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Data mining of the dog genome reveals novel Canine Endogenous Retroviruses(CfERVs)
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. (Bongcam-Rudloff)
Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Virology.
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(English)Manuscript (preprint) (Other (popular science, discussion, etc.))
Abstract [en]

Mining the dog genome for canine endogenous retroviruses (CfERV) using the program RetroTector© identified 407 CfERVs (0.15% of the total genome size). Phylogenetic analysis showed that the majority of these CfERVs belong to the gammaretroviridae (n=313) genus. In this group, we found 33 integrated CfERVs with similarity to the human HERV-Fc1. Eighteen of them had conserved open reading frames open and seven of the 18 were recent integrations (≤ 5% LTR divergence). Some of these CfERVs may have potential for active retrotransposition and could actively contribute to the plasticity of canine genomes. Similar to other vertebrates, betaretroviruses (n=28) was the second most common group. In addition, four spuma-like and four gypsy-like CfERVs were identified, the latter group being rare in vertebrate genomes. Moreover, we identified 55 CfERVs that could not be classified unambiguously to any known retroviral genera. The integration landscape shows that all dog chromosomes have CfERV integrations with non-uniform distribution both along and across chromosomes. Some regions were essentially devoid of CfERVs whereas other regions had large numbers. Notably, in a comparison between dog and human genomes, CfERV were approximately one fifth of the amount of HERVs found. Species-specific mechanisms for purging and protection against retroviral infections are suggested to act in the dog genome. The CfERV integration pattern showed that a substantial fraction of annotated genes were found within 100 kb distance from annotated proviruses. The majority of such integrations were placed in antisense orientation relative to the transcriptional direction of the neighboring chromosomal genes. In conclusion, our results from Canis familiaris genome analysis support the notion that different mammals may interact distinctively with endogenous retroviruses.

Keyword [en]
endogenous retroviruses, ERV, dog, canine
National Category
Bioinformatics and Systems Biology Microbiology in the medical area
Research subject
Medical Virology
URN: urn:nbn:se:uu:diva-112125OAI: oai:DiVA.org:uu-112125DiVA: diva2:284979
Available from: 2010-01-09 Created: 2010-01-09 Last updated: 2011-06-28
In thesis
1. Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies
Open this publication in new window or tab >>Novel Bioinformatics Applications for Protein Allergology, Genome-Wide Association and Retrovirology Studies
2010 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Recently, the pace of growth in the amount of data sources within Life Sciences has increased exponentially until pose a difficult problem to efficiently manage their integration. The data avalanche we are experiencing may be significant for a turning point in science, with a change of orientation from proprietary to publicly available data and a concomitant acceptance of studies based on the latter. To investigate these issues, a Network of Excellence (EMBRACE) was launched with the aim to integrate the major databases and the most popular bioinformatics software tools. The focus of this thesis is therefore to approach the problem of seamlessly integrating varied data sources and/or distributed research tools.

In paper I, we have developed a web service to facilitate allergenicity risk assessment, based on allergen descriptors, in order to characterize proteins with the potential for sensitization and cross-reactivity.

In paper II, a web service was developed which uses a lightweight protocol to integrate human endogenous retrovirus (ERV) data within a public genome browser. This new data catalogue and many other publicly available sources were integrated and tested in a bioinformatics-rich client application.

In paper III, GeneFinder, a distributed tool for genome-wide association studies, was developed and tested. Useful information based on a particular genomic region can be easily retrieved and assessed.

Finally, in paper IV, we developed a prototype pipeline to mine the dog genome for endogenous retroviruses and displaying the transcriptional landscape of these retroviral integrations. Moreover, we further characterized a group that until this point was believed to be primate-specific. Our results also revealed that the dog has been very effective in protecting itself from such integrations.

This work integrates different applications in the fields of protein allergology, biotechnology, genome association studies and endogenous retroviruses.

Place, publisher, year, edition, pages
Uppsala: Acta Universitatis Upsaliensis, 2010. 103 p.
Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology, ISSN 1651-6214 ; 703
data integration, web services, protein allergology, risk assessment, cross reactivity, endogenous retroviruses, ERV, dog, canine, GWAS, genome-wide association studies
urn:nbn:se:uu:diva-111932 (URN)978-91-554-7694-6 (ISBN)
Public defence
2010-01-29, C8:301, BMC, Husargatan 3, Uppsala, 09:30 (English)
Available from: 2010-01-08 Created: 2009-12-31 Last updated: 2010-01-11Bibliographically approved

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Martinez Barrio, AlvaroJern, Patric
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The Linnaeus Centre for BioinformaticsDepartment of Medical Biochemistry and MicrobiologyClinical VirologyPhysiology
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