Abstract
The genus Rosa comprises more than 100 woody species characterized by intensive hybridization, introgression, and an overall complex evolutionary history. Besides many diploid species (2n = 2x = 14) polyploids ranging from 3x to 10x are frequently found. Here we analyzed 5S ribosomal DNA in 19 species covering two subgenera and the major sections within subg. Rosa. In addition to diploids and polyploids with regular meiosis, we focused on 5x dogroses (Rosa sect. Caninae), which exhibit an asymmetric meiosis differentiating between bivalent- and univalent-forming chromosomes. Using genomic resources, we reconstructed 5S rDNA units to reveal their phylogenetic relationships. Additionally, we designed locus-specific probes derived from intergenic spacers (IGSs) and determined the position and number of 5S rDNA families on chromosomes. Two major 5S rDNA families (termed 5S_A and 5S_B, respectively) were found at variable ratios in both diploid and polyploid species including members of the early diverging subgenera, Rosa persica and Rosa minutifolia. Within subg. Rosa species of sect. Rosa amplified the 5S_A variant only, while taxa of other sections contained both variants at variable ratios. The 5S_B family was often co-localized with 35S rDNA at the nucleolar organizer regions (NOR) chromosomes, whereas the co-localization of the 5S_A family with NOR was only exceptionally observed. The allo-pentaploid dogroses showed a distinct distribution of 5S rDNA families between bivalent- and univalent-forming chromosomes. In conclusion, two divergent 5S rDNA families dominate rose genomes. Both gene families apparently arose in the early history of the genus, already 30 myrs ago, and apparently survived numerous speciation events thereafter. These observations are consistent with a relatively slow genome turnover in the Rosa genus.
Highlights
Ribosomal RNA genes encoding 5S, 5.8S, 18S, and 26S ribosomal RNA are ubiquitous in plants and are organized into arrays containing hundreds to thousands of tandem units at one or more genomic loci (Hemleben et al, 1988; Nieto Feliner and Rossello, 2012; Roa and Guerra, 2012)
Intragenomic homogeneity was high, and no significant SNPs were revealed in mapping experiments
We found that the genus is dominated by essentially two 5S rDNA families which markedly differ in intergenic spacers (IGSs) and date back to the genus’ base
Summary
Ribosomal RNA genes (rDNA) encoding 5S, 5.8S, 18S, and 26S ribosomal RNA are ubiquitous in plants and are organized into arrays containing hundreds to thousands of tandem units at one or more genomic loci (Hemleben et al, 1988; Nieto Feliner and Rossello, 2012; Roa and Guerra, 2012). The units within the 5S arrays retain a high degree of identity due to homogenizing forces referred to as concerted evolution (Dover, 1982; Eickbush and Eickbush, 2007) where unequal crossing-over and gene conversion are major forces driving the process. Regardless of the mechanism, numerous factors such as the number of arrays, their mutation rate, formation of new variants, the intensity of natural selection, or efficient population size can affect homogenization of repeats (Dover, 1982; Ohta, 1984; Nagylaki, 1990). Two or more variants differing in the length and nucleotide sequence may simultaneously exist per genome (Cronn et al, 1996; Volkov et al, 2001, 2017; Fulnecek et al, 2002; Pastova et al, 2019; Benson et al, 2020)
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