title: Rickettsia phylogenomics: unwinding the intricacies of obligate intracellular life.
abstract: BACKGROUND
  Completed genome sequences are rapidly increasing for Rickettsia, obligate intracellular alpha-proteobacteria responsible for various human diseases, including epidemic typhus and Rocky Mountain spotted fever. In light of phylogeny, the establishment of orthologous groups (OGs) of open reading frames (ORFs) will distinguish the core rickettsial genes and other group specific genes (class 1 OGs or C1OGs) from those distributed indiscriminately throughout the rickettsial tree (class 2 OG or C2OGs).
  
  
  RESULTS
  We present 1823 representative (no gene duplications) and 259 non-representative (at least one gene duplication) rickettsial OGs. While the highly reductive (approximately 1.2 MB) Rickettsia genomes range in predicted ORFs from 872 to 1512, a core of 752 OGs was identified, depicting the essential Rickettsia genes. Unsurprisingly, this core lacks many metabolic genes, reflecting the dependence on host resources for growth and survival. Additionally, we bolster our recent reclassification of Rickettsia by identifying OGs that define the AG (ancestral group), TG (typhus group), TRG (transitional group), and SFG (spotted fever group) rickettsiae. OGs for insect-associated species, tick-associated species and species that harbor plasmids were also predicted. Through superimposition of all OGs over robust phylogeny estimation, we discern between C1OGs and C2OGs, the latter depicting genes either decaying from the conserved C1OGs or acquired laterally. Finally, scrutiny of non-representative OGs revealed high levels of split genes versus gene duplications, with both phenomena confounding gene orthology assignment. Interestingly, non-representative OGs, as well as OGs comprised of several gene families typically involved in microbial pathogenicity and/or the acquisition of virulence factors, fall predominantly within C2OG distributions.
  
  
  CONCLUSIONS
  Collectively, we determined the relative conservation and distribution of 14354 predicted ORFs from 10 rickettsial genomes across robust phylogeny estimation. The data, available at PATRIC (PathoSystems Resource Integration Center), provide novel information for unwinding the intricacies associated with Rickettsia pathogenesis, expanding the range of potential diagnostic, vaccine and therapeutic targets.
authors.affiliation: Virginia Bioinformatics Institute at Virginia Tech, Blacksburg, VA, USA. pvittata@hotmail.com
authors.forename: Joseph J
authors.initials: JJ
authors.lastname: Gillespie
authors.forename: Kelly
authors.initials: K
authors.lastname: Williams
authors.forename: Maulik
authors.initials: M
authors.lastname: Shukla
authors.forename: Eric E
authors.initials: EE
authors.lastname: Snyder
authors.forename: Eric K
authors.initials: EK
authors.lastname: Nordberg
authors.forename: Shane M
authors.initials: SM
authors.lastname: Ceraul
authors.forename: Chitti
authors.initials: C
authors.lastname: Dharmanolla
authors.forename: Daphne
authors.initials: D
authors.lastname: Rainey
authors.forename: Jeetendra
authors.initials: J
authors.lastname: Soneja
authors.forename: Joshua M
authors.initials: JM
authors.lastname: Shallom
authors.forename: Nataraj Dongre
authors.initials: ND
authors.lastname: Vishnubhat
authors.forename: Rebecca
authors.initials: R
authors.lastname: Wattam
authors.forename: Anjan
authors.initials: A
authors.lastname: Purkayastha
authors.forename: Michael
authors.initials: M
authors.lastname: Czar
authors.forename: Oswald
authors.initials: O
authors.lastname: Crasta
authors.forename: Joao C
authors.initials: JC
authors.lastname: Setubal
authors.forename: Abdu F
authors.initials: AF
authors.lastname: Azad
authors.forename: Bruno S
authors.initials: BS
authors.lastname: Sobral
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D016366:Open Reading Frames; D010802:Phylogeny; D010957:Plasmids / Q000378:metabolism; D012281:Rickettsia / Q000378:metabolism* / Q000502:physiology*; D013987:Ticks / Q000235:genetics