Genomic plasticity and the diversity of polyploid plants

Spatio-temporal patterns of genome evolution in allotetraploid species of the genus Oryza

Despite knowledge that polyploidy is widespread and a major evolutionary force in flowering plant diversification, detailed comparative molecular studies on polyploidy have been confined to only a few species and families. The genus Oryza is composed of 23 species that are classified into ten distinct 'genome types' (six diploid and four polyploid), and is emerging as a powerful new model system to study polyploidy. Here we report the identification, sequence and comprehensive comparative annotation of eight homoeologous genomes from a single orthologous region (Adh1-Adh2) from four allopolyploid species representing each of the known Oryza genome types (BC, CD, HJ and KL). Detailed comparative phylogenomic analyses of these regions within and across species and ploidy levels provided several insights into the spatio-temporal dynamics of genome organization and evolution of this region in 'natural' polyploids of Oryza. The major findings of this study are that: (i) homoeologous genomic regions within the same nucleus experience both independent and parallel evolution, (ii) differential lineage-specific selection pressures do not occur between polyploids and their diploid progenitors, (iii) there have been no dramatic structural changes relative to the diploid ancestors, (iv) a variation in the molecular evolutionary rate exists between the two genomes in the BC complex species even though the BC and CD polyploid species appear to have arisen <2 million years ago, and (v) there are no clear distinctions in the patterns of genome evolution in the diploid versus polyploid species.

Radiative evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae)

*The micro-evolutionary mechanisms that drive large-scale radiations are not completely understood, partly because of a shortage of population-level studies aimed at identifying putative causes of rapid evolutionary change. The Dianthus broteri complex, representing the largest polyploid series known to date for any species in the genus (2x, 4x, 6x and 12x cytotypes), belongs to a lineage that was recently found to have diversified at unusually rapid rates. *We used a combination of genome sequencing (internal transcribed spacer (ITS), plus chloroplast DNA (cpDNA) regions trnH-psbA, psbA-trnK and trnK-matK) and amplified fragment length polymorphism (AFLP) fingerprinting in 25 populations to infer the evolutionary history of extant polyploid races. *The haplotype, ribotype and AFLP reconstructions showed a star-shaped arrangement suggesting a pattern of radiative evolution. The major, widespread haplotype occurred at all ploidy levels, whereas 20 minor haplotypes were restricted to single populations and cytotypes. In addition, AFLP analyses retrieved well-supported cytogeographic groups: six clades were clearly differentiated in terms of ploidy level and geography. Molecular data indicate that gene flow among different cytotypes is rare or nonexistent. *Our study supports a scenario of rapid diversification in carnations in which autopolyploidy and allopolyploidy, in interaction with geography and/or isolation, have played prominent roles.

Reticulate evolution in diploid and tetraploid species of Polystachya (Orchidaceae) as shown by plastid DNA sequences and low-copy nuclear genes

BACKGROUND AND AIMS

Here evidence for reticulation in the pantropical orchid genus Polystachya is presented, using gene trees from five nuclear and plastid DNA data sets, first among only diploid samples (homoploid hybridization) and then with the inclusion of cloned tetraploid sequences (allopolyploids). Two groups of tetraploids are compared with respect to their origins and phylogenetic relationships.

METHODS

Sequences from plastid regions, three low-copy nuclear genes and ITS nuclear ribosomal DNA were analysed for 56 diploid and 17 tetraploid accessions using maximum parsimony and Bayesian inference. Reticulation was inferred from incongruence between gene trees using supernetwork and consensus network analyses and from cloning and sequencing duplicated loci in tetraploids.

KEY RESULTS

Diploid trees from individual loci showed considerable incongruity but little reticulation signal when support from more than one gene tree was required to infer reticulation. This was coupled with generally low support in the individual gene trees. Sequencing the duplicated gene copies in tetraploids showed clearer evidence of hybrid evolution, including multiple origins of one group of tetraploids included in the study.

CONCLUSIONS

A combination of cloning duplicate gene copies in allotetraploids and consensus network comparison of gene trees allowed a phylogenetic framework for reticulation in Polystachya to be built. There was little evidence for homoploid hybridization, but our knowledge of the origins and relationships of three groups of allotetraploids are greatly improved by this study. One group showed evidence of multiple long-distance dispersals to achieve a pantropical distribution; another showed no evidence of multiple origins or long-distance dispersal but had greater morphological variation, consistent with hybridization between more distantly related parents.

Genome structure affects the rate of autosyndesis and allosyndesis in AABC, BBAC and CCAB Brassica interspecific hybrids

Gene introgression into allopolyploid crop species from diploid or polyploid ancestors can be accomplished through homologous or homoeologous chromosome pairing during meiosis. We produced trigenomic Brassica interspecific hybrids (genome complements AABC, BBAC and CCAB) from the amphidiploid species Brassica napus (AACC), Brassica juncea (AABB) and Brassica carinata (BBCC) in order to test whether the structure of each genome affects frequencies of homologous and homoeologous (both allosyndetic and autosyndetic) pairing during meiosis. AABC hybrids produced from three genotypes of B. napus were included to assess the genetic control of homoeologous pairing. Multi-colour fluorescent in situ hybridisation was used to quantify homologous pairing (e.g. A-genome bivalents in AABC), allosyndetic associations (e.g. B-C in AABC) and autosyndetic associations (e.g. B-B in AABC) at meiosis. A high percentage of homologous chromosomes formed pairs (97.5-99.3%), although many pairs were also involved in autosyndetic and allosyndetic associations. Allosyndesis was observed most frequently as A-C genome associations (mean 4.0 per cell) and less frequently as A-B genome associations (0.8 per cell) and B-C genome associations (0.3 per cell). Autosyndesis occurred most frequently in the haploid A genome (0.75 A-A per cell) and least frequently in the haploid B genome (0.13 B-B per cell). The frequency of C-C autosyndesis was greater in BBAC hybrids (0.75 per cell) than in any other hybrid. The frequency of A-B, A-C and B-C allosyndesis was affected by the genomic structure of the trigenomic hybrids. Frequency of allosyndesis was also influenced by the genotype of the B. napus paternal parent for the three AABC (B. juncea × B. napus) hybrid types. Homoeologous pairing between the Brassica A, B and C genomes in interspecific hybrids may be influenced by complex interactions between genome structure and allelic composition.

Complete switchgrass genetic maps reveal subgenome collinearity, preferential pairing and multilocus interactions

Polyploidy is an important aspect of the evolution of flowering plants. The potential of gene copies to diverge and evolve new functions is influenced by meiotic behavior of chromosomes leading to segregation as a single locus or duplicated loci. Switchgrass (Panicum virgatum) linkage maps were constructed using a full-sib population of 238 plants and SSR and STS markers to access the degree of preferential pairing and the structure of the tetraploid genome and as a step toward identification of loci underlying biomass feedstock quality and yield. The male and female framework map lengths were 1645 and 1376 cM with 97% of the genome estimated to be within 10 cM of a mapped marker in both maps. Each map coalesced into 18 linkage groups arranged into nine homeologous pairs. Comparative analysis of each homology group to the diploid sorghum genome identified clear syntenic relationships and collinear tracts. The number of markers with PCR amplicons that mapped across subgenomes was significantly fewer than expected, suggesting substantial subgenome divergence, while both the ratio of coupling to repulsion phase linkages and pattern of marker segregation indicated complete or near complete disomic inheritance. The proportion of transmission ratio distorted markers was relatively low, but the male map was more extensively affected by distorted transmission ratios and multilocus interactions, associated with spurious linkages.

