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Gene insertions and deletions in closely related genomes can be inferred by looking at the phyletic patterns of gene presence or absence on a phylogenetic tree.
Studies have primarily relied upon PCR amplification to evaluate gene presence (Callicott and Cotty 2015; Chang et al. 2005; Kusumoto et al. 2000; Tominaga et al. 2006).
Isolates were serotyped at molecular level based on capsular polysaccharide (cps) serotyping and analyzed for pilus island profiles, scpB gene, and hvgA gene presence.
This is an unavoidable cost of designing an array to detect broad patterns of gene presence.
Gene presence and divergence was determined using the algorithm described previously [20].
Vancanneyt et al. have reported beta haemolytic activity in 5 E. faecium isolates (n = 78) but no link could be established between haemolytic activity and gene presence [40].
Similar(20)
The gene presence-absence analysis seemed to be dominated by the phenotypic signal, primarily that from gene loss.
The third cluster was characterized by bbp-gene presence and above average susceptibility to penicillin.
Three common characteristics of this cluster were penicillin resistance, cna-gene presence, and biofilm formation on fibronectin-coated surfaces.
The gene presence/absence pattern in the fatty acid degradation pathway are suggestive of a possibility that the fatty acid generated by the cyanobacterium might supply the carbon and energy source for the heterotrophies in the coculture.
We chose NimbleGen microarray CGR as it does not only detect gene presence/absence, but potentially can also detect sequence variation in comparison to traditional microarray technology.
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