After a dozen years of progress the origin of angiosperms is still a great mystery

Reciprocal expression of MADS-box genes and DNA methylation reconfiguration initiate bisexual cones in spruce

The naturally occurring bisexual cone of gymnosperms has long been considered a possible intermediate stage in the origin of flowers, but the mechanisms governing bisexual cone formation remain largely elusive. Here, we employed transcriptomic and DNA methylomic analyses, together with hormone measurement, to investigate the molecular mechanisms underlying bisexual cone development in the conifer Picea crassifolia. Our study reveals a "bisexual" expression profile in bisexual cones, especially in expression patterns of B-class, C-class and LEAFY genes, supporting the out of male model. GGM7 could be essential for initiating bisexual cones. DNA methylation reconfiguration in bisexual cones affects the expression of key genes in cone development, including PcDAL12, PcDAL10, PcNEEDLY, and PcHDG5. Auxin likely plays an important role in the development of female structures of bisexual cones. This study unveils the potential mechanisms responsible for bisexual cone formation in conifers and may shed light on the evolution of bisexuality.

Handling Logical Character Dependency in Phylogenetic Inference: Extensive Performance Testing of Assumptions and Solutions Using Simulated and Empirical Data

Logical character dependency is a major conceptual and methodological problem in phylogenetic inference of morphological data sets, as it violates the assumption of character independence that is common to all phylogenetic methods. It is more frequently observed in higher-level phylogenies or in data sets characterizing major evolutionary transitions, as these represent parts of the tree of life where (primary) anatomical characters either originate or disappear entirely. As a result, secondary traits related to these primary characters become "inapplicable" across all sampled taxa in which that character is absent. Various solutions have been explored over the last three decades to handle character dependency, such as alternative character coding schemes and, more recently, new algorithmic implementations. However, the accuracy of the proposed solutions, or the impact of character dependency across distinct optimality criteria, has never been directly tested using standard performance measures. Here, we utilize simple and complex simulated morphological data sets analyzed under different maximum parsimony optimization procedures and Bayesian inference to test the accuracy of various coding and algorithmic solutions to character dependency. This is complemented by empirical analyses using a recoded data set on palaeognathid birds. We find that in small, simulated data sets, absent coding performs better than other popular coding strategies available (contingent and multistate), whereas in more complex simulations (larger data sets controlled for different tree structure and character distribution models) contingent coding is favored more frequently. Under contingent coding, a recently proposed weighting algorithm produces the most accurate results for maximum parsimony. However, Bayesian inference outperforms all parsimony-based solutions to handle character dependency due to fundamental differences in their optimization procedures-a simple alternative that has been long overlooked. Yet, we show that the more primary characters bearing secondary (dependent) traits there are in a data set, the harder it is to estimate the true phylogenetic tree, regardless of the optimality criterion, owing to a considerable expansion of the tree parameter space. [Bayesian inference, character dependency, character coding, distance metrics, morphological phylogenetics, maximum parsimony, performance, phylogenetic accuracy.].

The origin and evolution of carpels and fruits from an evo-devo perspective

The flower is an evolutionary innovation in angiosperms that drives the evolution of biodiversity. The carpel is integral to a flower and develops into fruits after fertilization, while the perianth, consisting of the calyx and corolla, is decorative to facilitate pollination and protect the internal organs, including the carpels and stamens. Therefore, the nature of flower origin is carpel and stamen origin, which represents one of the greatest and fundamental unresolved issues in plant evolutionary biology. Here, we briefly summarize the main progress and key genes identified for understanding floral development, focusing on the origin and development of the carpels. Floral ABC models have played pioneering roles in elucidating flower development, but remain insufficient for resolving flower and carpel origin. The genetic basis for carpel origin and subsequent diversification leading to fruit diversity also remains elusive. Based on current research progress and technological advances, simplified floral models and integrative evolutionary-developmental (evo-devo) strategies are proposed for elucidating the genetics of carpel origin and fruit evolution. Stepwise birth of a few master regulatory genes and subsequent functional diversification might play a pivotal role in these evolutionary processes. Among the identified transcription factors, AGAMOUS (AG) and CRABS CLAW (CRC) may be the two core regulatory genes for carpel origin as they determine carpel organ identity, determinacy, and functionality. Therefore, a comparative identification of their protein-protein interactions and downstream target genes between flowering and non-flowering plants from an evo-devo perspective may be primary projects for elucidating carpel origin and development.