Evolutionary rate variation, genomic dominance and duplicate gene expression evolution during allotetraploid cotton speciation

Here, we describe the evolution of gene expression among a diversified cohort of five allopolyploid species in the cotton genus (Gossypium). Using this phylogenetic framework and comparisons with expression changes accompanying F(1) hybridization, we provide a temporal perspective on expression diversification following a shared genome duplication. Global patterns of gene expression were studied by the hybridization of petal RNAs to a custom microarray. This platform measures total expression for c. 42 000 duplicated genes, and genome-specific expression for c. 1400 homoeologs (genes duplicated by polyploidy). We report homoeolog expression bias favoring the allopolyploid D genome over the A genome in all species (among five polyploid species, D biases ranging from c. 54 to 60%), in addition to conservation of biases among genes. Furthermore, we find surprising levels of transgressive up- and down-regulation in the allopolyploids, a diminution of the level of bias in genomic expression dominance but not in its magnitude, and high levels of rate variation among allotetraploid species. We illustrate how phylogenetic and temporal components of expression evolution may be partitioned and revealed following allopolyploidy. Overall patterns of expression evolution are similar among the Gossypium allotetraploids, notwithstanding a high level of interspecific rate variation, but differ strikingly from the direction of genomic expression dominance patterns in the synthetic F(1) hybrid.

Fall and rise of satellite repeats in allopolyploids of Nicotiana over c. 5 million years

Allopolyploids represent natural experiments in which DNA sequences from different species are combined into a single nucleus and then coevolve, enabling us to follow the parental genomes, their interactions and evolution over time. Here, we examine the fate of satellite DNA over 5 million yr of divergence in plant genus Nicotiana (family Solanaceae). We isolated subtelomeric, tandemly repeated satellite DNA from Nicotiana diploid and allopolyploid species and analysed patterns of inheritance and divergence by sequence analysis, Southern blot hybridization and fluorescent in situ hybridization (FISH). We observed that parental satellite sequences redistribute around the genome in allopolyploids of Nicotiana section Polydicliae, formed c. 1 million yr ago (Mya), and that new satellite repeats evolved and amplified in section Repandae, which was formed c. 5 Mya. In some cases that process involved the complete replacement of parental satellite sequences. The rate of satellite repeat replacement is faster than theoretical predictions assuming the mechanism involved is unequal recombination and crossing-over. Instead we propose that this mechanism occurs with the deletion of large chromatin blocks and reamplification, perhaps via rolling circle replication.

Evolutionary consequences of autopolyploidy

Autopolyploidy is more common in plants than traditionally assumed, but has received little attention compared with allopolyploidy. Hence, the advantages and disadvantages of genome doubling per se compared with genome doubling coupled with hybridizations in allopolyploids remain unclear. Autopolyploids are characterized by genomic redundancy and polysomic inheritance, increasing effective population size. To shed light on the evolutionary consequences of autopolyploidy, we review a broad range of studies focusing on both synthetic and natural autopolyploids encompassing levels of biological organization from genes to evolutionary lineages. The limited evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor wide reorganization of gene expression during the first generations following genome doubling, but that these processes may become more important in the longer term. Biogeographic and ecological surveys point to an association between the formation of autopolyploid lineages and environmental change. We thus hypothesize that polysomic inheritance may provide a short-term evolutionary advantage for autopolyploids compared to diploid relatives when environmental change enforces range shifts. In addition, autopolyploids should possess increased genome flexibility, allowing them to adapt and persist across heterogeneous landscapes in the long run.

Newly synthesized wheat allohexaploids display progenitor-dependent meiotic stability and aneuploidy but structural genomic additivity

To understand key mechanisms leading to stabilized allopolyploid species, we characterized the meiotic behaviour of wheat allohexaploids in relation to structural and genetic changes. For that purpose, we analysed first generations of synthetic allohexaploids obtained through interspecific hybridization, followed by spontaneous chromosome doubling, between several genotypes of Triticum turgidum and Aegilops tauschii wheat species, donors of AB and D genomes, respectively. As expected for these Ph1 (Pairing homoeologous 1) gene-carrying allopolyploids, chromosome pairing at metaphase I of meiosis essentially occurs between homologous chromosomes. However, the different synthetic allohexaploids exhibited progenitor-dependent meiotic irregularities, such as incomplete homologous pairing, resulting in univalent formation and leading to aneuploidy in the subsequent generation. Stability of the synthetic allohexaploids was shown to depend on the considered genotypes of both AB and D genome progenitors, where few combinations compare to the natural wheat allohexaploid in terms of regularity of meiosis and euploidy. Aneuploidy represents the only structural change observed in these synthetic allohexaploids, as no apparent DNA sequence elimination or rearrangement was observed when analysing euploid plants with molecular markers, developed from expressed sequence tags (ESTs) as well as simple sequence repeat (SSR) and transposable element sequences.

Impact of transposable elements on the organization and function of allopolyploid genomes

Transposable elements (TEs) represent an important fraction of plant genomes and are likely to play a pivotal role in fuelling genome reorganization and functional changes following allopolyploidization. Various processes associated with allopolyploidy (i.e. genetic redundancy, bottlenecks during the formation of allopolyploids or genome shock following genome merging) may allow accumulation of TE insertions. Our objective in carrying out a survey of the literature and a comparative analysis across different allopolyploid systems is to shed light on the structural, epigenetic and functional modifications driven by TEs during allopolyploidization and subsequent diploidization. The available evidence indicates that TE proliferation in the short or the long term after allopolyploidization may be restricted to a few TEs, in specific polyploid systems. By contrast, data indicate major structural changes in the TE genome fraction immediately after allopolyploidization, mainly through losses of TE sequences as a result of recombination. Emerging evidence also suggests that TEs are targeted by substantial epigenetic changes, which may impact gene expression and genome stability. Furthermore, TEs may directly or indirectly support the evolution of new functionalities in allopolyploids during diploidization. All data stress allopolyploidization as a shock associated with drastic genome reorganization. Mechanisms controlling TEs during allopolyploidization as well as their impact on diploidization are discussed.

Tissue-specific silencing of homoeologs in natural populations of the recent allopolyploid Tragopogon mirus

Recent years have seen rapid advances in our knowledge of the transcriptomic consequences of allopolyploidy, primarily through the study of polyploid crops and model systems. However, few studies have distinguished between homoeologs and between tissues, and still fewer have examined young natural allopolyploid populations of independent origin, whose parental species are still present in the same location. Here, we examined the expression of 13 homoeolog pairs in seven tissues of 10 plants of allotetraploid Tragopogon mirus from two natural populations formed by independent polyploidizations between Tragopogon dubius and Tragopogon porrifolius c. 40 generations ago. We compare these with patterns of expression in the diploid parental species from the same locality. Of the 910 assays in T. mirus, 576 (63%) showed expression of both homoeologs, 63 (7%) showed no expression of either homoeolog, 186 (20%) showed nonexpression of one homoeolog across all tissues of a plant, and 72 (8%) showed non-expression of a homoeolog in a particular tissue within a plant. We found two cases of reciprocal tissue-specific expression between homoeologs, potentially indicative of subfunctionalization. Our study shows that tissue-specific silencing, and even apparent subfunctionalization, can arise rapidly in the early generations of natural allopolyploidy.

