Identification of Repetitive Elements in the Genome of Oreochromis niloticus: Tilapia Repeat Masker |
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| Authors: | Andrey Shirak Manfred Grabherr Federica Di Palma Kerstin Lindblad-Toh Gideon Hulata Micha Ron Tom D Kocher Eyal Seroussi |
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| Institution: | (1) Agricultural Research Organization, Institute of Animal Science, Bet Dagan, 50250, Israel;(2) Broad Institute of Harvard and MIT, 320 Charles Street, Cambridge, MA 02141, USA;(3) Department of Biology, University of Maryland, College Park, MD 20742, USA; |
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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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