Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

BMC Bioinformatics
Oleg N Reva, Burkhard Tümmler

Abstract

Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. In this paper we analyzed oligonucleotide usage (OU) biases in a comprehensive collection of 155 completely sequenced bacterial chromosomes, 316 plasmids and 104 phages. Two global features were analyzed: pattern skew (PS) and variance of OU deviations normalized by mononucleotide content of the sequence (OUV). OUV reflects the strength of OU biases and taxonomic signals. PS denotes asymmetry of OU in direct and reverse DNA strands. A trend towards minimal PS was observed for almost all complete sequences of bacterial chromosomes and plasmids, however, PS was substantially higher in separate genomic loci and several types of plasmids and phages characterized by long stretches of non-coding DNA and/or asymmetric gene distribution on the two DNA strands. Five of the 155 bacterial chromosomes have anomalously high PS, of which the chromosomes of Xylella fastidiosa 9a5c and Prochlorococcus marinus MIT9313 exhibit extreme PS values suggesting an intermediate unstable state of these two genomes. Strand symmetry as indicated by minimal PS is a universally conserved feature o...Continue Reading

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Citations

Sep 12, 2012·Briefings in Bioinformatics·Hanno Teeling, Frank Oliver Glöckner
Jul 14, 2010·Applied and Environmental Microbiology·Ana BeloquiPeter N Golyshin
Dec 30, 2006·Journal of Bacteriology·Jens KlockgetherBurkhard Tümmler
Oct 18, 2005·BMC Bioinformatics·Oleg N Reva, Burkhard Tümmler
Aug 10, 2010·BMC Genomics·Jon BohlinDavid W Ussery
Apr 19, 2008·PLoS Computational Biology·Jon BohlinDavid W Ussery
Dec 4, 2009·PloS One·Jon Bohlin, Eystein Skjerve
Mar 31, 2010·PloS One·Colin F Davenport, Burkhard Tümmler
Sep 7, 2013·PeerJ·Aaron D Skewes, Roy D Welch
Feb 2, 2008·Environmental Microbiology·Oleg Reva, Burkhard Tümmler
Dec 18, 2007·Environmental Microbiology·Oleg N RevaDavid W Ussery
Jan 24, 2009·Environmental Microbiology·Colin F DavenportBurkhard Tümmler
Jan 26, 2010·Photosynthesis Research·Colin DavenportBurkhard Tümmler
Aug 8, 2018·BMC Genomics·Jon BohlinKristian Alfsnes
Feb 14, 2007·Reviews in Medical Virology·Eric L Delwart

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Methods Mentioned

BETA
restriction-modification

Software Mentioned

Python
DataFit7

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