Serial Section-Based Three-Dimensional Reconstruction of Anaxagorea (Annonaceae) Carpel Vasculature and Implications for the Morphological Relationship between the Carpel and the Ovule

Elucidating the origin of flowers has been a challenge in botany for a long time. One of the central questions surrounding the origin of flowers is how to interpret the carpel, especially the relationship between the phyllome part (carpel wall) and the ovule. Recently, consensus favors the carpel originating from the fusion of an ovule-bearing part and the phyllome part that subtends it. Considering the carpel is a complex organ, the accurate presentation of the anatomical structure of the carpel is necessary for resolving this question. Anaxagorea is the most basal genus in a primitive angiosperm family, Annonaceae. The conspicuous stipe at the base of each carpel makes it an ideal material for exploring the histological relationships among the receptacle, the carpel, and the ovule. In the present study, floral organogenesis and vasculature were delineated in Anaxagorea luzonensis and Anaxagorea javanica, and a three-dimensional model of the carpel vasculature was reconstructed based on serial sections. The results show that in Anaxagorea, the vasculature in the carpel branches in the form of shoots. The radiosymmetrical vasculature pattern is repeatedly presented in the receptacle, the carpel, and the funiculus of the ovule. This provides anatomical evidence of the composite origin of the carpel.

Mesozoic cupules and the origin of the angiosperm second integument

The second integument of the angiosperm ovule is unique among seed plants, with developmental genetics that are distinct from those of the inner integument¹. Understanding how the second integument should be compared to structures in other seed plants is therefore crucial to resolving the long-standing question of the origin of angiosperms^2-6. Attention has focused on several extinct plants with recurved cupules that are reminiscent of the anatropous organization of the basic bitegmic ovules of angiosperms^1-6, but interpretations have been hampered by inadequate information on the relevant fossils. Here we describe abundant exceptionally well-preserved recurved cupules from a newly discovered silicified peat dating to the Early Cretaceous epoch (around 125.6 million years ago) in Inner Mongolia, China. The new material, combined with re-examination of potentially related fossils, indicates that the recurved cupules of several groups of Mesozoic plants are all fundamentally comparable, and that their structure is consistent with the recurved form and development of the second integument in the bitegmic anatropous ovules of angiosperms. Recognition of these angiosperm relatives (angiophytes) provides a partial answer to the question of angiosperm origins, will help to focus future work on seed plant phylogenetics and has important implications for ideas on the origin of the angiosperm carpel.

Reconstructing the ancestral flower of extant angiosperms: the 'war of the whorls' is heating up

The origin of the angiosperm flower is a long-standing problem of botany and evolutionary biology. One widely accepted milestone towards solving it is the reconstruction of the ancestral flower of extant angiosperms, here termed 'AFEA'. A recent approach employing novel methods gave results that were not anticipated. Most notably the reconstructed phyllotaxis of AFEA soon was criticized and sparked a heated debate in the literature. To better explain, clarify, and perhaps cool the debate, we first summarize the results of previous attempts to reconstruct AFEA and contrast them with the more recent, controversial prediction of its structure. We then outline the major arguments made by contrasting parties in the recent debate. Finally, we discuss two key topics, the molecular mechanism of phyllotaxis and the role of gene regulatory networks during flower development and evolution, that may help to clarify the issue in the intermediate future.

A genome for gnetophytes and early evolution of seed plants

Gnetophytes are an enigmatic gymnosperm lineage comprising three genera, Gnetum, Welwitschia and Ephedra, which are morphologically distinct from all other seed plants. Their distinctiveness has triggered much debate as to their origin, evolution and phylogenetic placement among seed plants. To increase our understanding of the evolution of gnetophytes, and their relation to other seed plants, we report here a high-quality draft genome sequence for Gnetum montanum, the first for any gnetophyte. By using a novel genome assembly strategy to deal with high levels of heterozygosity, we assembled >4 Gb of sequence encoding 27,491 protein-coding genes. Comparative analysis of the G. montanum genome with other gymnosperm genomes unveiled some remarkable and distinctive genomic features, such as a diverse assemblage of retrotransposons with evidence for elevated frequencies of elimination rather than accumulation, considerable differences in intron architecture, including both length distribution and proportions of (retro) transposon elements, and distinctive patterns of proliferation of functional protein domains. Furthermore, a few gene families showed Gnetum-specific copy number expansions (for example, cellulose synthase) or contractions (for example, Late Embryogenesis Abundant protein), which could be connected with Gnetum's distinctive morphological innovations associated with their adaptation to warm, mesic environments. Overall, the G. montanum genome enables a better resolution of ancestral genomic features within seed plants, and the identification of genomic characters that distinguish Gnetum from other gymnosperms.

