Frequencies of Ty1-copia and Ty3-gypsy retroelements within the Triticeae EST databases

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Abstract

The frequency of Ty1-copia-type and Ty3-gypsy-type retrotransposons in the International Triticeae EST Consortium database and the DuPont EST database was estimated using BLASTN searches. These ESTs were obtained from 94 cDNA libraries from different tissues and different growing conditions, excluding subtracted and normalized cDNA libraries. Triticeae EST databases were screened using four different Ty1-copia-type, 12 reverse transcriptase sequences, and three Ty3-gypsy-type Triticeae retrotransposon sequences. Using a selection threshold of BLASTN scores higher than 100 or E values smaller than e-20, 0.145% of the ESTs were found to be significantly similar to at least one of the retrotransposons used in the search. This percentage increased to 0.176% when the BLASTN threshold was changed to E

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