title: Low-pass sequencing for microbial comparative genomics.
abstract: BACKGROUND
  We studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile Haloarcula marismortui; (2) the non-pigmented Natrialba asiatica; (3) the psychrophile Halorubrum lacusprofundi and (4) the Dead Sea isolate Halobaculum gomorrense. Approximately one thousand single pass genomic sequences per genome were obtained. The data were analyzed by comparative genomic analyses using the completed Halobacterium sp. NRC-1 genome as a reference. Low-pass shotgun sequencing is a simple, inexpensive, and rapid approach that can readily be performed on any cultured microbe.
  
  
  RESULTS
  As expected, the four archaeal halophiles analyzed exhibit both bacterial and eukaryotic characteristics as well as uniquely archaeal traits. All five halophiles exhibit greater than sixty percent GC content and low isoelectric points (pI) for their predicted proteins. Multiple insertion sequence (IS) elements, often involved in genome rearrangements, were identified in H. lacusprofundi and H. marismortui. The core biological functions that govern cellular and genetic mechanisms of H. sp. NRC-1 appear to be conserved in these four other halophiles. Multiple TATA box binding protein (TBP) and transcription factor IIB (TFB) homologs were identified from most of the four shotgunned halophiles. The reconstructed molecular tree of all five halophiles shows a large divergence between these species, but with the closest relationship being between H. sp. NRC-1 and H. lacusprofundi.
  
  
  CONCLUSIONS
  Despite the diverse habitats of these species, all five halophiles share (1) high GC content and (2) low protein isoelectric points, which are characteristics associated with environmental exposure to UV radiation and hypersalinity, respectively. Identification of multiple IS elements in the genome of H. lacusprofundi and H. marismortui suggest that genome structure and dynamic genome reorganization might be similar to that previously observed in the IS-element rich genome of H. sp. NRC-1. Identification of multiple TBP and TFB homologs in these four halophiles are consistent with the hypothesis that different types of complex transcriptional regulation may occur through multiple TBP-TFB combinations in response to rapidly changing environmental conditions. Low-pass shotgun sequence analyses of genomes permit extensive and diverse analyses, and should be generally useful for comparative microbial genomics.
authors.affiliation: Institute for Systems Biology, Seattle, Washington 98103, USA. ygoo@systemsbiology.org
authors.forename: Young Ah
authors.initials: YA
authors.lastname: Goo
authors.forename: Jared
authors.initials: J
authors.lastname: Roach
authors.forename: Gustavo
authors.initials: G
authors.lastname: Glusman
authors.forename: Nitin S
authors.initials: NS
authors.lastname: Baliga
authors.forename: Kerry
authors.initials: K
authors.lastname: Deutsch
authors.forename: Min
authors.initials: M
authors.lastname: Pan
authors.forename: Sean
authors.initials: S
authors.lastname: Kennedy
authors.forename: Shiladitya
authors.initials: S
authors.lastname: DasSarma
authors.forename: Wailap Victor
authors.initials: WV
authors.lastname: Ng
authors.forename: Leroy
authors.initials: L
authors.lastname: Hood
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics*; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics; D001482:Base Composition; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D014644:Genetic Variation; D020745:Genome, Archaeal; D023281:Genomics / Q000379:methods*; D019613:Haloarcula / Q000235:genetics; D007526:Isoelectric Point; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000379:methods*; D014157:Transcription Factors / Q000235:genetics
chemical_list: D019843:Archaeal Proteins; D019641:DNA, Archaeal; D012336:RNA, Ribosomal, 16S; D014157:Transcription Factors