Abstract
A nest of long terminal repeat (LTR) retrotransposons (RTRs), discovered by LTR_STRUC analysis, is near core genes encoding the NPR1 disease resistance-activating factor and a heat-shock-factor-(HSF-) like protein in sugarbeet hybrid US H20. SCHULTE, a 10 833 bp LTR retrotransposon, with 1372 bp LTRs that are 0.7% divergent, has two ORFs with unexpected introns but encoding a reverse transcriptase with rve and Rvt2 domains similar to Ty1/copia-type retrotransposons and a hypothetical protein. SCHULTE produced significant nucleotide BLAST alignments with repeat DNA elements from all four families of plants represented in the TIGR plant repeat database (PRD); the best nucleotide sequence alignment was to ToRTL1 in Lycopersicon esculentum. A second sugarbeet LTR retrotransposon, SCHMIDT, 11 565 bp in length, has 2561 bp LTRs that share 100% identity with each other and share 98-99% nucleotide sequence identity over 10% of their length with DRVs, a family of highly repetitive, relatively small DNA sequences that are widely dispersed over the sugarbeet genome. SCHMIDT encodes a complete gypsy-like polyprotein in a single ORF. Analysis using LTR_STRUC of an in silico deletion of both of the above two LTR retrotransposons found that SCHULTE and SCHMIDT had inserted within an older LTR retrotransposon, resulting in a nest that is only about 10 Kb upstream of NPR1 in sugarbeet hybrid US H20.
Highlights
Retrotransposons are recognized as movers and shapers of plant genome evolution
That retrotransposon elements account for much of the sugarbeet (Beta vulgaris L.) genome was shown by the identification [3] of repetitive DNA sequences in Beta vulgaris similar to long interspersed nuclear elements (LINEs), a type of retrotransposon without long terminal repeats (LTRs), and other repetitive DNA sequences that resembled LTR retrotransposons of the Ty1-copia class
A genomic NPR1 disease resistance priming gene-carrying bacterial artificial chromosome (BAC) [7,8,9] was subjected to LTR STRUC and LTR FINDER analyses, and two distinct full-length LTR retrotransposons were identified (Figure 1)
Summary
Retrotransposons are recognized as movers and shapers of plant genome evolution (see reviews [1, 2]). That retrotransposon elements account for much of the sugarbeet (Beta vulgaris L.) genome was shown by the identification [3] of repetitive DNA sequences in Beta vulgaris similar to long interspersed nuclear elements (LINEs), a type of retrotransposon without long terminal repeats (LTRs), and other repetitive DNA sequences that resembled LTR retrotransposons of the Ty1-copia class. Prior to the present study, pDRV sequences [5] were known as a family of short highly amplified DNA repeats shown by fluorescent in situ hybridization (FISH). Polymerase chain reaction (PCR) and fluorescent in situ hybridization (FISH) were used [6] to identify and to establish an abundance of En/Spm-like transposons in sugarbeet
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