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

Détails

Ressource 1Télécharger: serval:BIB_84FABFF05093.P001 (224.15 [Ko])
Etat: Public
Version: de l'auteur
Licence: Non spécifiée
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ID Serval
serval:BIB_84FABFF05093
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Institution
Titre
Solving ambiguities in contig assembly of Idiomarina loihiensis L2TR chromosome by in silico analyses.
Périodique
FEMS Microbiology Letters
Auteur(s)
Collyn F., Roten C.A., Guy L.
ISSN
0378-1097[print], 0378-1097[linking]
Statut éditorial
Publié
Date de publication
2007
Volume
271
Numéro
2
Pages
187-192
Langue
anglais
Résumé
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.
Mots-clé
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
Oui
Création de la notice
24/01/2008 14:07
Dernière modification de la notice
25/09/2019 6:09
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