STRUCTURE AND COMPARATIVE-ANALYSIS OF THE RDNA INTERGENIC SPACER OF BRASSICA-RAPA - IMPLICATIONS FOR THE FUNCTION AND EVOLUTION OF THE CRUCIFERAE SPACER

The sequence of the intergenic spacer (IGS) of the Brassica rapa rDNA was determined and compared with those of other Cruciferae species. In the 3012-bp IGS, two segments of mostly unique sequence flank a 1.5-k b region consisting of two tandem arrays of repeats. A putative transc ription initiation site (TIS) was identified by sequence comparison, 3 95 bp downstream from the repeat region. The intercalating segment dis plays unusual sequence patterns, and modelling of its topology predict s intrinsically bent DNA, with two elements of bending centered at pos itions -118 and -288 relative to the TIS. Comparative analysis of spac ers from Cruciferae, revealed a common organization and high sequence similarity in their 5' and, particularly, 3' regions, whereas the repe at region upstream of TIS diverges rapidly. The conservation of struct ural elements, including the bent DNA upstream from the TIS, is discus sed in light of their possible involvement in the IGS functions and st ructure of spacers in common ancestors. Examination of the Cruciferae spacers shows that, in addition to unequal crossover and gene conversi on, insertional mutagenesis and replication slippage are molecular mec hanisms significantly contributing to their evolution.