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Haloferax volcanii DS2 (Haloferax volcanii DS2) Genome Browser Gateway
 
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About the Haloferax volcanii DS2 Mar 30 2010 (haloVolc1) assembly (sequences)
 

Species Information

The Haloferax volcanii DS2 genome is 4.01 Million bp long and contains approximately 4130 predicted genes. The genome is complete and being publicly released by Jonathan Eisen before journal publication while genome annotation is in progress. H. volcanii is a chemoorganotroph requiring complex nutrient medium and 1.5-2.5 M NaCl for growth. Cultures will grow at 37C, but optimal growth is at 42C.

Taxonomy: Archaea; Euryarchaeota; Halobacteria; Halobacteriales; Halobacteriaceae; Haloferax.

Sequencing: The sequence was released Mar 30 2010 by the TIGR, and was described in PLoS One 5:e9605 (2010) Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, et al. "The complete genome sequence of Haloferax volcanii DS2, a model archaeon."

Abstract: BACKGROUND: Haloferax volcanii is an easily culturable moderate halophile that grows on simple defined media, is readily transformable, and has a relatively stable genome. This, in combination with its biochemical and genetic tractability, has made Hfx. volcanii a key model organism, not only for the study of halophilicity, but also for archaeal biology in general. METHODOLOGY/PRINCIPAL FINDINGS: We report here the sequencing and analysis of the genome of Hfx. volcanii DS2, the type strain of this species. The genome contains a main 2.848 Mb chromosome, three smaller chromosomes pHV1, 3, 4 (85, 438, 636 kb, respectively) and the pHV2 plasmid (6.4 kb). CONCLUSIONS/SIGNIFICANCE: The completed genome sequence, presented here, provides an invaluable tool for further in vivo and in vitro studie... [Click above reference link for full abstract]

Isolation: Arch Microbiol 104:207-14 (1975) Mullakhanbhai MF, Larsen H, "Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement."

Abstract: A halophilic bacterium was isolated from bottom sediment from the Dead Sea. The organism possessed the properties of the halobacteria, but differed from the known species in two important respects, 1) the cells were disc shaped and often cupped when grown under optimum conditions, 2) the optimum requirements for sodium chloride was in the range 1.7--2.5 molar which is about half of that generally reported for the halobacteria. The organism was assigned to the genus Halobacterium and described as Halobacterium volcanni spec. rov. The optimum sodium chloride concentration for growth was close to that found in the Dead Sea. The tolerance for magnesium chloride was very high; the organism grew well in media containing magnesium chloride in the concentrations found in the Dead Sea. Halobacteriu... [Click above reference link for full abstract]

Sequenced related species/strains: Halalkalicoccus jeotgali, Halobacterium NRC, Halogeometricum borinquense, Haloarcula hispanica, Halorubrum lacusprofundi, Haloarcula marismortui, Halomicrobium mukohataei, Halobacterium salinarum, Haloterrigena turkmenica, Halorhabdus utahensis, Haloquadratum walsbyi, Halopiger xanaduensis, Natrialba magadii, Natronomonas pharaonis

Browse Specific Gene/Feature Sets

Sample position queries

A genome position can be specified by chromosomal coordinate range, COGID, or keywords from the GenBank or TIGR description of a gene. The available chromosome/plasmid names are:

Browser Chrom/Plasmid NameLength (bp)GC Content (%)Gene CountNCBI RefSeq Accession
chr284775766.643021NC_013967
pHV18509255.5088NC_013968
pHV2635956.066NC_013965
pHV343790665.56380NC_013964
pHV463578661.67635NC_013966

The following list shows examples of valid position queries for thisgenome: 

Request:Genome Browser Response:
chrDisplays the entire sequence "chr" in the browser window
chr:1-10000    Displays first ten thousand bases of the sequence "chr"
transporter    Lists all genes with "transporter" in the name or description
HVO_0010Display genome at position of gene HVO_0010

Phylogenetic tree of related species based on multiple-genome alignment in browser:

Phylogeny tree

Credits

The Archaeal Genome Browsers at UCSC were developed by members of theLowe Lab (Kevin Schneider,Katherine Pollard, Andy Pohl, Todd Lowe) and Robert Baertsch, with significant support fromthe UCSC Human GenomeBrowser group.The Archaeal Browsers are run by a slightly modifiedversion of the UCSC Human GenomeBrowser system. All queries, bug reports, content corrections, suggested improvements,and new track data submissions should be sent to Todd Lowe (lowe@soe.ucsc.edu).

If you use the browser in your published research, please cite ourpublication in the Nucleic Acids Research DatabaseIssue. Citations and positive feedback will help us obtain fundingto continue development of this community resource.