Repeats in the transcribed regions: Comprehensive characterization and comparison of Citrus spp

Abstract

A large number of expressed sequences tags are available for Citrus spp., which provides an opportunity to understand genomic organization of the transcribed regions. Here, we report a detailed analysis of repetitive elements including tandem repeats (TRs) and transposable elements (TEs) in the transcribed region of the Citrus spp. On average, 22% of the expressed sequence tags (ESTs) contain TRs. The relative density of TR classes is highly taxon-specific. For instance, Citrus limonia has a high relative density of mononucleotide repeats, whereas dinucleotide repeats are rare. The proportions of 2-6, 7-30 and 31-50 bp repeats were almost identical in all studied species except for C. limonia and C. limettioides. We found that < 1% of the citrus ESTs have a similarity with transposable elements. Transcriptional activity of transposable element families varied even within the same class of elements. A high proportion of transcriptional activity was observed for gypsy-like TEs compare to other TE classes. While TEs are relatively rare, TRs are abundant elements in ESTs of citrus. The high proportion of TRs that have a unit size longer than 6 bp raises the question about a possible functional or evolutionary role of these elements.