Polyploidy, the possession of more than 2 complete genomes, is a major force in plant evolution known to affect the genetic and genomic constitution and the phenotype of an organism, which will have consequences for its ecology and geography as well as for lineage diversification and speciation. In this review, we discuss phylogenetic patterns in the incidence of polyploidy including possible underlying causes, the role of polyploidy for diversification, the effects of polyploidy on geographical and ecological patterns, and putative underlying mechanisms as well as chromosome evolution and evolution of repetitive DNA following polyploidization. Spurred by technological advances, a lot has been learned about these aspects both in model and increasingly also in nonmodel species. Despite this enormous progress, long-standing questions about polyploidy still cannot be unambiguously answered, due to frequently idiosyncratic outcomes and insufficient integration of different organizational levels (from genes to ecology), but likely this will change in the near future. See also the sister article focusing on animals by Choleva and Janko in this themed issue.

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Evolutionary Consequences, Constraints and Potential of Polyploidy in Plants

Summary
The perennial sunflower Helianthus tuberosus, known as Jerusalem Artichoke or Sunchoke, was cultivated in eastern North America before European contact. As such, it represents one of the few taxa that can support an independent origin of domestication in this region. Its tubers were adopted as a source of food and forage when the species was transferred to the Old World in the early 1600s, and are still used today.
Despite the cultural and economic importance of this tuber crop species, its origin is debated. Competing hypotheses implicate the occurrence of polyploidization with or without hybridization, and list the annual sunflower H. annuus and five distantly related perennial sunflower species as potential parents.
Here, we test these scenarios by skimming the genomes of diverse populations of Jerusalem Artichoke and its putative progenitors. We identify relationships among Helianthus taxa using complete plastomes (151 551 bp), partial mitochondrial genomes (196 853 bp) and 35S (8196 bp) and 5S (514 bp) ribosomal DNA.
Our results refute the possibility that Jerusalem Artichoke is of H. annuus ancestry. We provide the first genetic evidence that this species originated recursively from perennial sunflowers of central-eastern North America via hybridization between tetraploid Hairy Sunflower and diploid Sawtooth Sunflower.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12560

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

 Premise of the study: Hybridization and polyploidization (allopolyploidy) are ubiquitous in the evolution of plants, but tracing the origins and subsequent evolution of the constituent genomes of allopolyploids has been challenging. Genome doubling greatly complicates genetic analyses, and this has long hindered investigation in that most allopolyploid species are “ nonmodel ” organisms. However, recent advances in sequencing and genomics technologies now provide unprecedented opportunities to analyze numerous genetic markers in multiple individuals in any organism.  Methods: Here we review the application of next-generation sequencing technologies to the study of three aspects of allopolyploid genome evolution: duplicated gene loss and expression in two recently formed Tragopogon allopolyploids, intergenomic interactions and chromosomal evolution in Tragopogon miscellus , and repetitive DNA evolution in Nicotiana allopolyploids.  Key results: For the fi rst time, we can explore on a genomic scale the evolutionary processes that are ongoing in natural allopolyploids and not be restricted to well-studied crops and genetic models.  Conclusions: These approaches can be easily and inexpensively applied to many other plant species — making any evolutionarily provocative system a new “ model ” system.

https://bsapubs.onlinelibrary.wiley.com/doi/pdf/10.3732/ajb.1100395

Next-generation sequencing and genome evolution in allopolyploids.

Paphiopedilum is a horticulturally and ecologically important genus of ca. 80 species of lady's slipper orchids native to Southeast Asia. These plants have long been of interest regarding their chromosomal evolution, which involves a progressive aneuploid series based on either fission or fusion of centromeres. Chromosome number is positively correlated with genome size, so rearrangement processes must include either insertion or deletion of DNA segments. We have conducted Fluorescence In Situ Hybridization (FISH) studies using 5S and 25S ribosomal DNA (rDNA) probes to survey for rearrangements, duplications, and phylogenetically-correlated variation within Paphiopedilum. We further studied sequence variation of the non-transcribed spacers of 5S rDNA (5S-NTS) to examine their complex duplication history, including the possibility that concerted evolutionary forces may homogenize diversity. 5S and 25S rDNA loci among Paphiopedilum species, representing all key phylogenetic lineages, exhibit a considerable diversity that correlates well with recognized evolutionary groups. 25S rDNA signals range from 2 (representing 1 locus) to 9, the latter representing hemizygosity. 5S loci display extensive structural variation, and show from 2 specific signals to many, both major and minor and highly dispersed. The dispersed signals mainly occur at centromeric and subtelomeric positions, which are hotspots for chromosomal breakpoints. Phylogenetic analysis of cloned 5S rDNA non-transcribed spacer (5S-NTS) sequences showed evidence for both ancient and recent post-speciation duplication events, as well as interlocus and intralocus diversity. Paphiopedilum species display many chromosomal rearrangements - for example, duplications, translocations, and inversions - but only weak concerted evolutionary forces among highly duplicated 5S arrays, which suggests that double-strand break repair processes are dynamic and ongoing. These results make the genus a model system for the study of complex chromosomal evolution in plants.