Extending the scope of Darwin's 'abominable mystery': integrative approaches to understanding angiosperm origins and species richness

Background and aims

Angiosperms are the most species-rich group of land plants, but their origins and fast and intense diversification still require an explanation.

Scope

Extending research scopes can broaden theoretical frameworks and lines of evidence that can lead to solving this 'abominable mystery'. Solutions lie in understanding evolutionary trends across taxa and throughout the Phanerozoic, and integration between hypotheses and ideas that are derived from multiple disciplines.

Key Findings

Descriptions of evolutionary chronologies should integrate between molecular phylogenies, descriptive palaeontology and palaeoecology. New molecular chronologies open new avenues of research of possible Palaeozoic angiosperm ancestors and how they evolved during as many as 200Myr until the emergence of true angiosperms. The idea that 'biodiversity creates biodiversity' requires evidence from past and present ecologies, with changes in herbivory and resource availability throughout the Phanerozoic appearing to be particularly promising.

Conclusions

Promoting our understanding of angiosperm origins and diversification in particular, and the evolution of biodiversity in general, requires more profound understanding of the ecological past through integrating taxonomic, temporal and ecological scopes.

How to Evolve a Perianth: A Review of Cadastral Mechanisms for Perianth Identity

The flower of angiosperms is considered to be a major evolutionary innovation that impacted the whole biome. In particular, two properties of the flower are classically linked to its ecological success: bisexuality and a differentiated perianth with sepals and petals. Although the molecular basis for floral organ identity is well understood in extant species and summarized in the famous ABC model, how perianth identity appeared during evolution is still unknown. Here we propose that cadastral mechanisms that maintain reproductive organ identities to the center of the flower could have supported perianth evolution. In particular, repressing B- and C-class genes expression toward the inner whorls of the flower, is a key process to isolate domains with sepal and petal identity in the outer whorls. We review from the literature in model species the diverse regulators that repress B- and C-class genes expression to the center of the flower. This review highlights the existence of both unique and conserved repressors between species, and possible candidates to investigate further in order to shed light on perianth evolution.

A link between LEAFY and B-gene homologues in Welwitschia mirabilis sheds light on ancestral mechanisms prefiguring floral development

Flowering plants evolved from an unidentified gymnosperm ancestor. Comparison of the mechanisms controlling development in angiosperm flowers and gymnosperm cones may help to elucidate the mysterious origin of the flower. We combined gene expression studies with protein behaviour characterization in Welwitschia mirabilis to test whether the known regulatory links between LEAFY and its MADS-box gene targets, central to flower development, might also contribute to gymnosperm reproductive development. We found that WelLFY, one of two LEAFY-like genes in Welwitschia, could be an upstream regulator of the MADS-box genes APETALA3/PISTILLATA-like (B-genes). We demonstrated that, even though their DNA-binding domains are extremely similar, WelLFY and its paralogue WelNDLY exhibit distinct DNA-binding specificities, and that, unlike WelNDLY, WelLFY shares with its angiosperm orthologue the capacity to bind promoters of Welwitschia B-genes. Finally, we identified several cis-elements mediating these interactions in Welwitschia and obtained evidence that the link between LFY homologues and B-genes is also conserved in two other gymnosperms, Pinus and Picea. Although functional approaches to investigate cone development in gymnosperms are limited, our state-of-the-art biophysical techniques, coupled with expression studies, provide evidence that crucial links, central to the control of floral development, may already have existed before the appearance of flowers.

The ancestral flower of angiosperms and its early diversification

Recent advances in molecular phylogenetics and a series of important palaeobotanical discoveries have revolutionized our understanding of angiosperm diversification. Yet, the origin and early evolution of their most characteristic feature, the flower, remains poorly understood. In particular, the structure of the ancestral flower of all living angiosperms is still uncertain. Here we report model-based reconstructions for ancestral flowers at the deepest nodes in the phylogeny of angiosperms, using the largest data set of floral traits ever assembled. We reconstruct the ancestral angiosperm flower as bisexual and radially symmetric, with more than two whorls of three separate perianth organs each (undifferentiated tepals), more than two whorls of three separate stamens each, and more than five spirally arranged separate carpels. Although uncertainty remains for some of the characters, our reconstruction allows us to propose a new plausible scenario for the early diversification of flowers, leading to new testable hypotheses for future research on angiosperms.

