Allopolyploidy-Induced Rapid Genome Evolution in the Wheat (Aegilops–Triticum) Group

To better understand genetic events that accompany allopolyploid formation, we studied the rate and time of elimination of eight DNA sequences in F1 hybrids and newly formed allopolyploids of Aegilops and Triticum. In total, 35 interspecific and intergeneric F1 hybrids and 22 derived allopolyploids were analyzed and compared with their direct parental plants. The studied sequences exist in all the diploid species of the Triticeae but occur in only one genome, either in one homologous pair (chromosome-specific sequences [CSSs]) or in several pairs of the same genome (genome-specific sequences [GSSs]), in the polyploid wheats. It was found that rapid elimination of CSSs and GSSs is a general phenomenon in newly synthesized allopolyploids. Elimination of GSSs was already initiated in F1 plants and was completed in the second or third allopolyploid generation, whereas elimination of CSSs started in the first allopolyploid generation and was completed in the second or third generation. Sequence elimination started earlier in allopolyploids whose genome constitution was analogous to natural polyploids compared with allopolyploids that do not occur in nature. Elimination is a nonrandom and reproducible event whose direction was determined by the genomic combination of the hybrid or the allopolyploid. It was not affected by the genotype of the parental plants, by their cytoplasm, or by the ploidy level, and it did not result from intergenomic recombination. Allopolyploidy-induced sequence elimination occurred in a sizable fraction of the genome and in sequences that were apparently noncoding. This finding suggests a role in augmenting the differentiation of homoeologous chromosomes at the polyploid level, thereby providing the physical basis for the diploid-like meiotic behavior of newly formed allopolyploids. In our view, this rapid genome adjustment may have contributed to the successful establishment of newly formed allopolyploids as new species.     

The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis

Whole-genome duplication resulting from polyploidy is ubiquitous in the evolutionary history of plant species. Yet, polyploids must overcome the meiotic challenge of pairing, recombining, and segregating more than two sets of chromosomes. Using genomic sequencing of synthetic and natural allopolyploids of Arabidopsis thaliana and Arabidopsis arenosa, we determined that dosage variation and chromosomal translocations consistent with homoeologous pairing were more frequent in the synthetic allopolyploids. To test the role of structural chromosomal differentiation versus genetic regulation of meiotic pairing, we performed sequenced-based, high-density genetic mapping in F2 hybrids between synthetic and natural lines. This F2 population displayed frequent dosage variation and deleterious homoeologous recombination. The genetic map derived from this population provided no indication of structural evolution of the genome of the natural allopolyploid Arabidopsis suecica, compared with its predicted parents. The F2 population displayed variation in meiotic regularity and pollen viability that correlated with a single quantitative trait locus, which we named BOY NAMED SUE, and whose beneficial allele was contributed by A. suecica. This demonstrates that an additive, gain-of-function allele contributes to meiotic stability and fertility in a recently established allopolyploid and provides an Arabidopsis system to decipher evolutionary and molecular mechanisms of meiotic regularity in polyploids.     

Next-generation sequencing and genome evolution in allopolyploids

?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 first 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.     

Deleterious Mutations Accumulate Faster in Allopolyploid Than Diploid Cotton (Gossypium) and Unequally between Subgenomes

Whole-genome duplication (polyploidization) is among the most dramatic mutational processes in nature, so understanding how natural selection differs in polyploids relative to diploids is an important goal. Population genetics theory predicts that recessive deleterious mutations accumulate faster in allopolyploids than diploids due to the masking effect of redundant gene copies, but this prediction is hitherto unconfirmed. Here, we use the cotton genus (Gossypium), which contains seven allopolyploids derived from a single polyploidization event 1–2 Million years ago, to investigate deleterious mutation accumulation. We use two methods of identifying deleterious mutations at the nucleotide and amino acid level, along with whole-genome resequencing of 43 individuals spanning six allopolyploid species and their two diploid progenitors, to demonstrate that deleterious mutations accumulate faster in allopolyploids than in their diploid progenitors. We find that, unlike what would be expected under models of demographic changes alone, strongly deleterious mutations show the biggest difference between ploidy levels, and this effect diminishes for moderately and mildly deleterious mutations. We further show that the proportion of nonsynonymous mutations that are deleterious differs between the two coresident subgenomes in the allopolyploids, suggesting that homoeologous masking acts unequally between subgenomes. Our results provide a genome-wide perspective on classic notions of the significance of gene duplication that likely are broadly applicable to allopolyploids, with implications for our understanding of the evolutionary fate of deleterious mutations. Finally, we note that some measures of selection (e.g., dN/dS, π_N/π_S) may be biased when species of different ploidy levels are compared.     

