Molecular characterization of ribosomal DNA intergenic spacer (IGS) region in pomegranate ( Punica granatum L.).

The large intergenic spacer (IGS) region of rDNA is a valuable DNA sequence because it contains the signals for transcription and processing of rRNAs. In this study, we sequenced and analyzed the complete nucleotide of rDNA IGS region of pomegranate for the first time. This IGS sequence was 3,712 bp in length with GC content of 67.8 %. The sequence analysis indicated that the spacer could be divided into three main regions: a central repetitive region and two flanking unique domains on on both sides of the central area. Central region is composed of two repeat families (A and B), and the third region contained two short direct repeats (C1 and C2). By comparisons with the IGS sequence of other plant species and computer-aided searches, we determined the putative transcription initiation and termination sites, and the large number of methylable sites. The presence of some conserved motifs in this region may play an important role in regulation of rRNA transcription. Taken together, the pomegranate IGS revealed the complex structure. However, its organization and structure are similar to most other rDNA spacers studied. [ABSTRACT FROM AUTHOR]