The significance of developmental robustness for species diversity

BACKGROUND

The origin of new species and of new forms is one of the fundamental characteristics of evolution. However, the mechanisms that govern the diversity and disparity of lineages remain poorly understood. Particularly unclear are the reasons why some taxa are vastly more species-rich than others and the manner in which species diversity and morphological disparity are interrelated.

SCOPE AND CONCLUSIONS

Evolutionary innovations and ecological opportunities are usually cited as among the major factors promoting the evolution of species diversity. In many cases it is likely that these factors are positively reinforcing, with evolutionary innovations creating ecological opportunities that in turn foster the origin of new innovations. However, we propose that a third factor, developmental robustness, is very often essential for this reinforcement to be effective. Evolutionary innovations need to be stably and robustly integrated into the developmental genetic programme of an organism to be a suitable substrate for selection to 'explore' ecological opportunities and morphological 'design' space (morphospace). In particular, we propose that developmental robustness of the bauplan is often a prerequisite for the exploration of morphospace and to enable the evolution of further novelties built upon this bauplan Thus, while robustness may reduce the morphological disparity at one level, it may be the basis for increased morphological disparity and for evolutionary innovations at another level, thus fostering species diversity.

A transcriptomics investigation into pine reproductive organ development

The development of reproductive structures in gymnosperms is still poorly studied because of a lack of genomic information and useful genetic tools. The hermaphroditic reproductive structure derived from unisexual gymnosperms is an even less studied aspect of seed plant evolution. To extend our understanding of the molecular mechanism of hermaphroditism and the determination of sexual identity of conifer reproductive structures in general, unisexual and bisexual cones from Pinus tabuliformis were profiled for gene expression using 60K microarrays. Expression patterns of genes during progression of sexual cone development were analysed using RNA-seq. The results showed that, overall, the transcriptomes of male structures in bisexual cones were more similar to those of female cones. However, the expression of several MADS-box genes in the bisexual cones was similar to that of male cones at the more juvenile developmental stage, while despite these expression shifts, male structures of bisexual cones and normal male cones were histologically indistinguishable and cone development was continuous. This study represents a starting point for in-depth analysis of the molecular regulation of cone development and also the origin of hermaphroditism in pine.

Did Convergent Protein Evolution Enable Phytoplasmas to Generate 'Zombie Plants'?

Phytoplasmas are pathogenic bacteria that reprogram plant development such that leaf-like structures instead of floral organs develop. Infected plants are sterile and mainly serve to propagate phytoplasmas and thus have been termed 'zombie plants'. The developmental reprogramming relies on specific interactions of the phytoplasma protein SAP54 with a small subset of MADS-domain transcription factors. Here, we propose that SAP54 folds into a structure that is similar to that of the K-domain, a protein-protein interaction domain of MADS-domain proteins. We suggest that undergoing convergent structural and sequence evolution, SAP54 evolved to mimic the K-domain. Given the high specificity of resulting developmental alterations, phytoplasmas might be used to study flower development in genetically intractable plants.

Sequenced genomes and rapidly emerging technologies pave the way for conifer evolutionary developmental biology

Conifers, Ginkgo, cycads and gnetophytes comprise the four groups of extant gymnosperms holding a unique position of sharing common ancestry with the angiosperms. Comparative studies of gymnosperms and angiosperms are the key to a better understanding of ancient seed plant morphologies, how they have shifted over evolution to shape modern day species, and how the genes governing these morphologies have evolved. However, conifers and other gymnosperms have been notoriously difficult to study due to their long generation times, inaccessibility to genetic experimentation and unavailable genome sequences. Now, with three draft genomes from spruces and pines, rapid advances in next generation sequencing methods for genome wide expression analyses, and enhanced methods for genetic transformation, we are much better equipped to address a number of key evolutionary questions relating to seed plant evolution. In this mini-review we highlight recent progress in conifer developmental biology relevant to evo-devo questions. We discuss how genome sequence data and novel techniques might allow us to explore genetic variation and naturally occurring conifer mutants, approaches to reduce long generation times to allow for genetic studies in conifers, and other potential upcoming research avenues utilizing current and emergent techniques. Results from developmental studies of conifers and other gymnosperms in comparison to those in angiosperms will provide information to trace core molecular developmental control tool kits of ancestral seed plants, but foremost they will greatly improve our understanding of the biology of conifers and other gymnosperms in their own right.

Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT)

While gymnosperm ovules have one integument, in most angiosperms two integuments surround the ovules. Unitegmic ovules have arisen independently several times during the evolution of angiosperms, but the ultimate genetic cause of the presence of a single integument remains elusive. We compared species of the genus Prunus that have different numbers of integuments: bitegmic species, such as Prunus armeniaca (apricot) and Prunus persica (peach), and unitegmic species, such as Prunus incisa, analyzing the expression pattern of genes that are involved in integument development in Arabidopsis thaliana: INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT). Bitegmic and unitegmic species showed similar INO expression patterns, indicative of the conservation of an outer integument. However, expression of ETT, which occurs in the boundary of the outer and inner integuments, was altered in unitegmic ovules, which showed lack of ETT expression. These results strongly suggest that the presence of a single integument could be attributable to the amalgamation of two integuments and support the role of ETT in the fusion of the outer and inner integuments in unitegmic ovules, a situation that could be widespread in other unitegmic species of angiosperms.

Four hundred million years of silica biomineralization in land plants

Biomineralization plays a fundamental role in the global silicon cycle. Grasses are known to mobilize significant quantities of Si in the form of silica biominerals and dominate the terrestrial realm today, but they have relatively recent origins and only rose to taxonomic and ecological prominence within the Cenozoic Era. This raises questions regarding when and how the biological silica cycle evolved. To address these questions, we examined silica abundances of extant members of early-diverging land plant clades, which show that silica biomineralization is widespread across terrestrial plant linages. Particularly high silica abundances are observed in lycophytes and early-diverging ferns. However, silica biomineralization is rare within later-evolving gymnosperms, implying a complex evolutionary history within the seed plants. Electron microscopy and X-ray spectroscopy show that the most common silica-mineralized tissues include the vascular system, epidermal cells, and stomata, which is consistent with the hypothesis that biomineralization in plants is frequently coupled to transpiration. Furthermore, sequence, phylogenetic, and structural analysis of nodulin 26-like intrinsic proteins from diverse plant genomes points to a plastic and ancient capacity for silica accumulation within terrestrial plants. The integration of these two comparative biology approaches demonstrates that silica biomineralization has been an important process for land plants over the course of their >400 My evolutionary history.

Evolution of the Plant Reproduction Master Regulators LFY and the MADS Transcription Factors: The Role of Protein Structure in the Evolutionary Development of the Flower

Understanding the evolutionary leap from non-flowering (gymnosperms) to flowering (angiosperms) plants and the origin and vast diversification of the floral form has been one of the focuses of plant evolutionary developmental biology. The evolving diversity and increasing complexity of organisms is often due to relatively small changes in genes that direct development. These "developmental control genes" and the transcription factors (TFs) they encode, are at the origin of most morphological changes. TFs such as LEAFY (LFY) and the MADS-domain TFs act as central regulators in key developmental processes of plant reproduction including the floral transition in angiosperms and the specification of the male and female organs in both gymnosperms and angiosperms. In addition to advances in genome wide profiling and forward and reverse genetic screening, structural techniques are becoming important tools in unraveling TF function by providing atomic and molecular level information that was lacking in purely genetic approaches. Here, we summarize previous structural work and present additional biophysical and biochemical studies of the key master regulators of plant reproduction - LEAFY and the MADS-domain TFs SEPALLATA3 and AGAMOUS. We discuss the impact of structural biology on our understanding of the complex evolutionary process leading to the development of the bisexual flower.

Gene networks controlling Arabidopsis thaliana flower development

The formation of flowers is one of the main models for studying the regulatory mechanisms that underlie plant development and evolution. Over the past three decades, extensive genetic and molecular analyses have led to the identification of a large number of key floral regulators and to detailed insights into how they control flower morphogenesis. In recent years, genome-wide approaches have been applied to obtaining a global view of the gene regulatory networks underlying flower formation. Furthermore, mathematical models have been developed that can simulate certain aspects of this process and drive further experimentation. Here, we review some of the main findings made in the field of Arabidopsis thaliana flower development, with an emphasis on recent advances. In particular, we discuss the activities of the floral organ identity factors, which are pivotal for the specification of the different types of floral organs, and explore the experimental avenues that may elucidate the molecular mechanisms and gene expression programs through which these master regulators of flower development act.

Inside the gynoecium: at the carpel margin

The gynoecium, which is produced at the center of most flowers, is the female reproductive organ and consists of one or more carpels. The Arabidopsis gynoecium consists of two fused carpels. Its inner tissues possess meristematic characteristics and are called the carpel margin meristem (CMM), because they are located at the margins of the carpels and generate the 'marginal' tissues of the gynoecium (placenta, ovules, septum, transmitting tract, style, and stigma). A key question is which factors are guiding the correct development of all these tissues, many of which are essential for reproduction. Besides regulatory genes, hormones play an important part in the development of the marginal tissues, and recent reports have highlighted the role of cytokinins, as discussed in this review.