Intragenic recombination events and evidence for hybrid speciation in Nicotiana (Solanaceae)

Reticulate evolution may function both at the species level, through homoploid and polyploid hybridization, and below the species level, through inter and intragenic recombination. These processes represent challenges for the reconstruction of evolutionary relationships between species, because they cannot be represented adequately with bifurcating trees. We use data from low-copy nuclear genes to evaluate long-standing hypotheses of homoploid (interspecific) hybrid speciation in Nicotiana (Solanaceae) and reconstruct a complex series of reticulation events that have been important in the evolutionary history of this genus. Hybrid origins for three diploid species (Nicotiana glauca, N. linearis, and N. spegazzinii) are inferred on the basis of gene tree incongruence, evidence for interallelic recombination between likely parental alleles, and support for incompatible splits in Lento plots. Phylogenetic analysis of recombinant gene sequences illustrates that recombinants may be resolved with one of their progenitor lineages with a high posterior probability under Bayesian inference, and thus there is no indication of the conflict between phylogenetic signals that results from reticulation. Our results illustrate the importance of hybridization in shaping evolution in Nicotiana and also show that intragenic recombination may be relatively common. This finding demonstrates that it is important to investigate the possibility of recombination when aiming to detect hybrids from DNA-sequence data and reconstruct patterns of reticulate evolution between species.

The first meiosis of resynthesized Brassica napus, a genome blender

Polyploidy promotes the restructuring of merged genomes within initial generations of resynthesized Brassica napus, possibly caused by homoeologous recombination at meiosis. However, little is known about the impact of the first confrontation of two genomes at the first meiosis which could lead to genome exchanges in progeny. Here, we assessed the role of the first meiosis in the genome instability of synthetic B. napus. We used three different newly resynthesized B. napus plants and established meiotic pairing frequencies for the A and C genomes. We genotyped the three corresponding progenies in a cross to a natural B. napus on the two homoeologous A1 and C1 chromosomes. Pairing at meiosis in a set of progenies with various rearrangements was scored. Here, we confirmed that the very first meiosis of resynthesized plants of B. napus acts as a genome blender, with many of the meiotic-driven genetic changes transmitted to the progenies, in proportions that depend significantly on the cytoplasm background inherited from the progenitors. We conclude that the first meiosis generates rearrangements on both genomes and promotes subsequent restructuring in further generations. Our study advances the knowledge on the timing of genetic changes and the mechanisms that may bias their transmission.

Homoeologous recombination in allopolyploids: the polyploid ratchet

Polyploidization and recombination are two important processes driving evolution through the building and reshaping of genomes. Allopolyploids arise from hybridization and chromosome doubling among distinct, yet related species. Polyploids may display novel variation relative to their progenitors, and the sources of this variation lie not only in the acquisition of extra gene dosages, but also in the genomic changes that occur after divergent genomes unite. Genomic changes (deletions, duplications, and translocations) have been detected in both recently formed natural polyploids and resynthesized polyploids. In resynthesized Brassica napus allopolyploids, there is evidence that many genetic changes are the consequence of homoeologous recombination. Homoeologous recombination can generate novel gene combinations and phenotypes, but may also destabilize the karyotype and lead to aberrant meiotic behavior and reduced fertility. Thus, natural selection plays a role in the establishment and maintenance of fertile natural allopolyploids that have stabilized chromosome inheritance and a few advantageous chromosomal rearrangements. We discuss the evidence for genome rearrangements that result from homoeologous recombination in resynthesized B. napus and how these observations may inform phenomena such as chromosome replacement, aneuploidy, non-reciprocal translocations and gene conversion seen in other polyploids.

Expression and inheritance of sporophytic self-incompatibility in synthetic allohexaploid Senecio cambrensis (Asteraceae)

Allopolyploid speciation is common in plants and is frequently associated with shifts from outcrossing, for example self-incompatibility, to inbreeding (i.e. selfing). Senecio cambrensis is a recently evolved allohexaploid species that formed following hybridization between diploid self-incompatible S. squalidus and tetraploid self-compatible S. vulgaris. Studies of reproduction in wild populations of S. cambrensis have concluded that it is self-compatible. Here, we investigated self-compatibility in synthetic lines of S. cambrensis generated via hybridization and colchicine-induced polyploidization and wild S. cambrensis using controlled crossing experiments. Synthetic F(1)S. cambrensis individuals were all self-compatible but, in F(2) and later generations, self-incompatible individuals were identified at frequencies of 6.7-9.2%. Self-incompatibility was also detected in wild sampled individuals at a frequency of 12.2%. The mechanism and genetics of self-incompatibility were tested in synthetic S. cambrensis and found to be similar to those of its paternal parent S. squalidus (i.e. sporophytic). These results show, for the first time, that functional sporophytic self-incompatibility can be inherited and expressed in allopolyploids as early as the second (F(2)) generation. Wild S. cambrensis should therefore be considered as possessing a mixed mating system with the potential for evolution towards either inbreeding or outcrossing.

Epigenomic plasticity within populations: its evolutionary significance and potential

Epigenetics has progressed rapidly from an obscure quirk of heredity into a data-heavy 'omic' science. Our understanding of the molecular mechanisms of epigenomic regulation, and the extent of its importance in nature, are far from complete, but in spite of such drawbacks, population-level studies are extremely valuable: epigenomic regulation is involved in several processes central to evolutionary biology including phenotypic plasticity, evolvability and the mediation of intragenomic conflicts. The first studies of epigenomic variation within populations suggest high levels of phenotypically relevant variation, with the patterns of epigenetic regulation varying between individuals and genome regions as well as with environment. Epigenetic mechanisms appear to function primarily as genome defences, but result in the maintenance of plasticity together with a degree of buffering of developmental programmes; periodic breakdown of epigenetic buffering could potentially cause variation in rates of phenotypic evolution.

Nuclear DNA content variation associated with muscle fiber hypertrophic growth in decapod crustaceans

We tested the hypothesis that hypertrophic muscle growth in decapod crustaceans is associated with increases in both the number of nuclei per fiber and nuclear DNA content. The DNA-localizing fluorochrome DAPI (4′,6-diamidino-2-phenylindole) and chicken erythrocyte standards were used with static microspectrophotometry and image analysis to estimate nuclear DNA content in hemocytes and muscle fibers from eight decapod crustacean species: Farfantepenaeus aztecus , Palaemonetes pugio , Panulirus argus , Homarus americanus , Procambarus clarkii , Cambarus bartonii , Callinectes sapidus , and Menippe mercenaria . Mean diploid (2C) values in hemocytes ranged from 3.6 to 11.7 pg. Hemocyte 2C estimates were used to extrapolate ploidy level in the multinucleated skeletal muscle tissue of juvenile and adult animals. Across all species, mean muscle fiber diameters from adult animals were significantly larger than those in juveniles, and nuclear domains were greater in larger fibers. The number of nuclei per fiber increased with increasing fiber size, as hypothesized. Maximum nuclear DNA content per species in muscle ranged from 4C to 32C, consistent with endopolyploidy. Two patterns of body- and fiber-size-dependent shifts in ploidy were observed: four species had a significantly higher ploidy in the larger fibers of adults, while three species exhibited a significantly lower ploidy in adults than in juveniles. Thus, across species, there was no systematic relationship between nuclear domain size and nuclear DNA content.

