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Identification of Repetitive Elements in the Genome of Oreochromis niloticus: Tilapia Repeat Masker
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
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2009 (English)In: Marine Biotechnology, ISSN 1436-2228, E-ISSN 1436-2236, Vol. 12, no 2, 121-125 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2009. Vol. 12, no 2, 121-125 p.
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Natural Sciences
URN: urn:nbn:se:uu:diva-119725DOI: 10.1007/s10126-009-9236-8ISI: 000275754700001PubMedID: 19936833OAI: oai:DiVA.org:uu-119725DiVA: diva2:300745
Available from: 2010-03-01 Created: 2010-03-01 Last updated: 2011-08-23Bibliographically approved

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Grabherr, ManfredLindblad-Toh, Kerstin
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