Angiosperm-like pollen and Afropollis from the Middle Triassic (Anisian) of the Germanic Basin (Northern Switzerland)

Here we report on angiosperm-like pollen and Afropollis from the Anisian (Middle Triassic, 247.2-242.0 Ma) of a mid-latitudinal site in Northern Switzerland. Small monosulcate pollen grains with typical reticulate (semitectate) sculpture, columellate structure of the sexine and thin nexine show close similarities to early angiosperm pollen known from the Early Cretaceous. However, they differ in their extremely thin inner layer (nexine). Six different pollen types (I-VI) are differentiated based on size, reticulation pattern, and exine structure. The described pollen grains show all the essential features of angiosperm pollen. However, considering the lack of a continuous record throughout the lower part of the Mesozoic and the comparison with the oldest Cretaceous finds we suggest an affinity to an angiosperm stem group. Together with the previously published records from the Middle Triassic of the Barents Sea area the angiosperm-like pollen grains reflect a considerable diversity of the parent plants during the Middle Triassic. Sedimentological evidence and associated palynofloras also suggest a remarkable ecological range for these plants. Associated with these grains we found pollen comparable to the genus Afropollis. Representatives of this genus are commonly recorded in Lower Cretaceous sediments of low latitudes, but until now had no record from the lower part of the Mesozoic.

Darwin's naturalization hypothesis: scale matters in coastal plant communities

Darwin proposed two seemingly contradictory hypotheses for a better understanding of biological invasions. Strong relatedness of invaders to native communities as an indication of niche overlap could promote naturalization because of appropriate niche adaptation, but could also hamper naturalization because of negative interactions with native species ('Darwin's naturalization hypothesis'). Although these hypotheses provide clear and opposing predictions for expected patterns of species relatedness in invaded communities, so far no study has been able to clearly disentangle the underlying mechanisms. We hypothesize that conflicting past results are mainly due to the neglected role of spatial resolution of the community sampling. In this study, we corroborate both of Darwin's expectations by using phylogenetic relatedness as a measure of niche overlap and by testing the effects of sampling resolution in highly invaded coastal plant communities. At spatial resolutions fine enough to detect signatures of biotic interactions, we find that most invaders are less related to their nearest relative in invaded plant communities than expected by chance (phylogenetic overdispersion). Yet at coarser spatial resolutions, native assemblages become more invasible for closely-related species as a consequence of habitat filtering (phylogenetic clustering). Recognition of the importance of the spatial resolution at which communities are studied allows apparently contrasting theoretical and empirical results to be reconciled. Our study opens new perspectives on how to better detect, differentiate and understand the impact of negative biotic interactions and habitat filtering on the ability of invaders to establish in native communities.

Virus-induced gene silencing (VIGS) in plants: an overview of target species and the virus-derived vector systems

The analysis of gene functions in non-model plant species is often hampered by the fact that stable genetic transformation to downregulate gene expression is laborious and time-consuming, or, for some species, even not achievable. Virus-induced gene silencing (VIGS) can serve as an alternative to mutant collections or stable transgenic plants to allow the characterization of gene functions in a wide range of angiosperm species, albeit in a transient way. VIGS vector systems have been developed from both RNA and DNA plant viral sources to specifically silence target genes in plants. VIGS is nowadays widely used in plant genetics for gene knockdown due to its ease of use and the short time required to generating phenotypes. Here, we summarize successfully targeted eudicot and monocot plant species along with their specific VIGS vector systems which are already available for researchers.

Genomic profiling of rice sperm cell transcripts reveals conserved and distinct elements in the flowering plant male germ lineage

Genomic assay of sperm cell RNA provides insight into functional control, modes of regulation, and contributions of male gametes to double fertilization. Sperm cells of rice (Oryza sativa) were isolated from field-grown, disease-free plants and RNA was processed for use with the full-genome Affymetrix microarray. Comparison with Gene Expression Omnibus (GEO) reference arrays confirmed expressionally distinct gene profiles. A total of 10,732 distinct gene sequences were detected in sperm cells, of which 1668 were not expressed in pollen or seedlings. Pathways enriched in male germ cells included ubiquitin-mediated pathways, pathways involved in chromatin modeling including histones, histone modification and nonhistone epigenetic modification, and pathways related to RNAi and gene silencing. Genome-wide expression patterns in angiosperm sperm cells indicate common and divergent themes in the male germline that appear to be largely self-regulating through highly up-regulated chromatin modification pathways. A core of highly conserved genes appear common to all sperm cells, but evidence is still emerging that another class of genes have diverged in expression between monocots and dicots since their divergence. Sperm cell transcripts present at fusion may be transmitted through plasmogamy during double fertilization to effect immediate post-fertilization expression of early embryo and (or) endosperm development.

