Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.

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Serval ID
serval:BIB_84FABFF05093
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.
Journal
FEMS Microbiology Letters
Author(s)
Collyn F., Roten C.A., Guy L.
ISSN
0378-1097[print], 0378-1097[linking]
Publication state
Published
Issued date
2007
Volume
271
Number
2
Pages
187-192
Language
english
Abstract
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.
Keywords
Alteromonadaceae/genetics, Chromosome Inversion, Chromosomes, Bacterial/genetics, Computational Biology/methods, DNA, Bacterial/genetics, Genome, Bacterial/genetics, Polymerase Chain Reaction
Pubmed
Web of science
Open Access
Yes
Create date
24/01/2008 14:07
Last modification date
25/09/2019 6:09
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