Genome Sequence and Methylation Pattern of Haloterrigena salifodinae BOL5-1, an Extremely Halophilic Archaeon from a Bolivian Salt Mine.

The halophilic archaeon Haloterrigena salifodinae BOL5-1 was isolated from a Bolivian salt mine and sequenced using single-molecule real-time sequencing. The GC-rich genome was 5.1 Mbp, with a 4.2-Mbp chromosome and 5 plasmids ranging from 96 to 281 kbp. The genome annotation was incorporated into HaloWeb (https://halo.umbc.edu), and the methylation patterns were incorporated into REBASE (http://tools.neb.com/genomes/view.php?seq_id=99167&list=1).

Genome Sequence of Salarchaeum sp. Strain JOR-1, an Extremely Halophilic Archaeon from the Dead Sea.

An extremely halophilic archaeon, Salarchaeum sp. strain JOR-1, was isolated from the east coast of the Dead Sea, Kingdom of Jordan, and sequenced using single-molecule real-time (SMRT) sequencing. The GC-rich 2.5-Mbp genome was composed of a circular chromosome and a megaplasmid. The genome contained 2,633 genes and was incorporated into HaloWeb (https://halo.umbc.edu/).

Genome Sequences and Methylation Patterns of Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, Two Extremely Halophilic Archaea from a Bolivian Salt Mine.

Two extremely halophilic archaea, namely, Natrinema versiforme BOL5-4 and Natrinema pallidum BOL6-1, were isolated from a Bolivian salt mine and their genomes sequenced using single-molecule real-time sequencing. The GC-rich genomes of BOL5-4 and BOL6-1 were 4.6 and 3.8 Mbp, respectively, with large chromosomes and multiple megaplasmids. Genome annotation was incorporated into HaloWeb and methylation patterns incorporated into REBASE.

Methylomes of Two Extremely Halophilic Archaea Species, Haloarcula marismortui and Haloferax mediterranei.

The genomes of two extremely halophilic Archaea species, Haloarcula marismortui and Haloferax mediterranei, were sequenced using single-molecule real-time sequencing. The ∼4-Mbp genomes are GC rich with multiple large plasmids and two 4-methyl-cytosine patterns. Methyl transferases were incorporated into the Restriction Enzymes Database (REBASE), and gene annotation was incorporated into the Haloarchaeal Genomes Database (HaloWeb).

The information transfer system of halophilic archaea.

Information transfer is fundamental to all life forms. In the third domain of life, the archaea, many of the genes functioning in these processes are similar to their eukaryotic counterparts, including DNA replication and repair, basal transcription, and translation genes, while many transcriptional regulators and the overall genome structure are more bacterial-like. Among halophilic (salt-loving) archaea, the genomes commonly include extrachromosomal elements, many of which are large megaplasmids or minichromosomes. With the sequencing of genomes representing ten different genera of halophilic archaea and the availability of genetic systems in two diverse models, Halobacterium sp. NRC-1 and Haloferax volcanii, a large number of genes have now been annotated, classified, and studied. Here, we review the comparative genomic, genetic, and biochemical work primarily aimed at the information transfer system of halophilic archaea, highlighting gene conservation and differences in the chromosomes and the large extrachromosomal elements among these organisms.

HaloWeb: the haloarchaeal genomes database.

BACKGROUND: Complete genome sequencing together with post-genomic studies provide the opportunity for a comprehensive 'systems biology' understanding of model organisms. For maximum effectiveness, an integrated database containing genomic, transcriptomic, and proteomic data is necessary. DESCRIPTION: To improve data access and facilitate functional genomic studies on haloarchaea in our laboratory, a dedicated database and website, named HaloWeb, was developed. It incorporates all finished and publicly released haloarchaeal genomes, including gene, protein and RNA sequences and annotation data, as well as other features such as insertion element sequences. The HaloWeb database was designed for easy data access and mining, and includes tools for tasks such as genome map generation, sequence extraction, and sequence editing. Popular resources at other sites, e.g., NCBI PubMed and BLAST, COG and KOG protein clusters, KEGG pathways, and GTOP structures were dynamically linked. The HaloWeb site is located at http://halo4.umbi.umd.edu, and at a mirror site, http://halo5.umbi.umd.edu, with all public genomic data and NCBI, KEGG, and GTOP links available for use by the academic community. The database is curated and updated on a regular basis. CONCLUSIONS: The HaloWeb site includes all completely sequenced haloarchaeal genomes from public databases. It is currently being used as a tool for comparative genomics, including analysis of gene and genome structure, organization, and function. The database and website are up-to-date resources for researchers worldwide.