Genome Evolution Due to Allopolyploidization in Wheat

The wheat group has evolved through allopolyploidization, namely, through hybridization among species from the plant genera Aegilops and Triticum followed by genome doubling. This speciation process has been associated with ecogeographical expansion and with domestication. In the past few decades, we have searched for explanations for this impressive success. Our studies attempted to probe the bases for the wide genetic variation characterizing these species, which accounts for their great adaptability and colonizing ability. Central to our work was the investigation of how allopolyploidization alters genome structure and expression. We found in wheat that allopolyploidy accelerated genome evolution in two ways: (1) it triggered rapid genome alterations through the instantaneous generation of a variety of cardinal genetic and epigenetic changes (which we termed “revolutionary” changes), and (2) it facilitated sporadic genomic changes throughout the species’ evolution (i.e., evolutionary changes), which are not attainable at the diploid level. Our major findings in natural and synthetic allopolyploid wheat indicate that these alterations have led to the cytological and genetic diploidization of the allopolyploids. These genetic and epigenetic changes reflect the dynamic structural and functional plasticity of the allopolyploid wheat genome. The significance of this plasticity for the successful establishment of wheat allopolyploids, in nature and under domestication, is discussed.     

Analysis of 5S rDNA changes in synthetic allopolyploids <Emphasis Type="Italic">Triticum</Emphasis> × <Emphasis Type="Italic">Aegilops</Emphasis>

Changes of 5S rDNA at the early stage of allopolyploidization were investigated in three synthetic allopolyploids: Aegilops sharonensis × Ae. umbellulata (2n = 28), Triticum urartu × Ae. tauschii (2n = 28), and T. dicoccoides × Ae. tauschii (2n = 42). Fluorescent in situ hybridization (FISH) revealed quantitative changes affecting separate loci of one of the parental genomes in S₃ plants of each hybrid combination. Southern hybridization with genomic DNA of the allopolyploid T. urartu × Ae. tauschii (TMU38 × TQ27) revealed a lower intensity of signals from Ae. tauschii fragments compared with those derived from T. urartu. This confirmed the signal reduction revealed for chromosome 1D of this hybrid by FISH. Neither Southern hybridization nor PCR testing of 5–15 plants of the S₂-S₃ generations revealed an appearance of new 5S rDNA fragments or a complete disappearance of parental fragments from the allopolyploids under study. No changes were found by aligning nine 5S rDNA sequences of the allopolyploid TMU38 × TQ27 with corresponding sequences of the parental species. The similarity between one of the synthetic allopolyploids examined and a natural allopolyploid with the same genome composition points to an early formation of the 5S rDNA organization unique for each allopolyploid.     

Polyploidy and novelty: Gottlieb's legacy

Nearly four decades ago, Roose & Gottlieb (Roose & Gottlieb 1976 Evolution 30, 818–830. (doi:10.2307/2407821)) showed that the recently derived allotetraploids Tragopogon mirus and T. miscellus combined the allozyme profiles of their diploid parents (T. dubius and T. porrifolius, and T. dubius and T. pratensis, respectively). This classic paper addressed the link between genotype and biochemical phenotype and documented enzyme additivity in allopolyploids. Perhaps more important than their model of additivity, however, was their demonstration of novelty at the biochemical level. Enzyme multiplicity—the production of novel enzyme forms in the allopolyploids—can provide an extensive array of polymorphism for a polyploid individual and may explain, for example, the expanded ranges of polyploids relative to their diploid progenitors. In this paper, we extend the concept of evolutionary novelty in allopolyploids to a range of genetic and ecological features. We observe that the dynamic nature of polyploid genomes—with alterations in gene content, gene number, gene arrangement, gene expression and transposon activity—may generate sufficient novelty that every individual in a polyploid population or species may be unique. Whereas certain combinations of these features will undoubtedly be maladaptive, some unique combinations of newly generated variation may provide tremendous evolutionary potential and adaptive capabilities.     

