Length and sequence heterogeneity in 5S rDNA ofPopulus deltoides

Abstract

The 5S rRNA genes and their associated non-transcribed spacer (NTS) regions are present as repeat units arranged in tandem arrays in plant genomes. Length heterogeneity in 5S rDNA repeats was previously identified in Populus deltoides and was also observed in the present study. Primers were designed to amplify the 5S rDNA NTS variants from the P. deltoides genome. The PCR-amplified products from the two accessions of P. deltoides (G3 and G48) suggested the presence of length heterogeneity of 5S rDNA units within and among accessions, and the size of the spacers ranged from 385 to 434 bp. Sequence analysis of the non-transcribed spacer (NTS) revealed two distinct classes of 5S rDNA within both accessions: class 1, which contained GAA trinucleotide microsatellite repeats, and class 2, which lacked the repeats. The class 1 spacer shows length variation owing to the microsatellite, with two clones exhibiting 10 GAA repeat units and one clone exhibiting 16 such repeat units. However, distance analysis shows that class 1 spacer sequences are highly similar inter se, yielding nucleotide diversity (pi) estimates that are less than 0.15% of those obtained for class 2 spacers (pi = 0.0183 vs. 0.1433, respectively). The presence of microsatellite in the NTS region leading to variation in spacer length is reported and discussed for the first time in P. deltoides.

Characterization and physical mapping of nuclear ribosomal RNA (rRNA) genes in the haploid gametophytes of Saccharina japonica (Phaeophyta)

“…Within a single genome, different size classes of 5S rDNA repeat units were detected in other organisms such as Triticum spp. (Baum and Appels 1992), Populus deltoides (Negi et al 2002), and Beta vulgaris subsp. maritima (Turner and Brown 2005), but not in kelps.…”

PCR, sequencing and PCR–RFLP of the 5S‐rRNA‐NTS region as a tool for the DNA fingerprinting of medicinal and aromatic plants

“…[6] The gene is 120 bp long and is associated with spacers of various sizes to form the repeating unit of the tandem arrays. The 120 bp 5S-rRNA gene sequence is highly conserved across species, while the NTS region exhibits variation in base composition and length (in the range 100-800 bp) from species to species, [9] since it is apparently not under the same rigorous selection pressure as in the coding region. [10][11][12] The high level of conservation of the 5S-rRNA gene is associated with the precise function of 5S-rRNA as a component of the large ribosomal subunit in all eukaryotic organisms.…”

“…Some regions of the gene are more conserved than others, which is explained by the regulation of 5S-rRNA transcription. [9] Sequence conservation of the coding regions and high divergence in the spacer regions provide a good model for studying the organization and evolution of multigenes in diff erent plant species. [7,13] Based on these assumptions, variation in the NTS region has been used in a number of plant species for studying intraspecifi c variation, mapping 5S-rDNA arrays, genome evolution and phylogenetic reconstruction.…”

“…[7,13] Based on these assumptions, variation in the NTS region has been used in a number of plant species for studying intraspecifi c variation, mapping 5S-rDNA arrays, genome evolution and phylogenetic reconstruction. [9,10,14] …”

Molecular genetic features of 5S rDNA nontranscribed spacer in Hippophae rhamnoides L.

“…Ещё одной особенностью NTS 5S-рДНК Hippophae rhamnoides L. является присутствие микро-сателлитного локуса (GA) 9 в позиции -252/-235 от начала гена 5S-рРНК. Среди растений подоб-ное явление (но с другими микросателлитными мотивами) описано лишь у Populus deltoides (мотив (GAA) 10-13 ) и ещё у нескольких видов тополей, а также у Lens culinaris (мотив (TA) 6-21 ) [9, 16,17]. Поэтому можно заключить, что NTS 5S-рДНК с микросателлитным мотивом (GA) 9 у растений найден впервые.…”