Dynamics of polyploid formation in Tragopogon (Asteraceae): recurrent formation, gene flow, and population structure

Polyploidy is a major feature of angiosperm evolution and diversification. Most polyploid species have formed multiple times, yet we know little about the genetic consequences of recurrent formations. Among the clearest examples of recurrent polyploidy are Tragopogon mirus and T. miscellus (Asteraceae), each of which has formed repeatedly in the last approximately 80 years from known diploid progenitors in western North America. Here, we apply progenitor-specific microsatellite markers to examine the genetic contributions to each tetraploid species and to assess gene flow among populations of independent formation. These data provide fine-scale resolution of independent origins for both polyploid species. Importantly, multiple origins have resulted in considerable genetic variation within both polyploid species; however, the patterns of variation detected in the polyploids contrast with those observed in extant populations of the diploid progenitors. The genotypes detected in the two polyploid species appear to represent a snapshot of historical population structure in the diploid progenitors, rather than modern diploid genotypes. Our data also indicate a lack of gene flow among polyploid plants of independent origin, even when they co-occur, suggesting potential reproductive barriers among separate lineages in both polyploid species.

An efficient high-throughput flow cytometric method for estimating DNA ploidy level in plants

We present an efficient high-throughput flow cytometric method that builds on previously published methods and permits rapid ploidy discrimination in plants. By using Brassica napus L. microspore-derived plants as an example, we describe how 192 leaf tissue samples may be processed and analyzed comfortably by one operator in 6 h from tissue sampling to ploidy determination. The technique involves placing young leaf samples in two 96-well racks, using a bead-beating procedure to release nuclei into a lysis solution, filtering the samples on 96-well filter plates, staining with propidium iodide, and then rapidly estimating DNA ploidy using a plate loader on a BD FACS-Canto II flow cytometer. Throughout the sample preparation process, multichannel pipetting allows faster and less error-prone sample handling. In two 96-well plates of samples, the histogram peaks of DNA content from flow cytometry were wellresolved in 189 of 192 samples tested (98.4%), with CV values ranging from 2.98% to 6.20% with an average CV of 4.35% (SD = 0.68%). This new method is useful in doubled haploid plant breeding programs where early discrimination of haploid and doubled haploid (i.e., diploid) plantlets can confer significantly improved operational efficiencies. We discuss how this method could be further refined including adapting the method to robotic sample processing.

Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci

We conducted a sequence-level comparative analyses, at the scale of complete bacterial artificial chromosome (BAC) clones, between the genome of the most economically important Brassica species, Brassica napus (oilseed rape), and those of Brassica rapa, the genome of which is currently being sequenced, and Arabidopsis thaliana. We constructed a new B. napus BAC library and identified and sequenced clones that contain homoeologous regions of the genome including stearoyl-ACP desaturase-encoding genes. We sequenced the orthologous region of the genome of B. rapa and conducted comparative analyses between the Brassica sequences and those of the orthologous region of the genome of A. thaliana. The proportion of genes conserved (approximately 56%) is lower than has been reported previously between A. thaliana and Brassica (approximately 66%). The gene models for sets of conserved genes were used to determine the extent of nucleotide conservation of coding regions. This was found to be 84.2 +/- 3.9% and 85.8 +/- 3.7% between the B. napus A and C genomes, respectively, and that of A. thaliana, which is consistent with previous results for other Brassica species, and 97.5 +/- 3.1% between the B. napus A genome and B. rapa, and 93.1 +/- 4.9% between the B. napus C genome and B. rapa. The divergence of the B. napus genes from the A genome and the B. rapa genes was greater than anticipated and indicates that the A genome ancestor of the B. napus cultivar studied was relatively distantly related to the cultivar of B. rapa selected for genome sequencing.

Ribosomal DNA, heterochromatin, and correlation with genome size in diploid and polyploid North American endemic sagebrushes (Artemisia, Asteraceae)

Subgenus Tridentatae ( Artemisia , Asteraceae) can be considered a polyploid complex. Both polyploidy and hybridization have been documented in the Tridentatae. Fluorescent in situ hybridization (FISH) and fluorochrome banding were used to detect and analyze ribosomal DNA changes linked to polyploidization in this group by studying four diploid-polyploid species pairs. In addition, genome sizes and heterochromatin patterns were compared between these populations. The linked 5S and 35S rRNA genes are confirmed as characteristic for Artemisia, and a pattern at the diploid level of three rDNA loci located at telomeric positions proved to be typical. Loss of rDNA loci was observed in some polyploids, whereas others showed additivity with respect to their diploid relatives. Genome downsizing was observed in all polyploids. Banding patterns differed depending on the pair of species analysed, but some polyploid populations showed an increased number of heterochromatic bands. FISH and fluorochrome banding were useful in determining the systematic position of Artemisia bigelovii , for which a differential pattern was found as compared with the rest of the group. Additionally, FISH was used to detect the presence of the Arabidopsis-type telomere repeat for the first time in Artemisia.

Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina

*Transposable elements (TE) induce structural and epigenetic alterations in their host genome, with major evolutionary implications. These alterations are examined here in the context of allopolyploid speciation, on the recently formed invasive species Spartina anglica, which represents an excellent model to contrast plant genome dynamics following hybridization and genome doubling in natural conditions. *Methyl-sensitive transposon display was used to investigate the structural and epigenetic dynamics of TE insertion sites for several elements, and to contrast it with comparable genome-wide methyl-sensitive amplified polymorphism analyses. *While no transposition burst was detected, we found evidence of major structural and CpG methylation changes in the vicinity of TE insertions accompanying hybridization, and to a lesser extent, genome doubling. Genomic alteration appeared preferentially in the maternal subgenome, and the environment of TEs was specifically affected by large maternal-specific methylation changes, demonstrating that TEs fuel epigenetic alterations at the merging of diverged genomes. *Such genome changes indicate that nuclear incompatibilities in Spartina trigger immediate alterations, which are TE-specific with an important epigenetic component. Since most of this reorganization is conserved after genome doubling that produced a fertile invasive species, TEs certainly play a central role in the shock-induced dynamics of the genome during allopolyploid speciation.

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

Small RNAs, including microRNAs (miRNAs), small interfering RNAs (siRNAs), and trans-acting siRNAs (tasiRNAs), control gene expression and epigenetic regulation. Although the roles of miRNAs and siRNAs have been extensively studied, their expression diversity and evolution in closely related species and interspecific hybrids are poorly understood. Here, we show comprehensive analyses of miRNA expression and siRNA distributions in two closely related species Arabidopsis thaliana and Arabidopsis arenosa, a natural allotetraploid Arabidopsis suecica, and two resynthesized allotetraploid lines (F(1) and F(7)) derived from A. thaliana and A. arenosa. We found that repeat- and transposon-associated siRNAs were highly divergent between A. thaliana and A. arenosa. A. thaliana siRNA populations underwent rapid changes in F(1) but were stably maintained in F(7) and A. suecica. The correlation between siRNAs and nonadditive gene expression in allopolyploids is insignificant. In contrast, miRNA and tasiRNA sequences were conserved between species, but their expression patterns were highly variable between the allotetraploids and their progenitors. Many miRNAs tested were nonadditively expressed (deviating from the mid-parent value, MPV) in the allotetraploids and triggered unequal degradation of A. thaliana or A. arenosa targets. The data suggest that small RNAs produced during interspecific hybridization or polyploidization serve as a buffer against the genomic shock in interspecific hybrids and allopolyploids: Stable inheritance of repeat-associated siRNAs maintains chromatin and genome stability, whereas expression variation of miRNAs leads to changes in gene expression, growth vigor, and adaptation.

