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Identification of Repetitive Elements in the Genome of Oreochromis niloticus: Tilapia Repeat Masker

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Abstract

The large-scale bacterial artificial chromosome-end sequencing project of Nile tilapia (Oreochromis niloticus) has generated extensive sequence data that allowed the examination of the repeat content in this fish genome and building of a repeat library specific for this species. This library was established based on Tilapiini repeat sequences from GenBank, sequences orthologous to the repeat library of zebrafish in Repbase, and novel repeats detected by genome analysis using MIRA assembler. We estimate that repeats constitute about 14% of the tilapia genome and also give estimates for the occurrence of the different repeats based on the Basic Local Alignment Search Tool searches within the database of known tilapia sequences. The frequent occurrence of novel repeats in the tilapia genome indicates the importance of using the species-specific repeat masker prior to sequence analyses. A web tool based on the RepeatMasker software was designed to assist tilapia genomics.

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Acknowledgements

This is a contribution from the Agricultural Research Organization, Institute of Animal Science, Bet Dagan, Israel, No. 549/09. The research was supported by research grant IS-3995-07 from the USA-Israel Bi-national Agricultural Research and Development (BARD) Fund.

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Authors and Affiliations

  1. Agricultural Research Organization, Institute of Animal Science, Bet Dagan, 50250, Israel

    Andrey Shirak, Gideon Hulata, Micha Ron & Eyal Seroussi

  2. Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, MA, 02141, USA

    Manfred Grabherr, Federica Di Palma & Kerstin Lindblad-Toh

  3. Department of Biology, University of Maryland, College Park, MD, 20742, USA

    Tom D. Kocher

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  1. Andrey Shirak
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  2. Manfred Grabherr
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  3. Federica Di Palma
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  4. Kerstin Lindblad-Toh
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  5. Gideon Hulata
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  6. Micha Ron
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  7. Tom D. Kocher
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  8. Eyal Seroussi
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Correspondence to Eyal Seroussi.

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Shirak, A., Grabherr, M., Di Palma, F. et al. Identification of Repetitive Elements in the Genome of Oreochromis niloticus: Tilapia Repeat Masker. Mar Biotechnol 12, 121–125 (2010). https://doi.org/10.1007/s10126-009-9236-8

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  • DOI: https://doi.org/10.1007/s10126-009-9236-8

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