Coe1 in Beta vulgaris L. Has a Tnp2-Domain DNA Transposase Gene within Putative LTRs and Other Retroelement-Like Features

Abstract

We describe discovery in Beta vulgaris L. of Coe1, a DNA transposase gene within putative long terminal repeats (LTRs), and other retrotransposon-like features including both a retroviral-like hypothetical gene and an Rvt2-domain reverse transcriptase pseudogene. The central DNA transposase gene encodes, in eight exons, a predicted 160-KDa protein producing BLAST alignments with En/Spm-type transposons. Except for a stop signal, another ORF encodes a Ty1-copia-like reverse transcriptase with amino acid sequence domain YVDDIIL. Outside apparent LTRs, an 8-mer nucleotide sequence motif CACTATAA, near or within inverted repeat sequences, is hypothetical extreme termini. A genome scan of Arabidopsis thaliana found another example of a Tnp2-domain transposase gene within an apparent LTR-retrotransposon on chromosome 4.

A Nest of LTR Retrotransposons Adjacent the Disease Resistance‐Priming Gene NPR1 in Beta vulgaris L. U.S. Hybrid H20

“…A genomic NPR1 disease resistance priming gene-carrying BAC [7–9] was subjected to LTR_STRUC and LTR FINDER analyses, and two distinct full-length LTR retrotransposons were identified (Figure 1). Depicted are RTR1 and RTR2, two LTR retrotransposons that we also term SCHULTE and SCHMIDT, respectively, as well as a previously described element, Coe1 , a DNA transposase gene within apparent LTRs and other retrotransposon-like features [7].…”

“…Coe1 , a DNA transposon within apparent LTRs and other retrotransposon-like features, was discovered on a sugarbeet genomic BAC carrying the NPR1 disease resistance-priming gene [ 7 – 9 ]. This recent discovery in Beta vulgaris of a unique 16.3 Kb CACTA En/Spm -like transposon named Coe1 [ 7 ] was followed by the finding of conserved microsynteny of NPR1 with another core plant gene whose predicted product has high similarity to a DNA-binding HSF protein [ 8 ].…”

Conserved Microsynteny ofNPR1with Genes Encoding a Signal Calmodulin-Binding Protein and a CK1-Class Protein Kinase inBeta vulgarisand Two Other Eudicots

“…Coe1 , previously identified by our group using LTR_STRUC analysis as a novel composite of class I and class II elements [ 25 ], has three genes. Briefly, one gene has a single exon ORF1 ( Table 1 ), encoding a retroelement-like protein.…”

Root and Tuber Crops

“…A terminal constriction is on chromosome 1 and carries the major cluster of 18S-5.8S-25S ribosomal RNA genes. Highly repetitive DNA sequences comprise >60% of the beet genome (Flavell et al, 1974) and consist of numerous families of short (140-160 nt) repeating units present at high copy numbers (10 5 -10 6 copies/genome) (Schmidt and Heslop-Harrison, 1996), and various classes of transposable elements (Schmidt and Heslop-Harrison, 1998;Staginnus et al, 2001;Dechyeva and Schmidt, 2006;Kuykendall et al, 2008;Menzel et al, 2008;Kuykendall et al, 2009). Organization of centromeric regions has been of interest to understand the molecular processes of chromosome segregation, to understand the process of non-disjunction, and to create plant artificial chromosomes (Gindullis et al, 2001a;Menzel et al, 2008;Jacobs et al, 2009).…”