title: Comparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes.
abstract: The genomes of the 21 completely sequenced Thermococcales display a characteristic high level of rearrangements. As a result, the prediction of their origin and termination of replication on the sole basis of chromosomal DNA composition or skew is inoperative. Using a different approach based on biologically relevant sequences, we were able to determine oriC position in all 21 genomes. The position of dif, the site where chromosome dimers are resolved before DNA segregation could be predicted in 19 genomes. Computation of the core genome uncovered a number of essential gene clusters with a remarkably stable chromosomal position across species, in sharp contrast with the scrambled nature of their genomes. The active chromosomal reorganization of numerous genes acquired by horizontal transfer, mainly from mobile elements, could explain this phenomenon.
authors.affiliation: Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France.
authors.forename: Matteo
authors.initials: M
authors.lastname: Cossu
authors.affiliation: Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France.
authors.forename: Violette
authors.initials: V
authors.lastname: Da Cunha
authors.affiliation: Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Toffano-Nioche
authors.affiliation: Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Forterre
authors.affiliation: Institute of Integrative Cellular Biology, CEA, CNRS, Université Paris Sud, 91405 Orsay, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Oberto
mesh_terms: D001483:Base Sequence; D002875:Chromosomes / Q000235:genetics*; D055028:Comparative Genomic Hybridization; D019143:Evolution, Molecular; D015321:Gene Rearrangement; D019766:Genes, Archaeal / Q000235:genetics*; D016678:Genome; D008969:Molecular Sequence Data; D019709:Thermococcales / Q000235:genetics*
keywords: Archaea; Bioinformatics; Chromosomal landmarks; Genome evolution; Mobile elements; Thermococcales