908 non-core genes and 63 pseudogenes are currently derived from a set of 971 genes absent from at least one of five E. coli genomes (Davids, 2008). HT genes are also excluded from the non-core gene set by Davids (2008). Foreign prophage and IS genes remaining in the non-core set were removed from this EcoGene version of the non-core.
Non-core genes can derive from diverse processes. An ancestral common core gene can be lost from one genome, and thus be missing from its descendant genomes, constituting a lineage-specific gene loss. A lineage-specific gene gain can occur by paralogous evolution gene duplication and diversification, with both paralogs derived from one common core gene.
56 dubious genes with b numbers from the original GenBank U00096.1 have since been removed as very unlikely. A list of these now defunct b numbers will be made available soon on TopicPages including explanations for their rejections as true genes.