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Dynamic distribution patterns of ribosomal DNA and chromosomal evolution in Paphiopedilum , a lady's slipper orchid

The origin of Cardamine flexuosa (Wavy Bittercress) has been a
conundrum for more than six decades. Here we identify its
parental species, analyse its genome structure in comparison to
parental genomes and describe intergenomic structural
variations in C. flexuosa. Genomic in situ hybridization (GISH)
and comparative chromosome painting (CCP) uncovered the
parental genomes and the chromosome composition of C. flexuosa
and its presumed diploid progenitors. Cardamine flexuosa is an
allotetraploid (2n = 4x = 32), originating from two diploid
species, Cardamine amara and Cardamine hirsuta (2n = 2x = 16).
The two parental species display almost perfectly conserved
chromosomal collinearity for seven out of the eight
chromosomes. A 13 Mb pericentric inversion distinguishes
chromosome CA1 from CH1. A comparative cytomolecular map was
established for C. flexuosa by CCP/GISH. Whereas conserved
chromosome collinearity between the C. amara and C. hirsuta
subgenomes might have promoted intergenomic rearrangements
through homeologous recombination, only one reciprocal
translocation between two homeologues has occurred since the
origin of C. flexuosa. The genome of C. flexuosa demonstrates
that allopolyploids can maintain remarkably stable subgenomes
over 104–105 yr throughout a wide distribution range. By
contrast, the rRNA genes underwent genome-specific elimination
towards a diploid-like number of loci.

https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.12567

The widespread crucifer species Cardamine flexuosa is an allotetraploid with a conserved subgenomic structure.

Tragopogon mirus and T. miscellus are allotetraploids (2n = 24) that formed repeatedly during the past 80 years in eastern Washington and adjacent Idaho (USA) following the introduction of the diploids T. dubius, T. porrifolius, and T. pratensis (2n = 12) from Europe. In most natural populations of T. mirus and T. miscellus, there are far fewer 35S rRNA genes (rDNA) of T. dubius than there are of the other diploid parent (T. porrifolius or T. pratensis). We studied the inheritance of parental rDNA loci in allotetraploids resynthesized from diploid accessions. We investigate the dynamics and directionality of these rDNA losses, as well as the contribution of gene copy number variation in the parental diploids to rDNA variation in the derived tetraploids. Using Southern blot hybridization and fluorescent in situ hybridization (FISH), we analyzed copy numbers and distribution of these highly reiterated genes in seven lines of synthetic T. mirus (110 individuals) and four lines of synthetic T. miscellus (71 individuals). Variation among diploid parents accounted for most of the observed gene imbalances detected in F1 hybrids but cannot explain frequent deviations from repeat additivity seen in the allotetraploid lines. Polyploid lineages involving the same diploid parents differed in rDNA genotype, indicating that conditions immediately following genome doubling are crucial for rDNA changes. About 19% of the resynthesized allotetraploid individuals had equal rDNA contributions from the diploid parents, 74% were skewed towards either T. porrifolius or T. pratensis-type units, and only 7% had more rDNA copies of T. dubius-origin compared to the other two parents. Similar genotype frequencies were observed among natural populations. Despite directional reduction of units, the additivity of 35S rDNA locus number is maintained in 82% of the synthetic lines and in all natural allotetraploids. Uniparental reductions of homeologous rRNA gene copies occurred in both synthetic and natural populations of Tragopogon allopolyploids. The extent of these rDNA changes was generally higher in natural populations than in the synthetic lines. We hypothesize that locus-specific and chromosomal changes in early generations of allopolyploids may influence patterns of rDNA evolution in later generations.

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Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids

To study the relationship between uniparental rDNA (encoding 18S, 5.8S and 26S ribosomal RNA) silencing (nucleolar dominance) and rRNA gene dosage, we studied a recently emerged (within the last 80 years) allotetraploid Tragopogon mirus (2n=24), formed from the diploid progenitors T. dubius (2n=12, D-genome donor) and T. porrifolius (2n=12, P-genome donor). Here, we used molecular, cytogenetic and genomic approaches to analyse rRNA gene activity in two sibling T. mirus plants (33A and 33B) with widely different rRNA gene dosages. Plant 33B had ~400 rRNA genes at the D-genome locus, which is typical for T. mirus, accounting for ~25% of total rDNA. We observed characteristic expression dominance of T. dubius-origin genes in all organs. Its sister plant 33A harboured a homozygous macrodeletion that reduced the number of T. dubius-origin genes to about 70 copies (~4% of total rDNA). It showed biparental rDNA expression in root, flower and callus, but not in leaf where D-genome rDNA dominance was maintained. There was upregulation of minor rDNA variants in some tissues. The RNA polymerase I promoters of reactivated T. porrifolius-origin rRNA genes showed reduced DNA methylation, mainly at symmetrical CG and CHG nucleotide motifs. We hypothesise that active, decondensed rDNA units are most likely to be deleted via recombination. The silenced homeologs could be used as a ‘first reserve' to ameliorate mutational damage and contribute to evolutionary success of polyploids. Deletion and reactivation cycles may lead to bidirectional homogenisation of rRNA arrays in the long term.

/pdf/silenced-rrna-genes-are-activated-and-substitute-for-235eion043.pdf

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

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 allotetraploids, 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.

Hana Malinska

Papers

Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids

Silenced rRNA genes are activated and substitute for partially eliminated active homeologs in the recently formed allotetraploid, Tragopogon mirus (Asteraceae)

Ribosomal RNA genes evolution in Tragopogon: A story of New and Old World allotetraploids and the synthetic lines