Google Scholar
Gu, Z., Rifkin, S. A., White, K. P. & Li, W. H. Duplicate genes increase gene expression diversity within and between species. Nature Genet.36, 577–579 (2004) ArticleCAS Google Scholar
Kafri, R., Bar-Even, A. & Pilpel, Y. Transcription control reprogramming in genetic backup circuits. Nature Genet.37, 295–299 (2005) ArticleCAS Google Scholar
Maere, S. et al. Modeling gene and genome duplications in eukaryotes. Proc. Natl Acad. Sci. USA102, 5454–5459 (2005) ArticleADSCAS Google Scholar
Makova, K. D. & Li, W. H. Divergence in the spatial pattern of gene expression between human duplicate genes. Genome Res.13, 1638–1645 (2003) ArticleCAS Google Scholar
Papp, B., Pal, C. & Hurst, L. D. Dosage sensitivity and the evolution of gene families in yeast. Nature424, 194–197 (2003) ArticleADSCAS Google Scholar
Scannell, D. R., Byrne, K. P., Gordon, J. L., Wong, S. & Wolfe, K. H. Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature440, 341–345 (2006) ArticleADSCAS Google Scholar
He, X. & Zhang, J. Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics169, 1157–1164 (2005) Article Google Scholar
Dietrich, F. S. et al. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science304, 304–307 (2004) ArticleADSCAS Google Scholar
Galagan, J. E. et al. Sequencing of Aspergillus nidulans and comparative analysis with A.fumigatus and A.oryzae. Nature438, 1105–1115 (2005) ArticleADSCAS Google Scholar
Fusarium graminearum Sequencing Project. 〈http://www.broad.mit.edu〉 (Broad Institute of Harvard and MIT, 2003)
Dean, R. A. et al. The genome sequence of the rice blast fungus Magnaporthe grisea. Nature434, 980–986 (2005) ArticleADSCAS Google Scholar
Kellis, M., Birren, B. W. & Lander, E. S. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature428, 617–624 (2004) ArticleADSCAS Google Scholar
Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. S. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature423, 241–254 (2003) ArticleADSCAS Google Scholar
Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature415, 871–880 (2002) ArticleADSCAS Google Scholar
Arvestad, L., Berglund, A. C., Lagergren, J. & Sennblad, B. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics19 (Suppl. 1). i7–i15 (2003) Article Google Scholar
Chen, K., Durand, D. & Farach-Colton, M. NOTUNG: a program for dating gene duplications and optimizing gene family trees. J. Comput. Biol.7, 429–447 (2000) ArticleCAS Google Scholar
Dufayard, J. F. et al. Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics21, 2596–2603 (2005) ArticleCAS Google Scholar
Durand, D., Halldorsson, B. V. & Vernot, B. A hybrid micro-macroevolutionary approach to gene tree reconstruction. J. Comput. Biol.13, 320–335 (2006) ArticleMathSciNetCAS Google Scholar
Fitch, W. M. Distinguishing homologous from analogous proteins. Syst. Zool.19, 99–113 (1970) ArticleCAS Google Scholar
Jothi, R., Zotenko, E., Tasneem, A. & Przytycka, T. M. COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations. Bioinformatics22, 779–788 (2006) ArticleCAS Google Scholar
Kellis, M., Patterson, N., Birren, B., Berger, B. & Lander, E. S. Methods in comparative genomics: genome correspondence, gene identification and regulatory motif discovery. J. Comput. Biol.11, 319–355 (2004) ArticleCAS Google Scholar
Li, H. et al. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res.34, D572–D580 (2006) ArticleCAS Google Scholar
Remm, M., Storm, C. E. & Sonnhammer, E. L. Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J. Mol. Biol.314, 1041–1052 (2001) ArticleCAS Google Scholar
Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinform. 4, article no. 41 (2003)
Wapinski, I., Pfeffer, A., Friedman, N. & Regev, A. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics doi: 10.1093/bioinformatics/bmt193 (2007)
Byrne, K. P. & Wolfe, K. H. The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res.15, 1456–1461 (2005) ArticleCAS Google Scholar