Genetic structure of Aegilops cylindrica Host in its native range and in the United States of America

Chloroplast and nuclear microsatellite markers were used to study genetic diversity and genetic structure of Aegilops cylindrica Host collected in its native range and in adventive sites in the USA. Our analysis suggests that Ae. cylindrica, an allotetraploid, arose from multiple hybridizations between Ae. markgrafii (Greuter) Hammer. and Ae. tauschii Coss. presumably along the Fertile Crescent, where the geographic distributions of its diploid progenitors overlap. However, the center of genetic diversity of this species now encompasses a larger area including northern Iraq, eastern Turkey, and Transcaucasia. Although the majority of accessions of Ae. cylindrica (87%) had D-type plastomes derived from Ae. tauschii, accessions with C-type plastomes (13%), derived from Ae. markgrafii, were also observed. This corroborates a previous study suggesting the dimaternal origin of Ae. cylindrica. Model-based and genetic distance-based clustering using both chloroplast and nuclear markers indicated that Ae. tauschii ssp. tauschii contributed one of its D-type plastomes and its D genome to Ae. cylindrica. Analysis of genetic structure using nuclear markers suggested that Ae. cylindrica accessions could be grouped into three subpopulations (arbitrarily named N-K1, N-K2, and N-K3). Members of the N-K1 subpopulation were the most numerous in its native range and members of the N-K2 subpopulation were the most common in the USA. Our analysis also indicated that Ae. cylindrica accessions in the USA were derived from a few founder genotypes. The frequency of Ae. cylindrica accessions with the C-type plastome in the USA (approximately 24%) was substantially higher than in its native range of distribution (approximately 3%) and all C-type Ae. cylindrica in the USA except one belonged to subpopulation N-K2. The high frequency of the C-type plastome in the USA may reflect a favorable nucleo-cytoplasmic combination.

Speciation as an active force in promoting genetic evolution

There is a growing appreciation among evolutionary biologists that the rate and tempo of molecular evolution might often be altered at or near the time of speciation, i.e. that speciation is in some way a special time for genes. Molecular phylogenies frequently reveal increased rates of genetic evolution associated with speciation and other lines of investigation suggest that various types of abrupt genomic disruption can play an important role in promoting speciation via reproductive isolation. These phenomena are in conflict with the gradual view of molecular evolution that is implicit in much of our thinking about speciation and in the tools of modern biology. This raises the prospect of studying the molecular evolutionary consequences of speciation per se and studying the footprint of speciation as an active force in promoting genetic divergence. Here we discuss the reasons to believe that speciation can play such a role and elaborate on possible mechanisms for accelerated rates of evolution following speciation. We provide an example of how it is possible detect whether accelerated bursts of evolution occur in neutral and/or adaptive regions of genes and discuss the implications of rapid episodes of change for conventional models of molecular evolution. Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche.

Ploidy-mediated reduced segregation facilitates fixation of heterozygosity in the aromatic grass, Cymbopogon martinii (Roxb.)

In most medicinal and aromatic plants, the vegetative tissue (e.g., roots, stems, leaves) is the source of the economic product. These plants are inherently heterozygous (natural allelic hybrids) and maintain their genetic makeup in nature by obligate vegetative propagation. Under seed cultivation, these plants incur population heterogeneity that reduces biomass and hampers product quality. Therefore, fixation of heterozygosity is vital for maintaining uniformity in quality of the economic product and quantity of biomass under seed cultivation. Although seed-grown clonal progenies identical to the mother plant can be obtained in certain plants that show an unusual breeding system called apomixis, such a breeding system is rare in medicinal and aromatic plants of economic value. Here we show an effective experimental strategy based on a polyploid model that facilitates fixation of heterozygosity in obligate asexual species owing to tetrasomic inheritance and low segregation in C(1) progenies from high-fertility C(0) autopolyploids. Using an obligate asexual species of aromatic grass-Cymbopogon martinii, we demonstrated that progenitor diploids with distal chiasma localization and low chiasmate association in meiosis, when changed into tetraploids, entail high gametic/seed fertility reflected in high bivalent pairing and balanced anaphase segregation. Their seed progenies evince crop homogeneity owing to reduced segregation, indicating fixation of heterozygosity present in the source diploids. Because C. martinii could be maintained through obligate vegetative propagation, here is a unique opportunity to utilize the polyploid advantage through C(1) seed progenies for commercial cultivation, as well as maintenance of original C(0) stock for raising seeds without losing polyploid heterosis normally threatened in subsequent segregating progenies on account of aneuploidy and gametic instability.

Contrasting evolutionary dynamics between angiosperm and mammalian genomes

Continuing advances in genomics are revealing substantial differences between genomes of major eukaryotic lineages. Because most data (in terms of depth and phylogenetic breadth) are available for angiosperms and mammals, we explore differences between these groups and show that angiosperms have less highly compartmentalized and more diverse genomes than mammals. In considering the causes of these differences, four mechanisms are highlighted: polyploidy, recombination, retrotransposition and genome silencing, which have different modes and time scales of activity. Angiosperm genomes are evolutionarily more dynamic and labile, whereas mammalian genomes are more stable at both the sequence and chromosome level. We suggest that fundamentally different life strategies and development feedback on the genome exist, influencing dynamics and evolutionary trajectories at all levels from the gene to the genome.

Microspore culture preferentially selects unreduced (2n) gametes from an interspecific hybrid of Brassica napus L. x Brassica carinata Braun

We analysed the products of male meiosis in microspore-derived progeny from a Brassica napus (AAC(n)C(n)) x Brassica carinata (BBC(c)C(c)) interspecific hybrid (ABC(n)C(c)). Genotyping at 102 microsatellite marker loci and nuclear DNA contents provided strong evidence that 26 of the 28 progeny (93%) were derived from unreduced (2n) gametes. The high level of C(n)C(c) marker heterozygosity, and parallel spindles at Anaphase II in the ABC(n)C(c) hybrid, indicated that unreduced gametes were formed by first division restitution. The frequency of dyads at the tetrad stage of pollen development (2.6%) suggested that unreduced gametes were preferentially selected in microspore culture. Segregation of marker alleles in the microspore-derived progeny was consistent with homologous recombination between C(n) and C(c) chromosomes and homoeologous recombination involving A-, B- and C-genome chromosomes during meiosis in the ABC(n)C(c) hybrid. We discuss the potential for using microspore culture of unreduced gametes in interspecific hybrids to map Brassica centromeres through half-tetrad analysis.

Heterochronic development of the floret meristem determines grain number per spikelet in diploid, tetraploid and hexaploid wheats

BACKGROUND AND AIMS

The inflorescence of grass species such as wheat, rice and maize consists of a unique reproductive structure called the spikelet, which is comprised of one, a few, or several florets (individual flowers). When reproductive growth is initiated, the inflorescence meristem differentiates a spikelet meristem as a lateral branch; the spikelet meristem then produces a floret meristem as a lateral branch. Interestingly, in wheat, the number of fertile florets per spikelet is associated with ploidy level: one or two florets in diploid, two or three in tetraploid, and more than three in hexaploid wheats. The objective of this study was to identify the mechanisms that regulate the architecture of the inflorescence in wheat and its relationship to ploidy level.

