title: Complete genome determination and analysis of Acholeplasma oculi strain 19L, highlighting the loss of basic genetic features in the Acholeplasmataceae.
abstract: BACKGROUND
  Acholeplasma oculi belongs to the Acholeplasmataceae family, comprising the genera Acholeplasma and 'Candidatus Phytoplasma'. Acholeplasmas are ubiquitous saprophytic bacteria. Several isolates are derived from plants or animals, whereas phytoplasmas are characterised as intracellular parasitic pathogens of plant phloem and depend on insect vectors for their spread. The complete genome sequences for eight strains of this family have been resolved so far, all of which were determined depending on clone-based sequencing.
  
  
  RESULTS
  The A. oculi strain 19L chromosome was sequenced using two independent approaches. The first approach comprised sequencing by synthesis (Illumina) in combination with Sanger sequencing, while single molecule real time sequencing (PacBio) was used in the second. The genome was determined to be 1,587,120 bp in size. Sequencing by synthesis resulted in six large genome fragments, while the single molecule real time sequencing approach yielded one circular chromosome sequence. High-quality sequences were obtained by both strategies differing in six positions, which are interpreted as reliable variations present in the culture population. Our genome analysis revealed 1,471 protein-coding genes and highlighted the absence of the F1FO-type Na+ ATPase system and GroEL/ES chaperone. Comparison of the four available Acholeplasma sequences revealed a core-genome encoding 703 proteins and a pan-genome of 2,867 proteins.
  
  
  CONCLUSIONS
  The application of two state-of-the-art sequencing technologies highlights the potential of single molecule real time sequencing for complete genome determination. Comparative genome analyses revealed that the process of losing particular basic genetic features during genome reduction occurs in both genera, as indicated for several phytoplasma strains and at least A. oculi. The loss of the F1FO-type Na+ ATPase system may separate Acholeplasmataceae from other Mollicutes, while the loss of those genes encoding the chaperone GroEL/ES is not a rare exception in this bacterial class.
authors.forename: Christin
authors.initials: C
authors.lastname: Siewert
authors.forename: Wolfgang R
authors.initials: WR
authors.lastname: Hess
authors.forename: Bojan
authors.initials: B
authors.lastname: Duduk
authors.forename: Bruno
authors.initials: B
authors.lastname: Huettel
authors.forename: Richard
authors.initials: R
authors.lastname: Reinhardt
authors.forename: Carmen
authors.initials: C
authors.lastname: Büttner
authors.affiliation: Humboldt-Universität zu Berlin, Faculty of Life Science, Thaer-Institute, Division Phytomedicine, Lentzeallee 55/57, 14195 Berlin, Germany. Michael.Kube@agrar.hu-berlin.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Kube
mesh_terms: D000127:Acholeplasma / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial / Q000235:genetics; D023281:Genomics; D017421:Sequence Analysis; D013045:Species Specificity