Ecological and genetic factors linked to contrasting genome dynamics in seed plants

The large-scale replacement of gymnosperms by angiosperms in many ecological niches over time and the huge disparity in species numbers have led scientists to explore factors (e.g. polyploidy, developmental systems, floral evolution) that may have contributed to the astonishing rise of angiosperm diversity. Here, we explore genomic and ecological factors influencing seed plant genomes. This is timely given the recent surge in genomic data. We compare and contrast the genomic structure and evolution of angiosperms and gymnosperms and find that angiosperm genomes are more dynamic and diverse, particularly amongst the herbaceous species. Gymnosperms typically have reduced frequencies of a number of processes (e.g. polyploidy) that have shaped the genomes of other vascular plants and have alternative mechanisms to suppress genome dynamism (e.g. epigenetics and activity of transposable elements). Furthermore, the presence of several characters in angiosperms (e.g. herbaceous habit, short minimum generation time) has enabled them to exploit new niches and to be viable with small population sizes, where the power of genetic drift can outweigh that of selection. Together these processes have led to increased rates of genetic divergence and faster fixation times of variation in many angiosperms compared with gymnosperms.

Evolution of the YABBY gene family with emphasis on the basal eudicot Eschscholzia californica (Papaveraceae)

YABBY genes are seed plant-specific transcriptional regulators that are involved in diverse aspects of leaf, shoot and flower development. A series of duplications gave rise to five gene groups found throughout flowering plants. In Arabidopsis and other species, expression of two gene groups, CRABS CLAW and INNER NO OUTER, is restricted to floral organs. In contrast, members of the FILAMENTOUS FLOWER, YABBY2 and YABBY5 gene groups are also expressed in leaves and have been termed 'vegetative YABBYs'. How the five paralogue groups evolved and how their expression and function diversified have remained largely unresolved, precluding a reconstruction of the natural history of this gene family. Here, we report new genes from Eschscholzia californica (Ranunculales, Papaveraceae) that we use together with currently available database sequences in a comprehensive phylogenetic re-evaluation of the YABBY gene family. Multilayered Bayesian analysis covering seed plants allowed us to locate Eschscholzia YABBY sequences within the gene family phylogeny. We established that vegetative YABBYs do not form a monophyletic clade, and that CRABS CLAW and FILAMENTOUS FLOWER arose from a common ancestor gene. INNER NO OUTER genes are sister to that ancestral gene. We identified several conserved motifs outside of known amino acid domains that define all five angiosperm YABBY gene clades. Further, we inferred the evolution of gene expression and provide evidence for release of purifying constraint in certain branches of the gene family tree. Finally, we report expression patterns for five Eschscholzia YABBY genes consistent with functional conservation between early-diverged and core eudicots.

RSS1 regulates the cell cycle and maintains meristematic activity under stress conditions in rice

Plant growth and development are sustained by continuous cell division in the meristems, which is perturbed by various environmental stresses. For the maintenance of meristematic functions, it is essential that cell division be coordinated with cell differentiation. However, it is unknown how the proliferative activities of the meristems and the coordination between cell division and differentiation are maintained under stressful conditions. Here we show that a rice protein, RSS1, whose stability is controlled by cell cycle phases, contributes to the vigour of meristematic cells and viability under salinity conditions. These effects of RSS1 are exerted by regulating the G1-S transition, possibly through an interaction of RSS1 with protein phosphatase 1, and are mediated by the phytohormone, cytokinin. RSS1 is conserved widely in plant lineages, except eudicots, suggesting that RSS1-dependent mechanisms might have been adopted in specific lineages during the evolutionary radiation of angiosperms.