METHODS

The floral anatomy of diploid (Triticum monococcum), tetraploid (T. turgidum ssp. durum) and hexaploid (T. aestivum) wheat species were investigated by light and scanning electron microscopy to describe floret development and to clarify the timing of the initiation of the floret primordia. In situ hybridization analysis using Wknox1, a wheat knotted1 orthologue, was performed to determine the patterning of meristem formation in the inflorescence.

KEY RESULTS

The recessive natural mutation of tetraploid (T. turgidum ssp. turgidum) wheat, branching head (bh), which produces branched inflorescences, was used to demonstrate the utility of Wknox1 as a molecular marker for meristematic tissue. Then an analysis of Wknox1 expression was performed in diploid, tetraploid and hexaploid wheats and heterochronic development of the floret meristems was found among these wheat species.

CONCLUSIONS

It is shown that the difference in the number of floret primordia in diploid, tetraploid and hexaploid wheats is caused by the heterochronic initiation of floret meristem development from the spikelet meristem.

Different genome-specific chromosome stabilities in synthetic Brassica allohexaploids revealed by wide crosses with Orychophragmus

BACKGROUND AND AIMS

In sexual hybrids between cultivated Brassica species and another crucifer, Orychophragmus violaceus (2n = 24), parental genome separation during mitosis and meiosis is under genetic control but this phenomenon varies depending upon the Brassica species. To further investigate the mechanisms involved in parental genome separation, complex hybrids between synthetic Brassica allohexaploids (2n = 54, AABBCC) from three sources and O. violaceus were obtained and characterized.

METHODS

Genomic in situ hybridization, amplified fragment length polymorphism (AFLP) and single-strand conformation polymorphism (SSCP) were used to explore chromosomal/genomic components and rRNA gene expression of the complex hybrids and their progenies.

KEY RESULTS

Complex hybrids with variable fertility exhibited phenotypes that were different from the female allohexaploids and expressed some traits from O. violaceus. These hybrids were mixoploids (2n = 34-46) and retained partial complements of allohexaploids, including whole chromosomes of the A and B genomes and some of the C genome but no intact O. violaceus chromosomes; AFLP bands specific for O. violaceus, novel for two parents and absent in hexaploids were detected. The complex hybrids produced progenies with chromosomes/genomic complements biased to B. juncea (2n = 36, AABB) and novel B. juncea lines with two genomes of different origins. The expression of rRNA genes from B. nigra was revealed in all allohexaploids and complex hybrids, showing that the hierarchy of nucleolar dominance (B. nigra, BB > B. rapa, AA > B. oleracea, CC) in Brassica allotetraploids was still valid in these plants.

CONCLUSIONS

The chromosomes of three genomes in these synthetic Brassica allohexaploids showed different genome-specific stabilities (B > A > C) under induction of alien chromosome elimination in crosses with O. violaceus, which was possibly affected by nucleolar dominance.

Phenotypic, genetic and genomic consequences of natural and synthetic polyploidization of Nicotiana attenuata and Nicotiana obtusifolia

BACKGROUND AND METHODS

Polyploidy results in genetic turmoil, much of which is associated with new phenotypes that result in speciation. Five independent lines of synthetic allotetraploid N. x obtusiata (N x o) were created from crosses between the diploid N. attenuata (Na) (male) and N. obtusifolia (No) (female) and the autotetraploids of Na (NaT) and No (NoT) were synthesized. Their genetic, genomic and phenotypic changes were then compared with those of the parental diploid species (Na and No) as well as to the natural allotetraploids, N. quadrivalvis (Nq) and N. clevelandii (Nc), which formed 1 million years ago from crosses between ancient Na and No.

KEY RESULTS

DNA fingerprinting profiles (by UP-PCR) revealed that the five N x o lines shared similar but not identical profiles. Both synthetic and natural polyploidy showed a dosage effect on genome size (as measured in seeds); however, only Nq was associated with a genome upsizing. Phenotypic analysis revealed that at the cellular level, N x o lines had phenotypes intermediate of the parental phenotypes. Both allo- and autotetraploidization had a dosage effect on seed and dry biomass (except for NaT), but not on stalk height at first flower. Nc showed paternal (Na) cellular phenotypes but inherited maternal (No) biomass and seed mass, whereas Nq showed maternal (No) cellular phenotypes but inherited paternal (Na) biomass and seed mass patterns. Principal component analysis grouped Nq with N x o lines, due to similar seed mass, stalk height and genome size. These traits separated Nc, No and Na from Nq and N x o lines, whereas biomass distinguished Na from N x o and Nq lines, and NaT clustered closer to Nq and N x o lines than to Na.

CONCLUSIONS

Both allo- and autotetraploidy induce considerable morphological, genetic and genomic changes, many of which are retained by at least one of the natural polyploids. It is proposed that both natural and synthetic polyploids are well suited for studying the evolution of adaptive responses.

Polyploidy creates higher diversity among Cynodon accessions as assessed by molecular markers

Developing a better understanding of associations among ploidy level, geographic distribution, and genetic diversity of Cynodon accessions could be beneficial to bermudagrass breeding programs, and would enhance our understanding of the evolutionary biology of this warm season grass species. This study was initiated to: (1) determine ploidy analysis of Cynodon accessions collected from Turkey, (2) investigate associations between ploidy level and diversity, (3) determine whether geographic and ploidy distribution are related to nuclear genome variation, and (4) correlate among four nuclear molecular marker systems for Cynodon accessions' genetic analyses. One hundred and eighty-two Cynodon accessions collected in Turkey from an area south of the Taurus Mountains along the Mediterranean cost and ten known genotypes were genotyped using sequence related amplified polymorphism (SRAP), peroxidase gene polymorphism (POGP), inter-simple sequence repeat (ISSR), and random amplified polymorphic DNA (RAPD). The diploids, triploids, tetraploids, pentaploids, and hexaploids revealed by flow cytometry had a linear present band frequency of 0.36, 0.47, 0.49, 0.52, and 0.54, respectively. Regression analysis explained that quadratic relationship between ploidy level and band frequency was the most explanatory (r = 0.62, P < 0.001). The AMOVA results indicated that 91 and 94% of the total variation resided within ploidy level and provinces, respectively. The UPGMA analysis suggested that commercial bermudagrass cultivars only one-third of the available genetic variation. SRAP, POGP, ISSR, and RAPD markers differed in detecting relationships among the bermudagrass genotypes and rare alleles, suggesting more efficiency of combinatory analysis of molecular marker systems. Elucidating Cynodon accessions' genetic structure can aid to enhance breeding programs and broaden genetic base of commercial cultivars.

Genomic expression dominance in allopolyploids

BACKGROUND

Allopolyploid speciation requires rapid evolutionary reconciliation of two diverged genomes and gene regulatory networks. Here we describe global patterns of gene expression accompanying genomic merger and doubling in inter-specific crosses in the cotton genus (Gossypium L.).

RESULTS

Employing a micro-array platform designed against 40,430 unigenes, we assayed gene expression in two sets of parental diploids and their colchicine-doubled allopolyploid derivatives. Up to half of all genes were differentially expressed among diploids, a striking level of expression evolution among congeners. In the allopolyploids, most genes were expressed at mid-parent levels, but this was achieved via a phenomenon of genome-wide expression dominance, whereby gene expression was either up- or down-regulated to the level of one of the two parents, independent of the magnitude of gene expression. This massive expression dominance was approximately equal with respect to direction (up- or down-regulation), and the same diploid parent could be either the dominant or the recessive genome depending on the specific genomic combination. Transgressive up- and down-regulation were also common in the allopolyploids, both for genes equivalently or differentially expressed between the parents.

