Abstract
BackgroundPolyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal structure, molecular organization and evolution of ribosomal DNA (rDNA) in nightshade, Atropa belladonna (fam. Solanaceae), one of the oldest known allohexaploids among flowering plants. Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies.ResultsMolecular cloning and nucleotide sequencing of A. belladonna 45S rDNA repeats revealed a general structure characteristic of other Solanaceae species, and a very high sequence similarity of two length variants, with the only difference in number of short IGS subrepeats. These results combined with the detection of three pairs of 45S rDNA loci on separate chromosomes, presumably inherited from both tetraploid and diploid ancestor species, example intensive sequence homogenization that led to substitution/elimination of rDNA repeats of one parent. Chromosome silver-staining revealed that only four out of six 45S rDNA sites are frequently transcriptionally active, demonstrating nucleolar dominance. For 5S rDNA, three size variants of repeats were detected, with the major class represented by repeats containing all functional IGS elements required for transcription, the intermediate size repeats containing partially deleted IGS sequences, and the short 5S repeats containing severe defects both in the IGS and coding sequences. While shorter variants demonstrate increased rate of based substitution, probably in their transition into pseudogenes, the functional 5S rDNA variants are nearly identical at the sequence level, pointing to their origin from a single parental species. Localization of the 5S rDNA genes on two chromosome pairs further supports uniparental inheritance from the tetraploid progenitor.ConclusionsThe obtained molecular, cytogenetic and phylogenetic data demonstrate complex evolutionary dynamics of rDNA loci in allohexaploid species of Atropa belladonna. The high level of sequence unification revealed in 45S and 5S rDNA loci of this ancient hybrid species have been seemingly achieved by different molecular mechanisms.
Highlights
Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes
After double Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) probes, hybridization signals specific for 5S rDNA and 45S rDNA were observed on separate chromosomes, indicating that there is no co-localization of 5S and 45S rDNA gene clusters
Chromosome staining with chromomycin A3 (CMA) and FISH experiments conducted in our study demonstrated that three loci of 45S rDNA are present on six different chromosomes
Summary
Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Solanaceae), one of the oldest known allohexaploids among flowering plants Because of their abundance and specific molecular organization (evolutionarily conserved coding regions linked to variable intergenic spacers, IGS), 45S and 5S rDNA are widely used in plant taxonomic and evolutionary studies. Recent advances in plant genome and genomics research clearly demonstrate that hybridization/ polyploidization involves intensive genomic rearrangements including exchanges between genomes, and loss or variation of gene copies and expression. These molecular processes are fundamental for species adaptive evolution and performance. To learn more about the origin and genome evolution of this ancient natural polyploid, we studied genomic and molecular organization of the Atropa belladonna ribosomal DNA (rDNA)
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