Fine organization of genomic regions tagged to the 5S rDNA locus of the bread wheat 5B chromosome

Abstract

BackgroundThe multigene family encoding the 5S rRNA, one of the most important structurally-functional part of the large ribosomal subunit, is an obligate component of all eukaryotic genomes. 5S rDNA has long been a favored target for cytological and phylogenetic studies due to the inherent peculiarities of its structural organization, such as the tandem arrays of repetitive units and their high interspecific divergence. The complex polyploid nature of the genome of bread wheat, Triticum aestivum, and the technically difficult task of sequencing clusters of tandem repeats mean that the detailed organization of extended genomic regions containing 5S rRNA genes remains unclear. This is despite the recent progress made in wheat genomic sequencing. Using pyrosequencing of BAC clones, in this work we studied the organization of two distinct 5S rDNA-tagged regions of the 5BS chromosome of bread wheat.ResultsThree BAC-clones containing 5S rDNA were identified in the 5BS chromosome-specific BAC-library of Triticum aestivum. Using the results of pyrosequencing and assembling, we obtained six 5S rDNA- containing contigs with a total length of 140,417 bp, and two sets (pools) of individual 5S rDNA sequences belonging to separate, but closely located genomic regions on the 5BS chromosome. Both regions are characterized by the presence of approximately 70–80 copies of 5S rDNA, however, they are completely different in their structural organization. The first region contained highly diverged short-type 5S rDNA units that were disrupted by multiple insertions of transposable elements. The second region contained the more conserved long-type 5S rDNA, organized as a single tandem array. FISH using probes specific to both 5S rDNA unit types showed differences in the distribution and intensity of signals on the chromosomes of polyploid wheat species and their diploid progenitors.ConclusionA detailed structural organization of two closely located 5S rDNA-tagged genomic regions on the 5BS chromosome of bread wheat has been established. These two regions differ in the organization of both 5S rDNA and the neighboring sequences comprised of transposable elements, implying different modes of evolution for these regions.Electronic supplementary materialThe online version of this article (doi: 10.1186/s12870-017-1120-5) contains supplementary material, which is available to authorized users.

The Ribosomal DNA Loci of the Ancient Monocot Pistia stratiotes L. (Araceae) Contain Different Variants of the 35S and 5S Ribosomal RNA Gene Units

“…Based on the deduced rRNA secondary structure ( Figure 4 ), these variants appear to be pseudogenes. Similar degraded 5S rDNA sequences have been described for many eukaryotic organisms, especially fishes ( Rebordinos et al, 2013 ; Barman et al, 2016 ), crustaceans ( Perina et al, 2011 ), and plants ( Sergeeva et al, 2017 ; Volkov et al, 2017 ). Other molecular pathways than those leading to “concerted evolution” likely contribute to shaping the landscape of plant 5S rDNA ( Nei and Rooney, 2005 ).…”

Mosaic Arrangement of the 5S rDNA in the Aquatic Plant Landoltia punctata (Lemnaceae)

“…The 5S rDNA is especially well suited for such studies, due to the smaller size of its repeat units, making the sequences technically easier to handle compared to the much larger 45S rDNA, and to the higher variability exhibited by 5S rDNA NTSs relative to those of the 45S rDNA. The 5S rDNA loci have been characterized for representatives of numerous plant taxa to reveal phylogenetic relationships ( Baker et al, 2000 ; Pan et al, 2000 ; Röser et al, 2001 ), genome evolution ( Kellogg and Appels, 1995 ; Allaby and Brown, 2001 ; Simon et al, 2018 ), and the subgenome composition of polyploids ( Kovarik et al, 2008 ; Baum and Feldman, 2010 ; Sergeeva et al, 2017 ; Volkov et al, 2017 ), natural hybrids, and artificial hybrids ( Zanke et al, 1995 ; Fulnecek et al, 2002 ; Matyácek et al, 2002 ; Volkov et al, 2007 ; Mahelka et al, 2013 ).…”

Features of the organization of bread wheat chromosome 5BS based on physical mapping

“…In particular, gaps between contigs if they are present, tend to overlap with regions of tandem repeats. The analysis of the position of ribosomal RNA genes based on sequencing of the 5B BAC clones showed that the gap between contigs coincides with the region of tandemly repeated 5S RNA genes [ 46 ]. Thus, the distribution of short contigs along the chromosome most likely suggests that these regions are enriched for tandem repeats and vice versa, the distribution of longer regions indicates the presence of extended gene-coding regions.…”