Structure and evolution of the intergenic region in a ribosomal DNA repeat unit of wheat

The complete nucleotide sequence of the intergenic region between the 25 S and 18 S wheat ribosomal RNA genes has been determined from a 4.6 kb EcoRI-BamHI fragment (1 kb = 10(3) bases or base-pairs) subcloned from the plasmid pTa71. Within this subclone the intergenic DNA is flanked by the 3' end of the 25 S and the 5' end of the 18 S ribosomal RNA sequences. Four repeat families are present within the intergenic region. The major repeat family A, consists of 12 direct repeat units of 135 or 136 base-pairs (bp) flanked by diverged truncated copies. Within each A repeat a subrepeat structure has been revealed. Family B, which is localized to the 5' side of the A repeats, contains three repeat units, one of 152 bp, the second of 150 bp and a truncated unit of 107 bp. Family C, which is localized in the transcribed rRNA precursor, consists of two direct repeat units of 172 and 174 bp and possesses some short subrepeat motifs. The C repeats may have evolved by and diverged from one another by the insertion of short transposable sequences. Family D consists of two direct repeat units of 30 bp located 5' to the start of transcription. Statistical analysis of repeat family A showed that there is a significant association between the similarity of any two repeat units and their distance apart in the array. The near identity of members of the A family is maintained presumably by processes such as unequal crossing over and gene conversion, but the members at each end of the array show more divergence. Sequence motifs in the A and C repeat families and in other regions including the 5' end of 18 S RNA are related, implying that much of the intergenic DNA may have evolved from a few short ancestral sequences. The B and D repeats or their equivalent are not found in a maize ribosomal DNA repeat unit. The DNA in the external transcribed spacer DNA 5' to the 18 S RNA sequence is longer in wheat than in maize. This is due principally to two duplications and insertion of a sequence with dyad symmetry in the wheat gene.