<i>Superior</i>: A Novel Repetitive DNA Element Dispersed in the Rye Genome

Abstract

A new class of rye-specific repetitive DNA elements designated Superior has been identified. The rye genome library was constructed by cleavage with EcoO109I, the recognition sites of which consisted of 5′-PuGGNCCPy-3′ multi-sequences and were present with high frequency in the rye repetitive families. A novel 495-bp segment enriched in the rye genome was successfully identified. Southern blot hybridization and fluorescence in situ hybridization using the repetitive element showed a dispersed array through all 7 chromosomes of rye. The repetitive DNA element did not share identity with known class I or class II transposable elements or known repetitive elements. Only several DNA segments in BACs and ESTs of barley showed partial similarity to the repetitive DNA element in all DNA databases of living species. The new class of dispersed repetitive elements was designated Superior. The entire structure of Superior was determined by using a rye genomic library of lambda FIXII screened by the 495-bp probe. The Superior family consisted of 1,292-bp, 1,324-bp, and 1,432-bp elements in which the 5′ regions had been destroyed, indicating the presence of considerable structural diversity. Superior might be a useful tool for studying genomic organization and differentiation.

Transposable elements and plant genome evolution

“…For example, this was demonstrated for retrotransposons BARE 1 in barley, Grande in maize, rider in tomato, and various TEs in sorghum (Suoniemi et al, 1996;Muthukumar, Ben netzen, 2004;Gómez et al, 2006;Cheng et al, 2009). Two new classes of transcriptionally active transposon like sequences Revolver and Superior were discovered in rye (Tomita et al, 2008(Tomita et al, , 2009.…”

Differential Effects of High-Temperature Stress on Nuclear Topology and Transcription of Repetitive Noncoding and Coding Rye Sequences

“…2); one of them -rice osa-MIR2921 (accession MI0013263) -is implicated in the plant stress response [Sanan-Mishra et al, 2009]. The Superior repetitive element dispersed throughout rye chromosomes was also shown by Northern blots to be actively transcribed, and their RNA stem structure was suggested to indicate a possible functional role [Tomita et al, 2009]. …”

Rye chromosome-specific polymerase chain reaction products developed by primers designed from theEcoO109I recognition site

“…To amplify chromosome-specific DNA fragments in PCR, we focused on the EcoO109I restriction enzyme site sequence, 5′-PuGGNCCPy-3′, which is scattered across the entire rye genome (Tomita et al 2009a(Tomita et al , 2009b(Tomita et al , 2010. There are 16 possible EcoO109I site sequences, owing to a combination of adenine or guanine at the 5′ end, any one of the four bases in the middle, and cytosine or thymine at the 3′ end.…”

“…On the basis of the analysis of the repetitive units, we speculated that a large number of EcoO109I restriction enzyme recognition sites are present in the rye genome (Tomita et al 2009a(Tomita et al , 2009b(Tomita et al , 2010. EcoO109I, originated from Escherichia coli bacterium H709c strain, recognizes 5′-PuGGNCCPy-3′ (Mise and Nakajima 1985).…”