Identification of repetitive elements in the genome of Oreochromis niloticus: tilapia repeat masker.
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.
Shirak
Andrey
A
Agricultural Research Organization, Institute of Animal Science, Bet Dagan, 50250, Israel.
Grabherr
Manfred
M
Di Palma
Federica
F
Lindblad-Toh
Kerstin
K
Hulata
Gideon
G
Ron
Micha
M
Kocher
Tom D
TD
Seroussi
Eyal
E
D000818:Animals; D022202:Chromosomes, Artificial, Bacterial; D023681:Cichlids / Q000235:genetics*; D019295:Computational Biology; D015723:Gene Library; D023281:Genomics; D020071:Interspersed Repetitive Sequences / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software