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Bugs in the genome
Genome Biologyvolume 2, Article number: spotlight-20010518-01 (2001)
There is much speculation about how lateral transfer - the exchange of genes between distantly related species - has shaped the evolution of the human genome. A recent publication estimated that as many as 223 bacterial genes can be found within the human genome sequence. In the May 17 ScienceExpress, Salzberg et al. report a careful re-evaluation of the number of putative bacterial-to-vertebrate transfers (BVTs; ScienceXpress 2001, 10.1126/science.1061036). The authors performed careful similarity searches to compare the proteomes from human, fruitfly, nematode worm, yeast, mustard weed, eukaryotic parasites and all completed prokaryotic genomes. They included both the Ensembl and Celera proteome sets (containing 31,780 and 26,544 proteins, respectively). Although their initial analysis revealed similar numbers to earlier estimates, careful statistical examination of the results whittled the final number of BVTs down to 41 (Ensembl) and 46 (Celera). Salzberg et al. show that the calculations are highly dependent on the number of non-vertebrate genomes screened (the number of BVTs decreases as the number of genomes rises). They conclude that gene loss and evolutionary rate variation are more likely to explain the sequence similarities than are true BVT events.
Phylogenetic classification and the universal tree.
Initial sequencing and analysis of the human genome.
The comprehensive microbial resource (CMR), [http://www.tigr.org/tigr-scripts/CMR2/CMRHomePage.spl]
International protein index, [http://www.ensembl.org/IPI]
Celera Genomics, [http://www.celera.com]