Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.
Nucleotide composition analyses of bacterial genomes such as cumulative GC skew highlight the atypical, strongly asymmetric architecture of the recently published chromosome of Idiomarina loihiensis L2TR, suggesting that an inversion of a 600-kb chromosomal segment occurred. The presence of 3.4-kb inverted repeated sequences at the borders of the putative rearrangement supports this hypothesis. Reverting in silico this segment restores (1) a symmetric chromosome architecture; (2) the co-orientation of transcription of all rRNA operons with DNA replication; and (3) a better conservation of gene order between this chromosome and other gamma-proteobacterial ones. Finally, long-range PCRs encompassing the ends of the 600-kb segment reveal the existence of the reverted configuration but not of the published one. This demonstrates how cumulative nucleotide-skew analyses can validate genome assemblies.
Collyn
François
F
Département de Microbiologie Fondamentale, Faculté de Biologie et Médecine, Université de Lausanne, Switzerland.
Roten
Claude-Alain H
CA
Guy
Lionel
L
D034241:Alteromonadaceae / Q000235:genetics*; D007446:Chromosome Inversion; D002876:Chromosomes, Bacterial / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D016133:Polymerase Chain Reaction
D004269:DNA, Bacterial