Genome evolution

Orthology prediction using only the relative levels of similarity of genes can be useful for quantitative estimates of certain genomic features such as the number of shared genes or the number of conserved gene pairs, rather than filling in their specific function, e.g., to predict the existence of a metabolic pathway. 

A number of analyses have pointed out the functional relations between genes that occur in clusters on the genome (see Section III,B). 

The local context of a gene in the genome and its conservation is an invaluable tool for the prediction of orthology and function. Not only does the conservation of local context decrease with phylogenetic distance, but also the amount of information in the local context varies 

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SEGMENTED VIRUS GENOMES EVOLUTION AND FUNCTIONAL SIGNIFICANCE... 

I. K. Jordan E. V. Koonin, Horizontal Gene Transfer and Prokaryotic Genome Evolution. In Microbial Evolution Gene Establishment, Survival, and Exchange R. V. Millner, M. J. Day, Eds. ASM Press Washington, DC, 2004 pp 319-338. 

Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unraveling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422 433 38... 

With the exception of micro-organisms, the cells then and now are not the same they are separated by 3 billion years of genomic refinement. This genomic evolution, the development of the complexity that led to macro-organisms, was driven by the thermodynamics of DNA/RNA chemistry towards an equilibrium point which was stable enough to persist. 

Organisms appear in the fossil record in the sequence in which they finished their genomic evolution, i.e., the simplest first. Many different clones of similar levels of complexity finish simultaneously in many places. Simple organisms appear first in one locality and spread from there slowly increasing in number and variety. Al 1 appear in succession, one from another. 

Donachie WD, Blakely GW (2003) Coupling the initiation of chromosome replication to cell size in Escherichia coli. Curr Opin Microbiol 6 146-150 Doolittle WF, Sapienza C (1980) Selfish genes, the phenotype paradigm and genome evolution. Nature 284 601-603... 

Boussau B, Karlberg EO, Frank AC, Legault B-A, Andersson SGE (2004) Computational inference of scenarios for alpha-proteobacterial genome evolution. Proc Natl Acad Sci USA... 

Lang BE, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33 351-397... 

DNA/retrotransposons from mammalian genomes. In addition, methods to characterize and study the phylogenetic distribution of these elements are presented. These methods are applicable to screening any mammalian genome and should facilitate the much needed examination of genome evolution in a wide variety of species. 

Huynen, M. a., Boek, P. (1998). Measuring genome evolution. Proc. Natl. Acad. Sci. USA 95, 5849-5856. 

Beck, M. A., Shi, Q., Morris, V, and Levander, O. (1995). Kapid genomic evolution of a non-virulent Coxsackievinis B3 in selenium-deficient mice results in selection of identical virulent isolates. Neture Med. 1,433-436-... 

Lee, D., Grant, A., Buchan, D., Orengo, C. A structural perspective on genome evolution. Curr. Opin. Struc. Biol. 2003,13, 359—369. 

Jain, R., Rivera, M. C., Moore, J. E. et al. Horizontal gene transfer in microbial genome evolution. Theoretical Population Biology, 61 (2002), 489-95. 

Gurtler V, Mayall BC (2001) Genetic transfer and genome evolution in MRSA. Microbiology 147 3195-3197... 

Sharp, P. M. and Matassi, G. (1994) Codon usage and genome evolution. Curr. Opin. Genet. Dev. 4, 851-860. 

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