Conservation and loss of ribosomal RNA gene sites in diploid and polyploid Fragaria (Rosaceae)

Abstract

BackgroundThe genus Fragaria comprises species at ploidy levels ranging from diploid (2n = 2x = 14) to decaploid (2n = 10x = 70). Fluorescence in situ hybridization with 5S and 25S rDNA probes was performed to gather cytogenetic information that illuminates genomic divergence among different taxa at multiple ploidy levels, as well as to explore the evolution of ribosomal RNA genes during polyploidization in Fragaria.ResultsRoot tip cells of diploid taxa were typified by two 5S and six 25S rDNA hybridization signals of varying intensities, providing a baseline for comparisons within the genus. In three exceptional diploid genotypes, F. nilgerrensis (CFRA 1358 and CFRA 1825) and F. vesca 'Yellow Wonder', two 5S but only four 25S rDNA sites were found but with differing site losses. The numbers of 5S and 25S rDNA signals, respectively were three and nine in a triploid F. ×bifera accession, and were four and twelve in three tetraploids, thus occurring in proportional 1.5× and 2× multiples of the typical diploid pattern. In hexaploid F. moschata, a proportional multiple of six 5S rDNA sites was observed, but the number of 25S rDNA sites was one or two less than the proportionate prediction of eighteen. This apparent tendency toward rDNA site loss at higher ploidy was markedly expanded in octoploids, which displayed only two 5S and ten 25S rDNA sites. In the two decaploids examined, the numbers of 5S and 25S rDNA signals, respectively, were four and fifteen in F. virginiana subsp. platypetala, and six and twelve in F. iturupensis.ConclusionsAmong diploid Fragaria species, a general consistency of rDNA site numbers implies conserved genomic organization, but highly variable 25S signal sizes and intensities and two instances of site loss suggest concurrent high dynamics of rDNA copy numbers among both homologs and non-homologs. General conservation of rDNA site numbers in lower ploidy, but marked site number reductions at higher ploidy levels, suggest complex evolution of rDNA sites during polyploidization and/or independent evolutionary pathways for 6x versus higher ploidy strawberries. Site number comparisons suggest common genomic composition among natural octoploids, and independent origins of the two divergent decaploid accessions.

Intraspecific polymorphism of ribosomal DNA loci number and morphology in Brachypodium pinnatum and Brachypodium sylvaticum

“…It was observed e.g. in Trifolium [45], Lupinus angustifolius [46] and Fragaria species [47]. Variety in rDNA hybridisation signal intensity between homologues is not common, but it was reported in Hypochaeris spathulata, where the mechanism of the changes was postulated to be mainly unequal crossing-over [48].…”

“…Moreover, the distal position of rDNA may facilitate sequence association during meiosis that could lead to unequal exchanges of rDNA repeats and eventually a change of copy number at both homologous and non-homologous sites. Variation in locus number limited only to terminally located rDNA sequences was observed in Phaseolus [49] and Fragaria [47], but in some species, e.g. Brassica, both types of rDNA are highly variable, irrespective of their chromosomal position [14].…”

FISH mapping of 35S and 5S rRNA genes inArtemisiasubgenusDracunculus(Asteraceae): changes in number of loci during polyploid evolution and their systematic implications

“…Furthermore, non‐proportional increases in rDNA loci number in polyploid taxa with respect to their diploid counterparts have been reported in several genera (e.g. Hanson et al ., ; Mishima et al ., ; Liu & Davis, ) and attributed to either unequal homoeologous exchange or spontaneous elimination of chromosome fragments (Zhang & Sang, ; Pontes et al ., ; Weiss‐Schneeweiss et al ., ). Whatever the explanation, it seems clear that the polyploid species belonging to this Eurasian grade of Artemisia spp.…”

Two reported cytotypes of the emergent orchid model species Erycina pusilla are two different species

“…Several cases of 5S rDNAderived sequences being found within transposable elements have been reported (Kapitonov and Jurka 2003;Kalendar et al 2008). By contrast, loss of rDNA loci during evolution has occurred in Brassicaceae and Rosaceae (Mishima et al 2002;Hasterok et al 2006;Liu and Davis 2011). However, the exact mechanism and biological consequence of the variable number of 5S rDNA loci between these two cytotypes remain unknown.…”