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Title: Comparative genomics of the Campylobacter lari group

item Miller, William - Bill
item Yee, Emma
item Chapman, Mary
item Smith, Timothy - Tim
item Bono, James - Jim
item Huynh, Steven
item Parker, Craig
item VANDAMME, PETER - Ghent University
item LUONG, KHAI - Pacific Biosciences Inc
item KORLACH, JONAS - Pacific Biosciences Inc

Submitted to: Genome Biology and Evolution
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/5/2014
Publication Date: 11/5/2014
Citation: Miller, W.G., Yee, E., Chapman, M.H., Smith, T.P., Bono, J.L., Huynh, S., Parker, C., Vandamme, P., Luong, K., Korlach, J. 2014. Comparative genomics of the Campylobacter lari group. Genome Biology and Evolution. doi: 10.1093/gbe/evu249.

Interpretive Summary: Campylobacter have been isolated from a wide variety of environments and warm-blooded animals (birds, mammals). One division within Campylobacter is generally isolated from fresh water or marine (shorebirds, sea water and shellfish) environments. The original member of this division to be characterized was the human pathogen Campylobacter lari; thus, this division has been termed the lari group. This study describes the complete DNA sequences of 12 members of the lari group, including at least one strain from each of the species that comprises this group. These DNA sequences were compared and characterized to determine if genes could be identified that were related to host-association or the association of these organisms to their particular environment, or to identify genes tentatively involved in pathogenicity. Comparison of this group determined that these organisms are highly related and share many features, including a set of proteins possibly associated with host-cell attachment and virulence. These common genetic features may play a role in the association of lari group organisms with coastal environments and watersheds.

Technical Abstract: The Campylobacter lari group is a phylogenetic clade within the epsilon subdivision of the Proteobacteria and is part of the thermotolerant campylobacters, a division within the genus that includes the human pathogen Campylobacter jejuni. The lari group is currently composed of five validly-named species (C. lari, C. insulaenigrae, C. volucris, C. subantarcticus and C. peloridis), as well a group of strains termed the urease-positive thermophilic campylobacters (UPTC) and other lari-like strains. Here we present the complete genome sequences of 11 lari group strains, including the five lari group species, four UPTC strains and a lari-like strain isolated in this study. The genome of C. lari subsp. lari strain RM2100 was described previously. Analysis of the lari group genomes indicates that this group is highly related genomically; of the 1495 protein-encoding genes identified in strain RM2100, orthologs of 1145 (77%) were core genes among the lari group. Furthermore, these genomes are highly syntenic with minor rearrangements occurring only in four of the twelve genomes studied. The lari group can be bifurcated, based on the flagella and flagellar modification genes. Additionally, the lari group contains a large number of genes encoding hemagglutination domain proteins, which are either contingency genes or linked to conserved contingency genes. Many of the features identified in strain RM2100, such as major deficiencies in amino acid biosynthesis and energy metabolism, are conserved across all 12 genomes, suggesting that these common features may play a role in the association of the lari group with coastal environments and watersheds.