The effect of domestication on the fungal proteome

Trends in Genetics

Volumn 25, Issue 2, 2009, Pages 60-63

  Rokas, Antonis ^a  

^a VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PROTEOME;

ASPERGILLUS FLAVUS; ASPERGILLUS ORYZAE; CELL LINEAGE; DOMESTICATION; FERMENTED PRODUCT; NONHUMAN; PRIORITY JOURNAL; SHORT SURVEY;

ASPERGILLUS FLAVUS; ASPERGILLUS ORYZAE; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENOME, FUNGAL; PROTEOME;

ANIMALIA; ASPERGILLUS FLAVUS; ASPERGILLUS ORYZAE; FUNGI;

EID: 59349083327     PISSN: 01689525     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tig.2008.11.003     Document Type: Short Survey

References (30)

1. Lu J., et al. The accumulation of deleterious mutations in rice genomes: a hypothesis on the cost of domestication. Trends Genet. 22 (2006) 126-131
2. Burger J.C., et al. Molecular insights into the evolution of crop plants. Am. J. Bot. 95 (2008) 113-122
3. Doebley J.F., et al. The molecular genetics of crop domestication. Cell 127 (2006) 1309-1321
4. Gu Z., et al. Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 1092-1097
5. Olson M.V. When less is more: gene loss as an engine of evolutionary change. Am. J. Hum. Genet. 64 (1999) 18-23
6. Hesseltine C.W. A Millennium of fungi food and fermentation. Mycologia 57 (1965) 149-197
7. Dobney K., and Larson G. Genetics and animal domestication: new windows on an elusive process. J. Zool. 269 (2006) 261-271
8. Cruz F., et al. The legacy of domestication: accumulation of deleterious mutations in the dog genome. Mol. Biol. Evol. 25 (2008) 2331-2336
9. Machida M., et al. Genomics of Aspergillus oryzae: learning from the history of Koji mold and exploration of its future. DNA Res. 15 (2008) 173-183
10. Baker S.E., and Bennett J.W. An overview of the genus Aspergillus. In: Goldman G.H., and Osmani S.A. (Eds). The Aspergilli: Genomics, Medical Applications, Biotechnology, and Research Methods (2008), CRC Press 3-13
11. Geiser D.M., et al. Cryptic speciation and recombination in the aflatoxin-producing fungus Aspergillus flavus. Proc. Natl. Acad. Sci. U. S. A. 95 (1998) 388-393
12. Klich M.A. Biogeography of Aspergillus species in soil and litter. Mycologia 94 (2002) 21-27
13. Payne G.A., et al. Whole genome comparison of Aspergillus flavus and A. oryzae. Med. Mycol. 44 Suppl (2006) 9-11
14. Rokas A., et al. What can comparative genomics tell us about species concepts in the genus Aspergillus?. Stud. Mycol. 59 (2007) 11-17
15. Machida M., et al. Genome sequencing and analysis of Aspergillus oryzae. Nature 438 (2005) 1157-1161
16. Abe K., et al. Impact of Aspergillus oryzae genomics on industrial production of metabolites. Mycopathologia 162 (2006) 143-153
17. Koonin E.V. Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39 (2005) 309-338
18. Thompson J.D., et al. Clustal-W - improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
19. Bininda-Emonds O.R. transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics 6 (2005) 156
20. Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13 (1997) 555-556
21. Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15 (1998) 568-573
22. Rokas A., and Galagan J.E. The Aspergillus nidulans genome and a comparative analysis of genome evolution in Aspergillus. In: Goldman G.H., and Osmani S.A. (Eds). The Aspergilli: Genomics, Medical Applications, Biotechnology, and Research Methods (2008), CRC Press 43-55
23. Mathe E., et al. Computational approaches for predicting the biological effect of p53 missense mutations: a comparison of three sequence analysis based methods. Nucleic Acids Res. 34 (2006) 1317-1325
24. Ruepp A., et al. The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res. 32 (2004) 5539-5545
25. Ronald J., et al. Genomewide evolutionary rates in laboratory and wild yeast. Genetics 174 (2006) 541-544
26. Fay J.C., and Benavides J.A. Evidence for domesticated and wild populations of Saccharomyces cerevisiae. PLoS Genet. 1 (2005) 66-71
27. Legras J.L., et al. Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history. Mol. Ecol. 16 (2007) 2091-2102
28. Taylor J.W., et al. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31 (2000) 21-32
29. Tsai I.J., et al. Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle. Proc. Natl. Acad. Sci. U. S. A. 105 (2008) 4957-4962
30. Lynch M., and Deng H.W. Genetic slippage in response to sex. Am. Nat. 144 (1994) 242-261