Identification and distribution of seven classes of middle-repetitive DNA in the Arabidopsis thaliana genome.

In order to analyse further the genomic distribution of repetitive sequences in the Arabidopsis genome, we have identified and characterized seven novel repetitive sequences. Analysis of genomic representation, genomic location and DNA sequence divided the seven repeated sequences into two classes. The first was represented by three cosmid subclones (182A, 74A, 191A) carrying sequences that hybridised to up to 20 genomic fragments and showed sequence homology to the genes, Arabidopsis CCR2, Arabidopsis MYB and to various ATP-binding transport proteins. These multigene families mapped to various positions within the genome, as judged by hybridization to YAC clones constituting the Arabidopsis physical map. The second class was represented by four cosmid subclones (106B, 164A, 163A, 278A) that hybridised to between 20 and 300 genomic fragments. One of these, 106B, is a diverged, partial copy of the LTR of the Arabidopsis retrotransposon Athila. The other three sequences showed no homology to known genes or proteins. The distribution of these sequences on chromosome 4 was analysed and sequences hybridizing to 106B, 164A and 163A were found exclusively at the centromeric region of this chromosome. Their detailed arrangement at the centromeric region of chromosome 4, relative to other repeated sequence families and single copy sequences, was determined.