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

Abstract

The frequency of Ty1-copia-type and Ty3-gypsy-type retrotransposons in the International Triticeae EST Consortium (ITEC) database (61,942 sequences: 82% wheat, 10% barley, 8% rye) and the DuPont EST database (86,628 wheat sequences) was estimated using BLASTN searches. These ESTs were obtained from 94 cDNA libraries from different tissues (leaves, roots, spikes, flowers and seeds) 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 (0.064% Ty1-copia, 0.081% Ty3-gypsy). This percentage increased to 0.176% when the BLASTN threshold was changed to E<e -10 . The percentage of ESTs similar to retrotransposons was significantly higher (P < 0.05) 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 (0.25% at E<e -20 , and 0.30% at E<e -10 ) was three to four folds higher (P < 0.0001) than in cDNA libraries from plants grown under normal conditions (0.07% at E<e -20 , and 0.09% at E<e -10 ). 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.

Analysis of the wheat endosperm transcriptome

“…Of the LTR retrotransposons, 38 are members (12), Latidu (2), Jeli (28), lfis (2), Hawi (2), Fatima (1), Erika (1), Laura (2)) and 7 are members of Ty1-copia family (Angel (3), Leojyg (2), WIS (1)), copia-like (1) and 2 are novel LTRs. The Ty3-gypsy and Ty1-copia elements are found in 0.35% (45 out of 17 949 ESTs) of endosperm ESTs, which is higher than what was reported earlier for sets of ESTs derived from other wheat cDNA libraries (Echenique et al 2002), including cDNA libraries constructed from tissues of plants subjected to stress. The Class II repetitive elements, which utilize a DNA-intermediate in a cut-and-paste transposition, are represented by CACTA (Wicker et al 2003) with 34 out of 112 ESTs similar to this repetitive element (30%).…”

“…Retrotransposons, transposable elements which move via an RNA transcript, have been shown to be present in wheat EST sequences (Echenique et al 2002;. To test whether any of the endosperm genes represent fragments of transposable elements that are abundant in the wheat genome , we compared the 17 949 EST sequences to the sequences of transposable elements reported in wheat.…”

Genomic organization of the complex α-gliadin gene loci in wheat

“…Surprisingly, it was found that abundant retroelements are rarely expressed, whereas those with a low copy number are often transcribed based on the analysis of the maize EST database (Meyers et al 2001). Although a detailed examination of the transcriptional activities of wheat retrotransposons has not yet been reported, analysis of the Triticeae EST database revealed that sequences homologous to both Ty3-copia and Ty1-copia retrotransposons are differentially expressed in the cDNA libraries from different tissues or under various biotic and abiotic stresses (Echenique et al 2002).…”

Reme1, a Copia retrotransposon in melon, is transcriptionally induced by UV light

“…Using RT-PCR, transcription of Reme1 in leaves was observed under normal conditions. This is fairly unusual for a low-copy retrotransposon such as Reme1; transcription in unstressed somatic tissues is typical for the abundant elements of the grasses (Suoniemi et al 1996;Meyers et al 2001;Vicient et al 2001;Echenique et al 2002;Araujo et al 2005;Gomez et al 2006). Transcripts in leaves, however, are unlikely to contribute to genome expansion because leaves do not generally give rise to floral meristems and consequently gametes.…”