Functional and evolutionary implications of gene orthology (original) (raw)

References

Fitch, W. M. Distinguishing homologous from analogous proteins. Systemat. Zool. 19, 99–106 (1970).
Article CAS Google Scholar
Fitch, W. M. Homology a personal view on some of the problems. Trends Genet. 16, 227–231 (2000).
Article CAS Google Scholar
Koonin, E. V. Walter Fitch and the orthology paradigm. Brief. Bioinform. 12, 377–378 (2011).
Article Google Scholar
Baldauf, S. L. Phylogeny for the faint of heart: a tutorial. Trends Genet. 19, 345–351 (2003).
Article CAS Google Scholar
Sonnhammer, E. L. & Koonin, E. V. Orthology, paralogy and proposed classification for paralog subtypes. Trends Genet. 18, 619–620 (2002).
Article CAS Google Scholar
Koonin, E. V. Orthologs, paralogs and evolutionary genomics. Annu. Rev. Genet. 39, 309–338 (2005).
Article CAS Google Scholar
Dolinski, K. & Botstein, D. Orthology and functional conservation in eukaryotes. Annu. Rev. Genet. 41, 465–507 (2007).
Article CAS Google Scholar
Studer, R. A. & Robinson-Rechavi, M. How confident can we be that orthologs are similar, but paralogs differ? Trends Genet. 25, 210–216 (2009).
Article CAS Google Scholar
Nehrt, N. L., Clark, W. T., Radivojac, P. & Hahn, M. W. Testing the ortholog conjecture with comparative functional genomic data from mammals. PLoS Comput. Biol. 7, e1002073 (2011).
Article CAS Google Scholar
Kuzniar, A., van Ham, R. C., Pongor, S. & Leunissen, J. A. The quest for orthologs: finding the corresponding gene across genomes. Trends Genet. 24, 539–551 (2008).
Article CAS Google Scholar
Gabaldón, T. Large-scale assignment of orthology: back to phylogenetics? Genome Biol. 9, 235 (2008).
Article Google Scholar
Altenhoff, A. M. & Dessimoz, C. Phylogenetic and functional assessment of orthologs inference projects and methods. PLoS Comput. Biol. 5, e1000262 (2009).
Article Google Scholar
Trachana, K. et al. Orthology prediction methods: a quality assessment using curated protein families. Bioessays 33, 769–780 (2011).
Article CAS Google Scholar
Kristensen, D. M., Wolf, Y. I., Mushegian, A. R. & Koonin, E. V. Computational methods for Gene Orthology inference. Brief. Bioinform. 12, 379–391 (2011).
Article Google Scholar
Gabaldón, T. et al. Joining forces in the quest for orthologs. Genome Biol. 10, 403 (2009).
Article Google Scholar
Dessimoz, C., Gabaldón, T., Roos, D. S., Sonnhammer, E. L. & Herrero, J. Toward community standards in the quest for orthologs. Bioinformatics 28, 900–904 (2012).
Article CAS Google Scholar
Descorps-Declere, S., Lemoine, F., Sculo, Q., Lespinet, O. & Labedan, B. The multiple facets of homology and their use in comparative genomics to study the evolution of genes, genomes, and species. Biochimie 90, 595–608 (2008).
Article CAS Google Scholar
Mahmood, K., Webb, G. I., Song, J., Whisstock, J. C. & Konagurthu, A. S. Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs. Nucleic Acids Res. 40, e44 (2012).
Article CAS Google Scholar
Roux, J. & Robinson-Rechavi, M. An ontology to clarify homology-related concepts. Trends Genet. 26, 99–102 (2010).
Article CAS Google Scholar
Tatusov, R. L., Koonin, E. V. & Lipman, D. J. A genomic perspective on protein families. Science 278, 631–637 (1997).
Article CAS 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).
Article CAS Google Scholar
Koonin, E. V., Aravind, L. & Kondrashov, A. S. The impact of comparative genomics on our understanding of evolution. Cell 101, 573–576 (2000).
Article CAS Google Scholar
Sjolander, K., Datta, R. S., Shen, Y. & Shoffner, G. M. Ortholog identification in the presence of domain architecture rearrangement. Brief. Bioinform. 12, 413–422 (2011).
Article Google Scholar
Forslund, K. & Sonnhammer, E. L. Evolution of protein domain architectures. Methods Mol. Biol. 856, 187–216 (2012).
Article CAS Google Scholar
Hartmann, B. & Valcarcel, J. Decrypting the genome's alternative messages. Curr. Opin. Cell Biol. 21, 377–386 (2009).
Article CAS Google Scholar
Irimia, M. & Blencowe, B. J. Alternative splicing: decoding an expansive regulatory layer. Curr. Opin. Cell Biol. 24, 323–332 (2012).
Article CAS Google Scholar
Basu, M. K., Poliakov, E. & Rogozin, I. B. Domain mobility in proteins: functional and evolutionary implications. Brief. Bioinform. 10, 205–216 (2009).
Article CAS Google Scholar
Ouzounis, C. Orthology: another terminology muddle. Trends Genet. 15, 445 (1999).
Article CAS Google Scholar