The timetable for allopolyploidy in flowering plants

Background

Our understanding of the processes and dynamics of allopolyploid speciation, the long-term consequences of ploidal change, and the genetic and chromosomal changes in new emerged allopolyploids has substantially increased during the past few decades. Yet we remain uncertain about the time since lineage divergence when two taxa are capable of spawning such entities. Indeed, the matter has seemed intractable. Knowledge of the window of opportunity for allopolyploid production is very important because it provides temporal insight into a key evolutionary process, and a temporal reference against which other modes of speciation may be measured.

Scope

This Viewpoint paper reviews and integrates published information on the crossability of herbaceous species and the fertility of their hybrids in relation to species'' divergence times. Despite limitations in methodology and sampling, the estimated times to hybrid sterility are somewhat congruent across disparate lineages. Whereas the waiting time for hybrid sterility is roughly 4–5 million years, the waiting time for cross-incompatibility is roughly 8–10 million years, sometimes considerably more. Strict allopolyploids may be formed in the intervening time window. The progenitors of several allopolyploids diverged between 4 and 6 million years before allopolyploid synthesis, as expected. This is the first study to propose a general temporal framework for strict allopolyploidy. This Viewpoint paper hopefully will stimulate interest in studying the tempo of speciation and the tempo of reproductive isolation in general.     

Natural variation and persistent developmental instabilities in geographically diverse accessions of the allopolyploid Arabidopsis suecica

Allopolyploids arise from the hybridization of two species concomitant to genome doubling. While established allopolyploids are common in nature and vigorous in growth, early generation allopolyploids are often less fertile than their progenitors and display frequent phenotypic instabilities. It is commonly assumed that new allopolyploid species must pass through a bottleneck from which only those lines emerge that have reconciled genomic incompatibilities inherited from their progenitors in their combined genome, yet little is known about the processes following allopolyploidization over evolutionary time. To address the question if a single allopolyploidization event leads to a single new homogeneous species or may result in diverse offspring lines, we have investigated 13 natural accessions of Arabidopsis suecica, a relatively recent allopolyploid derived from a single hybridization event. The studied accessions display low genetic diversity between lines, yet show evidence of heritable phenotypic diversity of traits, some of which may be adaptive. Furthermore, our data show that contrary to the notion that unstable phenotypes in neoallopolyploids are eliminated rapidly in the new species, some instabilities are carried along throughout the species' evolution, persisting in the established allopolyploid. In summary, our results suggest that a single allopolyploidization event may lay the foundation for diverse populations of the new allopolyploid species.     

Nuclear DNA amount and genome downsizing in natural and synthetic allopolyploids of the genera Aegilops and Triticum

Recent molecular studies in the genera Aegilops and Triticum showed that allopolyploidization (interspecific or intergeneric hybridization followed by chromosome doubling) generated rapid elimination of low-copy or high-copy, non-coding and coding DNA sequences. The aims of this work were to determine the amount of nuclear DNA in allopolyploid species of the group and to see to what extent elimination of DNA sequences affected genome size. Nuclear DNA amount was determined by the flow cytometry method in 27 natural allopolyploid species (most of which were represented by several lines and each line by several plants) as well as 14 newly synthesized allopolyploids (each represented by several plants) and their parental plants. Very small intraspecific variation in DNA amount was found between lines of allopolyploid species collected from different habitats or between wild and domesticated forms of allopolyploid wheat. In contrast to the constancy in nuclear DNA amount at the intraspecific level, there are significant differences in genome size between the various allopolyploid species, at both the tetraploid and hexaploid levels. In most allopolyploids nuclear DNA amount was significantly less than the sum of DNA amounts of the parental species. Newly synthesized allopolyploids exhibited a similar decrease in nuclear DNA amount in the first generation, indicating that genome downsizing occurs during and (or) immediately after the formation of the allopolyploids and that there are no further changes in genome size during the life of the allopolyploids. Phylogenetic considerations of the origin of the B genome of allopolyploid wheat, based on nuclear DNA amount, are discussed.     

