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Open Access Research article

Sequence analysis of an Archaeal virus isolated from a hypersaline lake in Inner Mongolia, China

Eulyn Pagaling1, Richard D Haigh1, William D Grant1, Don A Cowan2, Brian E Jones3, Yanhe Ma4, Antonio Ventosa5 and Shaun Heaphy1*

  • * Corresponding author: Shaun Heaphy sh1@le.ac.uk

  • † Equal contributors

Author Affiliations

1 Department of Infection Immunity and Inflammation, University of Leicester, University Road, Leicester, LE1 9HN, UK

2 Department of Biotechnology, University of the Western Cape, Bellville 7535, Cape Town, South Africa

3 Genencor International B, V., Archimedesweg 30, 2333 CN Leiden, The Netherlands

4 State Key Laboratory of Microbial Resource, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100080, China

5 Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Sevilla, 41012, Spain

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BMC Genomics 2007, 8:410  doi:10.1186/1471-2164-8-410

Published: 9 November 2007

Abstract

Background

We are profoundly ignorant about the diversity of viruses that infect the domain Archaea. Less than 100 have been identified and described and very few of these have had their genomic sequences determined. Here we report the genomic sequence of a previously undescribed archaeal virus.

Results

Haloarchaeal strains with 16S rRNA gene sequences 98% identical to Halorubrum saccharovorum were isolated from a hypersaline lake in Inner Mongolia. Two lytic viruses infecting these were isolated from the lake water. The BJ1 virus is described in this paper. It has an icosahedral head and tail morphology and most likely a linear double stranded DNA genome exhibiting terminal redundancy. Its genome sequence has 42,271 base pairs with a GC content of ~65 mol%. The genome of BJ1 is predicted to encode 70 ORFs, including one for a tRNA. Fifty of the seventy ORFs had no identity to data base entries; twenty showed sequence identity matches to archaeal viruses and to haloarchaea. ORFs possibly coding for an origin of replication complex, integrase, helicase and structural capsid proteins were identified. Evidence for viral integration was obtained.

Conclusion

The virus described here has a very low sequence identity to any previously described virus. Fifty of the seventy ORFs could not be annotated in any way based on amino acid identities with sequences already present in the databases. Determining functions for ORFs such as these is probably easier using a simple virus as a model system.