Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes.
The sequencing of prokaryotic genomes covering a wide taxonomic range has sparked renewed interest in intrachromosomal compositional (GC) heterogeneity, largely in view of lateral transfers. We present here a brief overview of some methods for visualizing and quantifying GC variation in prokaryotes. We used these methods to examine heterogeneity levels in sequenced prokaryotes, for a range of scales or stringencies. Some species are consistently homogeneous, whereas others are markedly heterogeneous in comparison, in particular Aeropyrum pernix, Xylella fastidiosa, Mycoplasma genitalium, Enterococcus faecalis, Bacillus subtilis, Pyrobaculum aerophilum, Vibrio vulnificus chromosome I, Deinococcus radiodurans chromosome II and Halobacterium. As we discuss here, the wide range of heterogeneities calls for reexamination of an accepted belief, namely that the endogenous DNA of bacteria and archaea should typically exhibit low intrachromosomal GC contrasts. Supplementary results for all species analyzed are available at our website: http://bioinfo2.ugr.es/prok.
Bernaola-Galván
Pedro
P
Dpto. de Física Aplicada II, Universidad de Málaga, E-29071, Málaga, Spain.
Oliver
José L
JL
Carpena
Pedro
P
Clay
Oliver
O
Bernardi
Giorgio
G
D000465:Algorithms; D001482:Base Composition / Q000235:genetics*; D020029:Base Pairing / Q000235:genetics; D002499:Centrifugation, Density Gradient; D002586:Cesium; D002712:Chlorides; D019847:Chromosomes, Archaeal / Q000235:genetics; D002876:Chromosomes, Bacterial / Q000235:genetics; D003062:Codon / Q000235:genetics; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D032085:Isochores / Q000235:genetics
D002712:Chlorides; D003062:Codon; D019641:DNA, Archaeal; D004269:DNA, Bacterial; D032085:Isochores; D002586:Cesium; C028019:cesium chloride