Recent and recurrent polyploidy in Tragopogon (Asteraceae): cytogenetic, genomic and genetic comparisons

Tragopogon mirus Ownbey and T. miscellus Ownbey are allopolyploids that formed repeatedly during the past 80 years following the introduction of three diploids (T. dubius Scop., T. pratensis L. and T. porrifolius L.) from Europe to western North America. These polyploid species of known parentage are useful for studying the consequences of recent and recurrent polyploidization. We summarize recent analyses of the cytogenetic, genomic and genetic consequences of polyploidy in Tragopogon. Analyses of rDNA ITS (internal transcribed spacer) + ETS (external transcribed spacer) sequence data indicate that the parental diploids are phylogenetically well separated within Tragopogon (a genus of perhaps 150 species), in agreement with isozymic and cpDNA data. Using Southern blot and cloning experiments on tissue from early herbarium collections of T. mirus and T. miscellus (from 1949) to represent the rDNA repeat condition closer to the time of polyploidization than samples collected today, we have demonstrated concerted evolution of rDNA. Concerted evolution is ongoing, but has not proceeded to completion in any polyploid population examined; rDNA repeats of the diploid T. dubius are typically lost or converted in both allopolyploids, including populations of independent origin. Molecular cytogenetic studies employing rDNA probes, as well as centromeric and subtelomeric repeats isolated from Tragopogon, distinguished all chromosomes among the diploid progenitors (2n = 12). The diploid chromosome complements are additive in both allopolyploids (2n = 24); there is no evidence of major chromosomal rearrangements in populations of either T. mirus or T. miscellus. cDNA‐AFLP display revealed differences in gene expression between T. miscellus and its diploid parents, as well as between populations of T. miscellus of reciprocal origin. Approximately 5% of the genes examined in the allopolyploid populations have been silenced, and an additional 4% exhibit novel gene expression relative to their diploid parents. Some of the differences in gene expression represent maternal or paternal effects. Multiple origins of a polyploid species not only affect patterns of genetic variation in natural populations, but also contribute to differential patterns of gene expression and may therefore play a major role in the long‐term evolution of polyploids. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 82 , 485–501.     

Effect of small coding genes on the circadian rhythms under elevated CO2 conditions in plants

Key Message

Differential expression of mi-RNAs targeting developmental processes and progressive downregulation of repeat-associated siRNAs following genome merger and genome duplication in the context of allopolyploid speciation in Spartina.

Abstract

The role of small RNAs on gene expression regulation and genome stability is arousing increased interest and is being explored in various plant systems. In spite of prominence of reticulate evolution and polyploidy that affects the evolutionary history of all plant lineages, very few studies analysed RNAi mechanisms with this respect. Here, we explored small RNAs diversity and expression in the context of recent allopolyploid speciation, using the Spartina system, which offers a unique opportunity to explore the immediate changes following hybridization and genome duplication. Small RNA-Seq analyses were conducted on hexaploid parental species (S. alterniflora and S. maritima), their F1 hybrid S. x townsendii, and the neoallododecaploid S. anglica. We identified 594 miRNAs, 2197 miRNA-target genes, and 3730 repeat-associated siRNAs (mostly targeting Class I/Copia-Ivana- Copia-SIRE and LINEs elements). For both mi- and ra-siRNAs, we detected differential expression patterns following genome merger and genome duplication. These misregulations include non-additive expression of miRNAs in the F1 hybrid and additional changes in the allopolyploid targeting developmental processes. Expression of repeat-associated siRNAs indicates a strengthen of transposable element repression during the allopolyploidization process. Altogether, these results confirm the central role small RNAs play in shaping regulatory changes in naturally formed recent allopolyploids.