Shokhrina & Gontcharov. Structure of the nuclear ribosomal intergenic spacer region (IGS) in some species of Crassulaceae DC. In: The East Asian Flora: and its role in the formation of the world’s vegetation

Structure of the nuclear ribosomal intergenic spacer region (IGS) in some species of Crassulaceae DC

Valentina SHOKHRINA¹ & Andrey GONTCHAROV²
¹ School of Natural Sciences, Far-Easter Federal University, Vladivostok, Russia
² Institute of Biology and Soil Science FEB RAS, Vladivostok, Russia

Eukaryotic rRNA genes are arranged in tandem repeats separated by intergenic spacer region. Typically in plants IGS varies in length from about 2 kb in to 12 kb and contains different internal subrepeats. Some of these repetitive sequences contain promoters and enhancers duplications playing an important role in transcription and processing of rRNA genes. We studied structure organization and evolution of the IGS rDNA in some representatives of the family Crassulaceae and assessed this region as a potential phylogenetic marker. IGS was amplified with primes as a complement to the conservative areas of 26S (domains G19 and H1) and the 5' end of 18S rDNA. Successful amplification and sequencing of the spacer was achieved only in 57 out of 117 studied specimens. These sequences ranged from ca. 1400 bp to 220-280 bp only in some specimens due to the extensive deletions in non-coding spacer region (predominantly 3'ETS) and in the 3' end of 26S exon. Only 120-280 bp corresponding to the 5'ETS (if present) were relatively conserved in the sequences obtained. Search for subrepeats in the crassulacean IGS revealed only short (10-15 bp) repeated motives positioned 140-600 bp apart from each other. It is unlikely that these motives represent true subrepeats that are typically much longer (> 100-150 bp) and follow one another in the IGS sequence. It should be noted that in the specimens studied TATA-motif(binding site of RNA polymerase I) was not conservative. Three variants of this motif were found and in some short sequences it was completely lacking. The sequences were grouped into 8 types according to the presence of deletions in the 3' end of 26S exon and specific TATA-motifsequence. Several sequences in our data set that shared features of two different IGS types. This fact suggests that some populations may have originated by hybridization. It is likely that rDNAintergenic spacer in the family Crassulaceae evolves by three different ways: extensive deletions in the spacer sometimes involving flanking portion of the 26S exon, point mutations and indels in the 5' ETS and exchange of large portions between parental IGS sequences during hybridization.