Theissen, G. Birth, life and death of developmental control genes: new challenges for the homology concept. Theory Biosci. 124, 199–212 (2005).
Article CAS Google Scholar
Bandyopadhyay, S., Sharan, R. & Ideker, T. Systematic identification of functional orthologs based on protein network comparison. Genome Res. 16, 428–435 (2006).
Article CAS Google Scholar
Singh, R., Xu, J. & Berger, B. Global alignment of multiple protein interaction networks with application to functional orthology detection. Proc. Natl Acad. Sci. USA 105, 12763–12768 (2008).
Article CAS Google Scholar
Huynen, M. A. & Bork, P. Measuring genome evolution. Proc. Natl Acad. Sci. USA 95, 5849–5856 (1998).
Article CAS Google Scholar
Bromham, L. & Penny, D. The modern molecular clock. Nature Rev. Genet. 4, 216–224 (2003).
Article CAS Google Scholar
Kumar, S. Molecular clocks: four decades of evolution. Nature Rev. Genet. 6, 654–662 (2005).
Article CAS Google Scholar
Koski, L. B. & Golding, G. B. The closest BLAST hit is often not the nearest neighbor. J. Mol. Evol. 52, 540–542 (2001).
Article CAS Google Scholar
Hulsen, T., Huynen, M. A., de Vlieg, J. & Groenen, P. M. Benchmarking ortholog identification methods using functional genomics data. Genome Biol. 7, R31 (2006).
Article Google Scholar
Wolf, Y. I. & Koonin, E. V. A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes. Genome Biol. Evol. 1286–1294 (2012).
Koonin, E. V. Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Rev. Microbiol. 1, 127–136 (2003).
Article CAS Google Scholar
Snel, B., Huynen, M. A. & Dutilh, B. E. Genome trees and the nature of genome evolution. Annu. Rev. Microbiol. 59, 191–209 (2005).
Article CAS 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
Makarova, K. S., Wolf, Y. I., Mekhedov, S. L., Mirkin, B. G. & Koonin, E. V. Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res. 33, 4626–4638 (2005).
Article CAS Google Scholar
Huerta-Cepas, J. & Gabaldón, T. Assigning duplication events to relative temporal scales in genome-wide studies. Bioinformatics 27, 38–45 (2011).
Article CAS Google Scholar
Forslund, K., Pekkari, I. & Sonnhammer, E. L. Domain architecture conservation in orthologs. BMC Bioinformatics 12, 326 (2011).
Article Google Scholar
Koonin, E. V. et al. A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes. Genome Biol. 5, R7 (2004).
Article Google Scholar
Peterson, M. E. et al. Evolutionary constraints on structural similarity in orthologs and paralogs. Protein Sci. 18, 1306–1315 (2009).
Article CAS Google Scholar
Mushegian, A. R. & Koonin, E. V. A minimal gene set for cellular life derived by comparison of complete bacterial genomes. Proc. Natl Acad. Sci. USA 93, 10268–10273 (1996).
Article CAS Google Scholar
Galperin, M. Y., Walker, D. R. & Koonin, E. V. Analogous enzymes: independent inventions in enzyme evolution. Genome Res. 8, 779–790 (1998).
Article CAS Google Scholar
Omelchenko, M. V., Galperin, M. Y., Wolf, Y. I. & Koonin, E. V. Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol. Direct 5, 31 (2010).
Article Google Scholar
Lynch, V. J. & Wagner, G. P. Resurrecting the role of transcription factor change in developmental evolution. Evolution 62, 2131–2154 (2008).
Article CAS Google Scholar
Casci, T. Functional genomics: Degrees of similarity. Nature Rev. Genet. 12, 522 (2011).
Article CAS Google Scholar
Thomas, P. D., Wood, V., Mungall, C. J., Lewis, S. E. & Blake, J. A. On the use of gene ontology annotations to assess functional similarity among orthologs and paralogs: a short report. PLoS Comput. Biol. 8, e1002386 (2012).
Article CAS Google Scholar
Altenhoff, A. M., Studer, R. A., Robinson-Rechavi, M. & Dessimoz, C. Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput. Biol. 8, e1002514 (2012).
Article CAS Google Scholar
Huerta-Cepas, J., Dopazo, J., Huynen, M. A. & Gabaldón, T. Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Brief. Bioinform. 12, 442–448 (2011).
Article CAS Google Scholar
Chen, X. & Zhang, J. The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data. PLoS Comput. Biol. 8, e1002784 (2012).
Article CAS Google Scholar
Mohd-Padil, H., Mohd-Adnan, A. & Gabaldón, T. Phylogenetic analyses uncover a novel clade of transferring in non-mammalian vertebrates. Mol. Biol. Evol. 30, 894–905 (2013).
Article CAS Google Scholar
Huerta-Cepas, J. et al. PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res. 39, D556–D560 (2011).
Article CAS Google Scholar
Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).
Article CAS Google Scholar

Download references