Quantifying intrachromosomal GC heterogeneity in prokaryotic genomes

Pedro Bernaola-Galván, José L. Oliver, Pedro Carpena, Oliver Clay, Giorgio Bernardi

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)121-133
Number of pages13
JournalGene
Volume333
Issue number1-2
DOIs
StatePublished - May 26 2004
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics

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