Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler.
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BACKGROUND: The rate of emergence of human pathogens is steadily increasing; most of these novel agents originate in wildlife. Bats, remarkably, are the natural reservoirs of many of the most pathogenic viruses in humans. There are two bat genome projects currently underway, a circumstance that promises to speed the discovery host factors important in the coevolution of bats with their viruses. These genomes, however, are not yet assembled and one of them will provide only low coverage, making the inference of most genes of immunological interest error-prone. Many more wildlife genome projects are underway and intend to provide only shallow coverage. RESULTS: We have developed a statistical method for the assembly of gene families from partial genomes. The method takes full advantage of the quality scores generated by base-calling software, incorporating them into a complete probabilistic error model, to overcome the limitation inherent in the inference of gene family members from partial sequence information. We validated the method by inferring the human IFNA genes from the genome trace archives, and used it to infer 61 type-I interferon genes, and single type-II interferon genes in the bats Pteropus vampyrus and Myotis lucifugus. We confirmed our inferences by direct cloning and sequencing of IFNA, IFNB, IFND, and IFNK in P. vampyrus, and by demonstrating transcription of some of the inferred genes by known interferon-inducing stimuli. CONCLUSION: The statistical trace assembler described here provides a reliable method for extracting information from the many available and forthcoming partial or shallow genome sequencing projects, thereby facilitating the study of a wider variety of organisms with ecological and biomedical significance to humans than would otherwise be possible.
Gene Expression Profiling
Interferon Type I
Reproducibility of Results
Sequence Analysis, DNA
Sequence Homology, Nucleic Acid
Published Version (Please cite this version)10.1186/1471-2164-11-444
Publication InfoHaines, A; Hudak, K; Kepler, TB; Ramsburg, Elizabeth A; Roach, J; Sample, C; & Walsh, A (2010). Chiropteran types I and II interferon genes inferred from genome sequencing traces by a statistical gene-family assembler. BMC Genomics, 11. pp. 444. 10.1186/1471-2164-11-444. Retrieved from https://hdl.handle.net/10161/4346.
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Adjunct Assistant Professor in the Department of Molecular Genetics and Microbiology
In principle, most viral infections can be prevented by effective and timely vaccination. In the past several decades however, the rapid emergence and spread into new geographical areas of viruses such as dengue, West Nile virus, HIV, and the highly pathogenic avian influenzas has outpaced the development of preventative vaccines. The major focus of research in the Ramsburg lab is to develop novel vaccines based on recombinant viruses for the prevention of viral diseases, and to better char
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