CONCLUSION

Our data provide novel insights into the architecture of gene expression in the allopolyploid nucleus, raise questions regarding the responsible underlying mechanisms of genome dominance, and provide clues into the enigma of the evolutionary prevalence of allopolyploids.

Faithful inheritance of cytosine methylation patterns in repeated sequences of the allotetraploid tobacco correlates with the expression of DNA methyltransferase gene families from both parental genomes

The widespread occurrence of epigenetic alterations in allopolyploid species deserves scrutiny that DNA methylation systems may be perturbed by interspecies hybridization and polyploidization. Here we studied the genes involved in DNA methylation in Nicotiana tabacum (tobacco) allotetraploid containing S and T genomes inherited from Nicotiana sylvestris and Nicotiana tomentosiformis progenitors. To determine the inheritance of DNA methyltransferase genes and their expression patterns we examined three major DNA methyltransferase families (MET1, CMT3 and DRM) from tobacco and the progenitor species. Using Southern blot hybridization and PCR-based methods (genomic CAPS), we found that the parental loci of these gene families are retained in tobacco. Homoeologous expression was found in all tissues examined (leaf, root, flower) suggesting that DNA methyltransferase genes were probably not themselves targets of uniparental epigenetic silencing for over thousands of generations of allotetraploid evolution. The level of CG and CHG methylation of selected high-copy repeated sequences was similar and high in tobacco and its diploid progenitors. We speculate that natural selection might favor additive expression of parental DNA methyltransferase genes maintaining high levels of DNA methylation in tobacco, which has a repeat-rich heterochromatic genome.

Gene loss and silencing in Tragopogon miscellus (Asteraceae): comparison of natural and synthetic allotetraploids

Whole-genome duplication (polyploidisation) is a widespread mechanism of speciation in plants. Over time, polyploid genomes tend towards a more diploid-like state, through downsizing and loss of duplicated genes (homoeologues), but relatively little is known about the timing of gene loss during polyploid formation and stabilisation. Several studies have also shown gene transcription to be affected by polyploidisation. Here, we examine patterns of gene loss in 10 sets of homoeologues in five natural populations of the allotetraploid Tragopogon miscellus that arose within the past 80 years following independent whole-genome duplication events. We also examine 44 first-generation synthetic allopolyploids of the same species. No cases of homoeologue loss arose in the first allopolyploid generation, but after 80 years, 1.6% of homoeologues were lost in natural populations. For seven homoeologue sets we also examined transcription, finding that 3.4% of retained homoeologues had been silenced in the natural populations, but none in the synthetic plants. The homoeologue losses and silencing events found were not fixed within natural populations and did not form a predictable pattern among populations. We therefore show haphazard loss and silencing of homoeologues, occurring within decades of polyploid formation in T. miscellus, but not in the initial generation.

Molecular phylogenetic analyses of nuclear and plastid DNA sequences support dysploid and polyploid chromosome number changes and reticulate evolution in the diversification of Melampodium (Millerieae, Asteraceae)

Chromosome evolution (including polyploidy, dysploidy, and structural changes) as well as hybridization and introgression are recognized as important aspects in plant speciation. A suitable group for investigating the evolutionary role of chromosome number changes and reticulation is the medium-sized genus Melampodium (Millerieae, Asteraceae), which contains several chromosome base numbers (x=9, 10, 11, 12, 14) and a number of polyploid species, including putative allopolyploids. A molecular phylogenetic analysis employing both nuclear (ITS) and plastid (matK) DNA sequences, and including all species of the genus, suggests that chromosome base numbers are predictive of evolutionary lineages within Melampodium. Dysploidy, therefore, has clearly been important during evolution of the group. Reticulate evolution is evident with allopolyploids, which prevail over autopolyploids and several of which are confirmed here for the first time, and also (but less often) on the diploid level. Within sect. Melampodium, the complex pattern of bifurcating phylogenetic structure among diploid taxa overlain by reticulate relationships from allopolyploids has non-trivial implications for intrasectional classification.

Analysis of the Nicotiana tabacum stigma/style transcriptome reveals gene expression differences between wet and dry stigma species

The success of plant reproduction depends on pollen-pistil interactions occurring at the stigma/style. These interactions vary depending on the stigma type: wet or dry. Tobacco (Nicotiana tabacum) represents a model of wet stigma, and its stigmas/styles express genes to accomplish the appropriate functions. For a large-scale study of gene expression during tobacco pistil development and preparation for pollination, we generated 11,216 high-quality expressed sequence tags (ESTs) from stigmas/styles and created the TOBEST database. These ESTs were assembled in 6,177 clusters, from which 52.1% are pistil transcripts/genes of unknown function. The 21 clusters with the highest number of ESTs (putative higher expression levels) correspond to genes associated with defense mechanisms or pollen-pistil interactions. The database analysis unraveled tobacco sequences homologous to the Arabidopsis (Arabidopsis thaliana) genes involved in specifying pistil identity or determining normal pistil morphology and function. Additionally, 782 independent clusters were examined by macroarray, revealing 46 stigma/style preferentially expressed genes. Real-time reverse transcription-polymerase chain reaction experiments validated the pistil-preferential expression for nine out of 10 genes tested. A search for these 46 genes in the Arabidopsis pistil data sets demonstrated that only 11 sequences, with putative equivalent molecular functions, are expressed in this dry stigma species. The reverse search for the Arabidopsis pistil genes in the TOBEST exposed a partial overlap between these dry and wet stigma transcriptomes. The TOBEST represents the most extensive survey of gene expression in the stigmas/styles of wet stigma plants, and our results indicate that wet and dry stigmas/styles express common as well as distinct genes in preparation for the pollination process.

Saltational evolution: hopeful monsters are here to stay

Since 150 years it is hypothesized now that evolution always proceeds in a countless number of very small steps (Darwin in On the origin of species by means of natural selection or the preservation of favoured races in the struggle of life, Murray, London, 1859), a view termed "gradualism". Few contemporary biologists will doubt that gradualism reflects the most frequent mode of evolution, but whether it is the only one remains controversial. It has been suggested that in some cases profound ("saltational") changes may have occurred within one or a few generations of organisms. Organisms with a profound mutant phenotype that have the potential to establish a new evolutionary lineage have been termed "hopeful monsters". Recently I have reviewed the concept of hopeful monsters in this journal mainly from a historical perspective, and provided some evidence for their past and present existence. Here I provide a brief update on data and discussions supporting the view that hopeful monsters and saltational evolution are valuable biological concepts. I suggest that far from being mutually exclusive scenarios, both gradual and saltational evolution are required to explain the complexity and diversity of life on earth. In my view, gradual changes represent the usual mode of evolution, but are unlikely to be able to explain all key innovations and changes in body plans. Saltational changes involving hopeful monsters are probably very exceptional events, but since they have the potential to establish profound novelties sometimes facilitating adaptive radiations, they are of quite some importance, even if they would occur in any evolutionary lineage less than once in a million years. From that point of view saltational changes are not more bizarre scenarios of evolutionary change than whole genome duplications, endosymbiosis or impacts of meteorites. In conclusion I argue that the complete dismissal of saltational evolution is a major historical error of evolutionary biology tracing back to Darwin that needs to be rectified.

