Malinska & al. • Evolution of rDNA in Tragopogon TAXON 60 (2) • April 2011: 348–354 Ribosomal RNA genes evolution in Tragopogon: A story of New and Old World allotetraploids and the synthetic lines Hana Malinska,1 Jennifer A. Tate,2 Evgeny Mavrodiev,2 Roman Matyasek,1 K. Yoong Lim,3 Andrew R. Leitch,3 Douglas E. Soltis,2 Pamela S. Soltis4 & Ales Kovarik1 1 Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i, Laboratory of Molecular Epigenetics, Královopolská 135, 61265 Brno, Czech Republic 2 Department of Botany, University of Florida, Gainesville, Florida 32611, U.S.A. 3 School of Biological Sciences, Queen Mary, University of London, E1 4NS, U.K. 4 Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611, U.S.A. Authors for correspondence: Hana Malinska, [email protected] and Ales Kovarik, [email protected] Abstract Tragopogon mirus Ownbey and Tragopogon miscellus Ownbey are recent allotetraploids that have formed recurrently within the last 80 years, following the introduction of the diploids T. dubius Scop., T. pratensis L. and T. porrifolius L. from Europe to North America. In some areas, the progenitor diploids still occur along with expanding populations of the allotetra- ploids, and the polyploids at those locations likely represent descendents of the nearby diploids. In most natural populations of T. mirus and T. miscellus, there are far fewer rDNA units of the common parent (T. dubius) than there are of the other diploid parent and in some rarely occurring individuals, one parental locus was >90% deleted. Nevertheless, in contrast to several ancient Old World allotetraploids, gene copies from both parents are readily detected by molecular methods in both T. mirus and T. miscellus. In one population of T. mirus and herbarium specimens collected at the time of species origin the gene ratios were balanced. Several lineages of T. mirus and T. miscellus were recently successfully resynthesized from diploid species. Among 181 synthetic individuals analyzed, we observed frequent deviations from copy­number additivity; that is in most cases, the T. dubius homeologs were reduced in copy number. At the epigenetic level, the genes of T. dubius origin dominate expression in most natural and synthetic allopolyploids. The fact that some rDNA genotypes seen in 80­year­old allopolyploids are already evident in the first generation of synthetic lines supports the hypothesis that the extent and tempo of rDNA homogenization in older allopolyploids is largely influenced by genetic and epigenetic changes in the early generations. Thus, T. mirus and T. miscellus that formed repeatedly in the wild within the last century represent a unique system to study the early stages of genome evolution following interspecific hybridization and genome duplication. This review summarizes recent works on the rDNA chromosomal organization, repeat and loci inheritance and gene expression. Keywords allopolyploid; homogenization; nucleolar dominance; ribosomal DNA; Tragopogon INTRODUCTION problems (Hadac, 1989; Ainouche & al., 2004). The success of newly formed angiosperm polyploids is partly attributable to In 1970, Susumu Ohno promoted the idea that gene and their highly plastic genome structure, as manifested by devia- genome duplications are the principle creative force in evolu- tions from Mendelian inheritance patterns of genetic loci and tion (Ohno, 1970). Perhaps no other group of living organisms chromosome aberrations (Leitch & Leitch, 2008). supports his hypothesis better than land plants. Chromosome Previous studies on natural and synthetic allopolyploids counts and other approaches suggest that between 30% and have shown that united parental genomes undergo active, fast, 100% of angiosperm species are polyploids (Masterson, 1994; and in some cases reproducible and directed processes of ge- Bennett, 2004; Soltis & al., 2009). Genomic studies have re- nome reorganization, probably due to intergenomic interactions vealed that all plant genomes sequenced to date have undergone (Soltis & Soltis, 1995). Reorganizations include both genetic one or more genome wide duplications in their evolutionary and epigenetic changes, which are observable after just a few history (Cui & al., 2006; Fawcett & al., 2009; Van de Peer & generations and even in F1 hybrids (e.g., Dadejova & al., 2007; al., 2009). Interspecific hybridization followed by multiplica- Kopecky & al., 2008; for review, see Chen & Ni, 2006). Most tion of parental chromosome sets is called allopolyploidy and genetic changes involve sequence loss or elimination often is believed to be a major driving force of angiosperm species associated with genome downsizing (Pestsova & al., 1998; evolution (Soltis & Soltis, 1995). Many economically important Kashkush & al., 2002), intergenomic chromosomal transloca- crops (e.g., wheat, oilseed rape, cotton, coffee, banana, tobacco) tions (Kenton & al., 1993), or the expansion of genome­specific are relatively recent allopolyploids (Leitch & Leitch, 2008). transposons (Zhao & al., 1998). Epigenetic silencing of parental The formation of allopolyploid species is, however, not always genes caused by the modification of chromatin is believed to beneficial since rapidly expanding populations of invasive allo­ reconcile regulatory incompatibilities between parental subge- polyploid weeds may cause severe ecological and economic nomes (Adams & Wendel, 2005). In contrast to the evolution of 348 TAXON 60 (2) • April 2011: 348–354 Malinska & al. • Evolution of rDNA in Tragopogon single­copy genes, members of multigene families do not often 2008). Eukaryotes regulate the effective dosage of their rRNA evolve independently, but in a concerted manner. In multigene genes, expressing fewer than half of the genes at the same families, limited sequence variability is often observed among time (Neves & al., 2005). Likewise, genetic hybrids displaying individual copies. Despite this high intraspecific homogeneity, nucleolar dominance transcribe rRNA genes inherited from interspecific divergence is not affected. This phenomenon has one parent, but silence the other parental set (Volkov & al., been called concerted evolution (Arnheim & al., 1980). The 2007). Interplay of DNA methylation, histone modification, underlying molecular processes are unequal crossing over and and chromatin­remodeling activities establishes silencing in gene conversion. The degree of homogenization is thus a result rDNA loci (Preuss & Pikaard, 2007). of the interplay between homogenization processes and novel The evolution of rDNA has stimulated much research. Ex- base substitutions (Schlotterer & Tautz, 1994). pression patterns of rRNA genes have been studied at inter­ In plants, nuclear ribosomal DNA (rDNA) units oc- phase by observing the behavior of nucleoli (Leitch, 2000). cur in tandem arrays at one or several loci (for review see Epigenetic processes can lead to inactivation of entire rDNA Hemleben & Zentgraf, 1994). These rRNA genes, frequently arrays (nucleolar dominance, Honjo & Reeder, 1973; Dadejova used as phylogeny markers, are organized on chromosomes & al., 2007; Preuss & Pikaard, 2007). Sequences can undergo as long arrays of tandemly arranged units. Each large 35S concerted evolution involving sequence homogenization (Do- rDNA unit contains the 18S, 5.8S and 26S rRNA genes, the ver, 1982; Wendel & al., 1995). Finally, the sequence data from internal transcribed spacers (ITS), and the intergenic spacer the internally transcribed spacers (nuclear ribosomal ITS) are (IGS) (Fig. 1). The large polycistronic 35S transcript is endo- regularly used to construct phylogenetic trees (Nieto Feliner nucleotically processed to produce mature rRNA molecules. & Rossello, 2007; Poczai & Hyvonen, 2010). The 5S genes encoding 120 nt transcripts are usually, but not In this review we will summarize the data from previous always (Garcia & al., 2009), located at different chromosomal and ongoing studies in recently formed Tragopogon allotetra- loci than 35S rDNA. The genic regions are highly conserved ploids, focusing on rDNA evolution. even between distally related species, whereas the intra and intergenic regions are highly variable. For example, the se- quence polymorphisms within IGS and ITS are sufficient to THE ORIGIN OF TRAGOPOGON resolve species relationships within most genera (e.g., Lihova ALLOTETRAPLOIDS & al., 2004; for review, see Alvarez & Wendel, 2003). The IGS, which contains the transcriptional start site as well as Tragopogon (Asteraceae) comprises approximately 100– genetic and epigenetic features that influence the regulation 150 species native to Eurasia. Most of them are diploids (2n = of the downstream genes, diverges rapidly, and substantial 12), but at least twelve species are ancient polyploids (2n = 24, differences in structure may occur even within a species (Ben- 36, 56–58) with generally unknown parentages (Mavrodiev nett & Smith, 1991; Skalicka & al., 2003; Komarova & al., & al., 2008). Fig. 1. The chromosomal and genomic structure of rDNA. Clusters of active rRNA genes are often located at the terminal part of the chromo- some, which is cytogenetically revealed as a secondary constriction (upper part). Note, two decondensed domains (arrows) are flanked by knobs of highly condensed rDNA chromatin. Each cluster is composed of hundreds to thousands of units arranged head to tail in tandem. Each unit is composed of conserved genic regions encoding 18S­5.8S­26S rRNA that are separated by the internally transcribed spacers (ITS1,