Dudley, A. M., Janse, D. M., Tanay, A., Shamir, R. & Church, G. M. A global view of pleiotropy and phenotypically derived gene function in yeast. Mol. Syst. Biol.1, 2005.0001 (2005) Article Google Scholar
Tzung, K. W. et al. Genomic evidence for a complete sexual cycle in Candida albicans. Proc. Natl Acad. Sci. USA98, 3249–3253 (2001) ArticleADSCAS Google Scholar
Ashburner, M. et al. Gene ontology: tool for the unification of biology. Nature Genet.25, 25–29 (2000) ArticleCAS Google Scholar
Segal, E., Friedman, N., Kaminski, N., Regev, A. & Koller, D. From signatures to models: understanding cancer using microarrays. Nature Genet.37 (Suppl.). S38–S45 (2005) ArticleCAS Google Scholar
Gavin, A. C. et al. Proteome survey reveals modularity of the yeast cell machinery. Nature440, 631–636 (2006) ArticleADSCAS Google Scholar
Deutschbauer, A. M. et al. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics169, 1915–1925 (2005) ArticleCAS Google Scholar
Hughes, T. R. et al. Functional discovery via a compendium of expression profiles. Cell102, 109–126 (2000) ArticleCAS Google Scholar
Newman, J. R. et al. Single-cell proteomic analysis of S.cerevisiae reveals the architecture of biological noise. Nature441, 840–846 (2006) ArticleADSCAS Google Scholar
Huisinga, K. L. & Pugh, B. F. A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol. Cell13, 573–585 (2004) ArticleCAS Google Scholar
Tirosh, I., Weinberger, A., Carmi, M. & Barkai, N. A genetic signature of interspecies variations in gene expression. Nature Genet.38, 830–834 (2006) ArticleCAS Google Scholar
Sopko, R. et al. Mapping pathways and phenotypes by systematic gene overexpression. Mol. Cell21, 319–330 (2006) ArticleADSCAS Google Scholar
Davis, J. C. & Petrov, D. A. Do disparate mechanisms of duplication add similar genes to the genome? Trends Genet.21, 548–551 (2005) ArticleCAS Google Scholar
Reguly, T. et al. Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.J. Biol. 5, article no. 11 (2006)
Kafri, R., Levy, M. & Pilpel, Y. The regulatory utilization of genetic redundancy through responsive backup circuits. Proc. Natl Acad. Sci. USA103, 11653–11658 (2006) ArticleADSCAS Google Scholar
Harbison, C. T. et al. Transcriptional regulatory code of a eukaryotic genome. Nature431, 99–104 (2004) ArticleADSCAS Google Scholar
Gerber, A. P., Herschlag, D. & Brown, P. O. Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast. PLoS Biol. 2, article no. E79 (2004)
Force, A. et al. The origin of subfunctions and modular gene regulation. Genetics170, 433–446 (2005) ArticleCAS Google Scholar
Pearson, W. R. & Lipman, D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA85, 2444–2448 (1988) ArticleADSCAS Google Scholar
Jones, D. T., Taylor, W. R. & Thornton, J. M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci.8, 275–282 (1992) CASPubMed Google Scholar
Saitou, N. & Nei, M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol.4, 406–425 (1987) CAS Google Scholar
Kurtzman, C. P. & Robnett, C. J. Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res.3, 417–432 (2003) ArticleCAS Google Scholar
Kuramae, E. E., Robert, V., Snel, B. & Boekhout, T. Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics88, 387–393 (2006) ArticleCAS Google Scholar
Felsenstein, J. PHYLIP—Phylogeny Inference Package (Version 3.2). Cladistics5, 164–166 (1989) Google Scholar
Ninio, M., Privman, E., Pupko, T. & Friedman, N. Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates. Bioinformatics23, e136–e141 (2007) ArticleCAS Google Scholar
Kanehisa, M. A database for post-genome analysis. Trends Genet.13, 375–376 (1997) ArticleCAS Google Scholar
Karp, P. D. et al. Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res.33, 6083–6089 (2005) ArticleCAS Google Scholar
Mewes, H. W. et al. MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res.34, D169–D172 (2006) ArticleCAS Google Scholar
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res.32, 1792–1797 (2004) ArticleCAS Google Scholar
Eddy, S. HMMER: Hidden Markov models for sequence profile analysis. 〈http://hmmer.janelia.org/〉 (2003)