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United States Department of Agriculture

Agricultural Research Service

Title: Frequencies of Ty1-Copia and Ty3-Gypsy Retroelements Within the Triticeae Est Databases

Authors
item Echenique, V - UC DAVIS, CA
item Stamova, B - UC DAVIS, CA
item Wolters, P - DUPONT, NEWARK, DE
item Lazo, Gerard
item Blake, Victoria
item Dubcovsky, J - UC DAVIS, CA

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 9, 2001
Publication Date: February 8, 2002

Interpretive Summary: With the recent increase in the abundance of wheat expressed sequence tags (ESTs), a survey was conducted to determine the frequency of Ty1-copia-type and Ty3-gypsy-type retrotransposons in the International Triticeae EST Cooperative (ITEC) database and the DuPont EST databases. Transposable elements may play a role in creating genetic diversity seen in plant species. These ESTs were obtained from cDNA libraries from different tissues and different growing conditions. 0.145% of the ESTs were found to be significantly similar to at least one of the retrotransposons used in the search. The percentage of ESTs similar to retrotransposons was significantly higher in libraries derived from leaf tissues than in libraries from roots, anthers, or spikes. In addition, the percentage of ESTs similar to retrotransposons in libraries from plants under stress conditions was three to four folds higher than in libraries from plants grown under normal conditions. Identification of retrotransposons within the Triticeae EST databases provides an indirect estimation of the patterns of transcriptional activity of these repetitive elements and is important to improve the annotation of genomic sequences used to search these EST databases.

Technical Abstract: The frequency of Ty1-copia-type and Ty3-gypsy-type retrotransposons in the International Triticeae EST Cooperative (ITEC) database and the DuPont EST database was estimated using BLASTN searches. These ESTs were obtained from cDNA libraries from different tissues and different growing conditions. Triticeae EST databases were screened using four different Ty1-copia-type, 12 reverse transcriptase, 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 < e-10. The percentage of ESTs similar to etrotransposons was significantly higher in cDNA libraries from leaf tissues than in cDNA libraries from roots, anthers, or spikes. In addition, the percentage of ESTs similar to retrotransposons in cDNA libraries from plants under stress conditions was three to four folds higher than in cDNA libraries from plants grown under normal conditions. Identification of retrotransposons within the Triticeae EST databases provides an indirect estimation of the patterns of transcriptional activity of these repetitive elements and is important to improve the annotation of genomic sequences used to search these EST databases.

Last Modified: 7/25/2014
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