Molecular cloning and characterization of an unusually large intergenic spacer from the Nor-B2 locus of hexaploid wheat

The Hordeum bulbosum 25S-18S rDNA region: comparison with Hordeum vulgare and other Triticeae

Hordeum vulgare and Hordeum bulbosum are two closely related barley species, which share a common H genome. H. vulgare has two nucleolar organizer regions (NORs), while the NOR of H. bulbosum is only one. We sequenced the 2.5 kb 25S-18S region in the rDNA of H. bulbosum and compared it to the same region in H. vulgare as well as to the other Triticeae. The region includes an intergenic spacer (IGS) with a number of subrepeats, a promoter, and an external transcribed spacer (5'ETS). The IGS of H. bulbosum downstream of 25S rRNA contains two 143-bp repeats and six 128-bp repeats. In contrast, the IGS in H. vulgare contains an array of seven 79-bp repeats and a varying number of 135-bp repeats. The 135-bp repeats in H. vulgare and the 128-bp repeats in H. bulbosum show similarity. Compared to H. vulgare, the 5'ETS of H. bulbosum is shorter. Additionally, the 5'ETS regions in H. bulbosum and H. vulgare diverged faster than in other Triticeae genera. Alignment of the Triticeae promoter sequences suggests that in Hordeum, as in diploid Triticum, transcription starts with guanine and not with adenine as it is in many other plants.

Mapping of unmethylated sites in rDNA repeats in barley NOR deletion line

Extensive cytosine methylation is characteristic of plant rDNA. Evidence exists, however, that the active rRNA genes are less methylated. In this work we report on the mapping of unmethylated CCGG sites in Hordeum vulgare rDNA repeats by digestion with methylation sensitive restriction enzyme HpaII and indirect end-labeling of the generated fragments. For mapping we used genomic DNA from barley deletion line with a single NOR on chromosome 5H. This NOR is more active in order to compensate for the missing NOR 6H. The enhanced NOR 5H activity in the deletion mutant is not due to higher multiplicity of the rRNA genes or, as sequencing showed, to changes in the subunit structure of the intergenic spacer. The HpaII sites in barley rDNA are heavily methylated. Nevertheless, a fraction of the rDNA repeats is hypomethylated with unmethylated CCGG sites at various positions. One unmethylated CCGG sequence is close to the transcription start site, downstream of the 135bp subrepeats. Unmethylated sites are also present in the external transcribed spacer and in the genes coding mature rRNAs. The patterns of unmethylated sites in the barley deletion line and in lines with two NORs were compared. It is hypothesized that the occurrence of unmethylated sites on a fixed subset of rDNA repeats correlates with their transcriptional activity.

Within- and between-individual length heterogeneity of the rDNA-IGS in Miscanthus sinensis var. glaber (Poaceae): phylogenetic analyses

The variability in the intergenic spacer (IGS) region between 17S and 25S rRNA genes of ribosomal DNA (rDNA) gene family was surveyed in Miscanthus sinensis var. glaber. Length heterogeneity, with sizes from 1782 to 2212 base pairs, of the IGS resulted from the variation of copy numbers of the A and B subrepeats. These repeated elements were located upstream of the presumptive polymeraseII promoter, which was the region corresponding to the nontranscribed spacer (NTS). Length heterogeneity was detected both within and between individuals of Miscanthus sinensis var. glaber. Neighbor-joining analyses of repetitive A elements indicated that both unequal crossing-over and preferential conversion may have affected the hot-spot regions of the IGS in concert. Within-individual polymorphism and the reconstructed phylogeny suggested that interspecific hybridization has also contributed to length heterogeneity.