Genome Sequence of Halorubrum sp. Strain T3, an Extremely Halophilic Archaeon Harboring a Virus-Like Element

Abstract

Halorubrum sp. strain T3, harboring a virus-like element, was isolated from a sample collected from a solar saltern in Yunnan, China. Several strains of Halorubrum pleomorphic viruses were reported in this genus recently; however, the virus-host interaction in haloarchaea remains unclear. To explore this issue, here we present the genome sequence of Halorubrum sp. strain T3 (3,168,011 bp, 68.48% G+C content).

GENOME ANNOUNCEMENT

Species of the genus Halorubrum are widely distributed, mainly in a hypersaline environment (14). Recently, four strains of Halorubrum pleomorphic viruses (HRPV-1, HRPV-2, HRPV-3 and HRPV-6) were reported (17, 18). However, the virus-host interaction in haloarchaea remains unclear. In our laboratory, tens of strains isolated from the Mohei solar saltern (Yunnan, People's Republic of China) have been shown to belong to the genus Halorubrum; however, only a single strain, viz, strain T3, contains a virus-like element, which is largely homologous with HRPV-3 (our unpublished data). The 16S rRNA sequence of strain T3 has a close relationship to Halorubrum chaoviator Halo-G^T (99.217% similarity) (15) and Halorubrum trapanicum NRC 34021^T (99.215%) (20). It can grow well in universal modified growth medium (MGM) under 37°C and can be easily transformed in laboratory without polyethylene glycol (PEG) mediation (2). Compared with Halorubrum lacusprofundi ATCC 49239, from which virus was absent, which has genome sequence accession no. CP001365.1 to CP001367.1 and was isolated from a deep lake in Antarctica, strain T3 was isolated from a typical hypersaline surroundings. To explore the virus-host interaction, we sequenced the genome of Halorubrum sp. strain T3.

The genome sequence of Halorubrum sp. strain T3 was determined by a whole-genome shotgun strategy using Illumina Hiseq2000 paired-end sequencing technology (16), a 500-bp-span paired-end library (∼300 Mb of available reads with ∼100-fold genome coverage), and a 2,000-bp-span paired-end library (∼150 Mb of available reads with ∼50-fold genome coverage). All reads were assembled into 16 contigs (>919 bp in size) and 10 scaffolds (>2,381 bp in size) by use of SOAP de novo v1.05 software (11). Genes were predicted by using Glimmer 3.0 (4). Noncoding RNAs (rRNA and tRNA) were determined by using tRNAscan-SE (13), RNAmmer (10), and the Rfam database (6). The repeat sequence annotation was obtained by using the RepeatMasker software and Repbase database (9). The gene annotation was achieved by BLAST (1), the Swiss-Prot and Clusters of Orthologous Groups (COG) databases (19), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) database (8). The prephage was predicted by using Prohinder software and the ACLAME database (12). Finally, clustered regularly interspaced short palindromic repeats (CRISPRs) were predicted by using CRISPRFinder software (7).

Halorubrum sp. strain T3 has a genome size of 3,168,011 bp (scaffold length) and 68.48% G+C content. A total of 3,369 coding sequences (CDSs) and 48 tRNAs were identified. Two rRNA operons, no small RNAs (sRNA), no potential prephages, and 2,630 tandem repeats were found. Among the 3,369 genes identified, 1,577 were classified into 21 certain functional COG sets or 1,563 were classified into 30 certain functional KEGG sets. Eighteen possible CRISPRs, resembling the mammalian adaptive immune system (3, 5), were found on the genome sequence. Analysis of the CRISPR-rich genome sequence of strain T3 and comparison with other genomes will provide further insights into the genetics and virus-host interaction of haloarchaea.

Nucleotide sequence accession numbers.

This Whole Genome Shotgun project has been deposited in the DDBJ, EMBL, and GenBank databases under accession no. ALWQ00000000. The version described in this article is the first version, ALWQ01000000. The accession number for the 16S rRNA gene is JQ936845.