Genetic regulation of meiotic cross-overs between related genomes in Brassica napus haploids and hybrids

Although the genetic regulation of recombination in allopolyploid species plays a pivotal role in evolution and plant breeding, it has received little recent attention, except in wheat (Triticum aestivum). PrBn is the main locus that determines the number of nonhomologous associations during meiosis of microspore cultured Brassica napus haploids (AC; 19 chromosomes). In this study, we examined the role played by PrBn in recombination. We generated two haploid x euploid populations using two B. napus haploids with differing PrBn (and interacting genes) activity. We analyzed molecular marker transmission in these two populations to compare genetic changes, which have arisen during meiosis. We found that cross-over number in these two genotypes was significantly different but that cross-overs between nonhomologous chromosomes showed roughly the same distribution pattern. We then examined genetic recombination along a pair of A chromosomes during meiosis of B. rapa x B. napus AAC and AACC hybrids that were produced with the same two B. napus genotypes. We observed significant genotypic variation in cross-over rates between the two AAC hybrids but no difference between the two AACC hybrids. Overall, our results show that PrBn changes the rate of recombination between nonhomologous chromosomes during meiosis of B. napus haploids and also affects homologous recombination with an effect that depends on plant karyotype.

Duplicate genes increase expression diversity in closely related species and allopolyploids

Polyploidy or whole genome duplication (WGD) provides raw genetic materials for sequence and expression evolution of duplicate genes. However, the mode and tempo of expression divergence between WGD duplicate genes in closely related species and recurrent allopolyploids are poorly understood. Arabidopsis is a suitable system for testing the hypothesis that duplicate genes increase expression diversity and regulatory networks. In Arabidopsis, WGD occurred more than once before the split between Arabidopsis thaliana and Arabidopsis arenosa, and both natural and human-made allotetraploids are available. Comparative genomic hybridization analysis indicated that single-copy and duplicate genes after WGD were well preserved in A. thaliana and A. arenosa. Analysis of gene expression microarrays showed that duplicate genes generally had higher levels of expression divergence between two closely related species than single-copy genes. The proportion of the progenitors' duplicate genes that were nonadditively expressed in the resynthesized and natural allotetraploids was significantly higher than that of single-copy genes. Duplicate genes related to environmental stresses tended to be differentially expressed, and multicopy duplicate genes were likely to diverge expression between progenitors and in the allotetraploids. Compared with single-copy genes, duplicate genes tended to contain TATA boxes and less DNA methylation in the promoter regions, facilitating transcriptional regulation by binding transcription factors and/or cis- and trans-acting proteins. The data suggest an important role of WGD duplicate genes in modulating diverse and novel gene expression changes in response to external environmental cues and internal genetic turmoil such as recurrent polyploidy events.

Hybrid speciation in angiosperms: parental divergence drives ploidy

Hybridization and polyploidy are now hypothesized to have regularly stimulated speciation in angiosperms, but individual or combined involvement of these two processes seems to involve significant differences in pathways of formation, establishment and evolutionary consequences of resulting lineages. We evaluate here the classical cytological hypothesis that ploidy in hybrid speciation is governed by the extent of chromosomal rearrangements among parental species. Within a phylogenetic framework, we calculate genetic divergence indices for 50 parental species pairs and use these indices as surrogates for the overall degree of genomic divergence (that is, as proxy for assessments of dissimilarity of the parental chromosomes). The results confirm that genomic differentiation between progenitor taxa influences the likelihood of diploid (homoploid) versus polyploid hybrid speciation because genetic divergence between parents of polyploids is found to be significantly greater than in the case of homoploid hybrid species. We argue that this asymmetric relationship may be reinforced immediately after hybrid formation, during stabilization and establishment. Underlying mechanisms potentially producing this pattern are discussed.

Polyploidy and angiosperm diversification

Polyploidy has long been recognized as a major force in angiosperm evolution. Recent genomic investigations not only indicate that polyploidy is ubiquitous among angiosperms, but also suggest several ancient genome-doubling events. These include ancient whole genome duplication (WGD) events in basal angiosperm lineages, as well as a proposed paleohexaploid event that may have occurred close to the eudicot divergence. However, there is currently no evidence for WGD in Amborella, the putative sister species to other extant angiosperms. The question is no longer "What proportion of angiosperms are polyploid?", but "How many episodes of polyploidy characterize any given lineage?" New algorithms provide promise that ancestral genomes can be reconstructed for deep divergences (e.g., it may be possible to reconstruct the ancestral eudicot or even the ancestral angiosperm genome). Comparisons of diversification rates suggest that genome doubling may have led to a dramatic increase in species richness in several angiosperm lineages, including Poaceae, Solanaceae, Fabaceae, and Brassicaceae. However, additional genomic studies are needed to pinpoint the exact phylogenetic placement of the ancient polyploidy events within these lineages and to determine when novel genes resulting from polyploidy have enabled adaptive radiations.

The role of hybridization in plant speciation

The importance of hybridization in plant speciation and evolution has been debated for decades, with opposing views of hybridization as either a creative evolutionary force or evolutionary noise. Hybrid speciation may occur at either the homoploid (i.e., between two species of the same ploidy) or the polyploid level, each with its attendant genetic and evolutionary consequences. Whereas allopolyploidy (i.e., resulting from hybridization and genome doubling) has long been recognized as an important mode of plant speciation, the implications of genome duplication have typically not been taken into account in most fields of plant biology. Recent developments in genomics are revolutionizing our views of angiosperm genomes, demonstrating that perhaps all angiosperms have likely undergone at least one round of polyploidization and that hybridization has been an important force in generating angiosperm species diversity. Hybridization and polyploid formation continue to generate species diversity, with several new allopolyploids having originated just within the past century or so. The origins of polyploid species-whether via hybridization between species or between genetically differentiated populations of a single species-and the immediate genetic consequences of polyploid formation are therefore receiving enthusiastic attention. The time is therefore right for a review of the role of hybridization in plant speciation.

Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean

The genomes of most, if not all, flowering plants have undergone whole genome duplication events during their evolution. The impact of such polyploidy events is poorly understood, as is the fate of most duplicated genes. We sequenced an approximately 1 million-bp region in soybean (Glycine max) centered on the Rpg1-b disease resistance gene and compared this region with a region duplicated 10 to 14 million years ago. These two regions were also compared with homologous regions in several related legume species (a second soybean genotype, Glycine tomentella, Phaseolus vulgaris, and Medicago truncatula), which enabled us to determine how each of the duplicated regions (homoeologues) in soybean has changed following polyploidy. The biggest change was in retroelement content, with homoeologue 2 having expanded to 3-fold the size of homoeologue 1. Despite this accumulation of retroelements, over 77% of the duplicated low-copy genes have been retained in the same order and appear to be functional. This finding contrasts with recent analyses of the maize (Zea mays) genome, in which only about one-third of duplicated genes appear to have been retained over a similar time period. Fluorescent in situ hybridization revealed that the homoeologue 2 region is located very near a centromere. Thus, pericentromeric localization, per se, does not result in a high rate of gene inactivation, despite greatly accelerated retrotransposon accumulation. In contrast to low-copy genes, nucleotide-binding-leucine-rich repeat disease resistance gene clusters have undergone dramatic species/homoeologue-specific duplications and losses, with some evidence for partitioning of subfamilies between homoeologues.