Survey of transposable elements in sugarcane expressed sequence tags (ESTs)

Abstract

The sugarcane expressed sequence tag (SUCEST) project has produced a large number of cDNA sequences from several plant tissues submitted or not to different conditions of stress. In this paper we report the result of a search for transposable elements (TEs) revealing a surprising amount of expressed TEs homologues. Of the 260,781 sequences grouped in 81,223 fragment assembly program (Phrap) clusters, a total of 276 clones showed homology to previously reported TEs using a stringent cut-off value of e-50 or better. Homologous clones to Copia/Ty1 and Gypsy/Ty3 groups of long terminal repeat (LTR) retrotransposons were found but no non-LTR retroelements were identified. All major transposon families were represented in sugarcane including Activator (Ac), Mutator (MuDR), Suppressor-mutator (En/Spm) and Mariner. In order to compare the TE diversity in grasses genomes, we carried out a search for TEs described in sugarcane related species O.sativa, Z. mays and S. bicolor. We also present preliminary results showing the potential use of TEs insertion pattern polymorphism as molecular markers for cultivar identification.

A Unique Set of 11,008 Onion Expressed Sequence Tags Reveals Expressed Sequence and Genomic Differences between the Monocot Orders Asparagales and Poales[W]

“…Of these, 25% (36 of 145) were homologous with transposases of class-I DNA elements ( Mutator , Ac/Ds, or En/Spm), and the remainder were homologous with polyproteins or reverse transcriptases of class-II RNA elements ( copia , gypsy , or non-long terminal repeat [LTR] retrotransposons). Rossi et al (2001) reported a similar range of TEs among sugarcane ESTs but did not detect non-LTR retroelements. The orientations of BLASTX alignments were inspected to determine whether ESTs matching TEs were products of directionally cloned transcripts and did not represent genomic contamination or read-through from neighboring retrotransposons (Elrouby and Bureau, 2001).…”

The Centromeric Retrotransposons of Rice Are Transcribed and Differentially Processed by RNA Interference

“…Few rice retrotransposon families (Tos10, Tos17-20) are transpositionally active under tissue culture conditions (Hirochika et al 1996;Hirochika 1997). Nevertheless, it has been demonstrated in several species that some retrotransposon families, or rather only some of their copies, are transcriptionally active (Suoniemi et al 1997;Meyers et al 2001;Rossi et al 2001;Vicient et al 2001a,b;Echenique et al 2002;Neumann et al 2003Neumann et al , 2005, which suggests that they can escape from the host silencing mechanisms. CRR transcripts were detected by RT-PCR in all three organs tested (root, leaf, panicle), suggesting that the CRR-related sequences are transcribed constitutively.…”

Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced

“…Although some recent papers describe transcriptional activity of retrotransposons in somatic cells (Rossi et al, 2001;Vicient et al, 2001a;Echenique et al, 2002), it contrasts with many plant retrotransposons, which are transcriptionally silent or are transcriptionally active only during certain stages of plant development (Pouteau et al, 1991;Suoniemi et al, 1996;Turcich et al, 1996) or stress conditions (Hirochika, 1993;Pearce et al, 1996;Grandbastien et al, 1997;Takeda et al, 1998;Kato et al, 1999;Beguiristain et al, 2001). As the transposition of retrotransposons is believed to be regulated mainly on the transcriptional level, such limited activity might evolve in order to suppress deleterious effects of element amplification in the genome (Kumar and Bennetzen, 1999).…”