Plant & Animal Genome IX Conference

Poster: Sequencing & EST
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FREQUENCY OF RETROELEMENTS WITHIN THE TRITICEAE DATABASES

¹ Dept. of Agronomy & Range Science, University of California, One Shields Ave, Davis, CA 95616. USA.

² Dept. de Agronomia, Univ. Nacional del Sur, San Andres 800 (8000) Bahia Blanca, Buenos Aires, Argentina

³ DuPont Ag Biotech, Delaware Technology Park, 1 Innovation Way, Newark, DE 19711. USA.

⁴ USDA-ARS, Western Regional Research Center, 800 Buchanan St, Albany, CA 94710. USA.

Frequency of different classes of retrotransposons in the International Triticeae EST Consortium (ITEC) database (65,186 sequences) and the DuPont wheat EST database (86,627 sequences) was estimated using BLAST searches. Subtracted and normalized cDNA libraries were excluded from the analysis. Copia-like ESTs were screened using BARE1, WIS-2-1A, and R1713 sequences from barley, wheat and rye, and a complete sequence from WIS-2-1A from T. monococcum. ESTs databases were also screened with gypsy-type retrotransposon sequences CEREBA, BAGY-1, WHRE1, CENTA, GRANDE1-4, and RIRE3 from barley, wheat, mays, and rice. BLAST scores higher than 100 or P< e-20 were used as selection thresholds. The percentage of significant ESTs in the DuPont database was 0.19% (0.08% Copia, 0.11% Gypsy) and in the ITEC database 0.14% (0.07% Copia, 0.08% Gypsy. Identification of these repetitive elements within the EST databases is important to avoid errors in the estimations of the number of genes present in BAC clones and to avoid their use as probes in mapping experiments. Quantification of their frequency can be also used as an indirect estimate of the level of activity of these repetitive elements in the Triticeae.