title: Genomic subtraction recovers rye-specific DNA elements enriched in the rye genome.
abstract: Repetitive DNA sequence families have been identified in methylated relic DNAs of rye. This study sought to isolate rye genome-specific repetitive elements regardless of the level of methylation, using a genomic subtraction method. The total genomic DNAs of rye-chromosome-addition-wheat lines were cleaved to short fragments with a methylation-insensitive 4-bp cutter, MboI, and then common DNA sequences between rye and wheat were subtracted by annealing with excess wheat genomic DNA. Four classes of rye-specific repetitive elements were successfully isolated from both the methylated and non-methylated regions of the genome. Annealing of the DNA mixture at a ratio of the enzyme-restricted fragments:the sonicated fragments (1:3-1:5) was key to this success. Two classes of repetitive elements identified here belong to representative repetitive families: the tandem 350-family and the dispersed R173 family. Southern blot hybridization patterns of the two repetitive elements showed distinct fragments in methylation-insensitive EcoO109I digests, but continuous smear signals in the methylation-sensitive PstI and SalI digests, indicating that both of the known families are contained in the methylated regions. The subtelomeric tandem 350-family is organized by multimers of a 380-bp-core unit defined by the restriction enzyme EcoO109I. The other two repetitive element classes had new DNA sequences (444, 89 bp) and different core-unit sizes, as defined by methylation-sensitive enzymes. The EcoO109I recognition sites consisting of PyCCNGGPu-multi sequences existed with high frequency in the four types of rye repetitive families and might be a useful tool for studying the genomic organization and differentiation of this species.
authors.affiliation: Tottori University, Koyama-cho, Japan. tomita@muses.tottori-u.ac.jp
authors.forename: Motonori
authors.initials: M
authors.lastname: Tomita
authors.forename: Keiichi
authors.initials: K
authors.lastname: Akai
authors.forename: Takayoshi
authors.initials: T
authors.lastname: Morimoto
mesh_terms: D018744:DNA, Plant / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*; D012434:Secale / Q000235:genetics*
chemical_list: D018744:DNA, Plant