title: Haloquadratum walsbyi: limited diversity in a global pond.
abstract: BACKGROUND
  Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.
  
  
  RESULTS
  Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.
  
  
  CONCLUSIONS
  Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.
authors.affiliation: Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany. mdyall-smith@csu.edu.au
authors.forename: Mike L
authors.initials: ML
authors.lastname: Dyall-Smith
authors.forename: Friedhelm
authors.initials: F
authors.lastname: Pfeiffer
authors.forename: Kathrin
authors.initials: K
authors.lastname: Klee
authors.forename: Peter
authors.initials: P
authors.lastname: Palm
authors.forename: Karin
authors.initials: K
authors.lastname: Gross
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: Markus
authors.initials: M
authors.lastname: Rampp
authors.forename: Dieter
authors.initials: D
authors.lastname: Oesterhelt
mesh_terms: D020745:Genome, Archaeal / Q000235:genetics; D006216:Halobacteriaceae / Q000145:classification / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S