The evolution and functional significance of leaf shape in the angiosperms

Angiosperm leaves manifest a remarkable diversity of shapes that range from developmental sequences within a shoot and within crown response to microenvironment to variation among species within and between communities and among orders or families. It is generally assumed that because photosynthetic leaves are critical to plant growth and survival, variation in their shape reflects natural selection operating on function. Several non-mutually exclusive theories have been proposed to explain leaf shape diversity. These include: thermoregulation of leaves especially in arid and hot environments, hydraulic constraints, patterns of leaf expansion in deciduous species, biomechanical constraints, adaptations to avoid herbivory, adaptations to optimise light interception and even that leaf shape variation is a response to selection on flower form. However, the relative importance, or likelihood, of each of these factors is unclear. Here we review the evolutionary context of leaf shape diversification, discuss the proximal mechanisms that generate the diversity in extant systems, and consider the evidence for each the above hypotheses in the context of the functional significance of leaf shape. The synthesis of these broad ranging areas helps to identify points of conceptual convergence for ongoing discussion and integrated directions for future research.

Conservation and canalization of gene expression during angiosperm diversification accompany the origin and evolution of the flower

The origin and rapid diversification of the angiosperms (Darwin's "Abominable Mystery") has engaged generations of researchers. Here, we examine the floral genetic programs of phylogenetically pivotal angiosperms (water lily, avocado, California poppy, and Arabidopsis) and a nonflowering seed plant (a cycad) to obtain insight into the origin and subsequent evolution of the flower. Transcriptional cascades with broadly overlapping spatial domains, resembling the hypothesized ancestral gymnosperm program, are deployed across morphologically intergrading organs in water lily and avocado flowers. In contrast, spatially discrete transcriptional programs in distinct floral organs characterize the more recently derived angiosperm lineages represented by California poppy and Arabidopsis. Deep evolutionary conservation in the genetic programs of putatively homologous floral organs traces to those operating in gymnosperm reproductive cones. Female gymnosperm cones and angiosperm carpels share conserved genetic features, which may be associated with the ovule developmental program common to both organs. However, male gymnosperm cones share genetic features with both perianth (sterile attractive and protective) organs and stamens, supporting the evolutionary origin of the floral perianth from the male genetic program of seed plants.

Flotation preferentially selects saccate pollen during conifer pollination

• Among many species of living conifers the presence of pollen with air bladders (saccate pollen) is strongly associated with downward-facing ovules and the production of pollination drops. This combination of features enables saccate pollen grains captured in the pollination drop to float upwards into the ovule. Despite the importance of this mechanism in understanding reproduction in living conifers and in extinct seed plants with similar morphologies, experiments designed to test its effectiveness have yielded equivocal results. • In vitro and in vivo pollination experiments using saccate and nonsaccate pollen were performed using modeled ovules and two Pinus species during their natural pollination period. • Buoyant saccate pollen readily floated through aqueous droplets, separating these grains from nonbuoyant pollen and spores. Ovules that received saccate pollen, nonsaccate pollen or a mixture of both all showed larger amounts and higher proportions of saccate pollen inside ovules after drop secretion. • These results demonstrate that flotation is an effective mechanism of pollen capture and transport in gymnosperms, and suggest that the prevalence of saccate grains and downward-facing ovules in the evolutionary history of seed plants is a result of the widespread use of this mechanism.

Floral genetic architecture: an examination of QTL architecture underlying floral (co)variation across environments

Genetic correlations are expected to be high among functionally related traits and lower between groups of traits with distinct functions (e.g., reproductive vs. resource-acquisition traits). Here, we explore the quantitative-genetic and QTL architecture of floral organ sizes, vegetative traits, and life history in a set of Brassica rapa recombinant inbred lines within and across field and greenhouse environments. Floral organ lengths were strongly positively correlated within both environments, and analysis of standardized G-matrices indicates that the structure of genetic correlations is ∼80% conserved across environments. Consistent with these correlations, we detected a total of 19 and 21 additive-effect floral QTL in the field and the greenhouse, respectively, and individual QTL typically affected multiple organ types. Interestingly, QTL×QTL epistasis also appeared to contribute to observed genetic correlations; i.e., interactions between two QTL had similar effects on filament length and two estimates of petal size. Although floral and nonfloral traits are hypothesized to be genetically decoupled, correlations between floral organ size and both vegetative and life-history traits were highly significant in the greenhouse; G-matrices of floral and vegetative traits as well as floral and life-history traits differed across environments. Correspondingly, many QTL (45% of those mapped in the greenhouse) showed environmental interactions, including approximately even numbers of floral and nonfloral QTL. Most instances of QTL×QTL epistasis for floral traits were environment dependent.

Testing the recent theories for the origin of the hermaphrodite flower by comparison of the transcriptomes of gymnosperms and angiosperms

Background

Different theories for the origin of the angiosperm hermaphrodite flower make different predictions concerning the overlap between the genes expressed in the male and female cones of gymnosperms and the genes expressed in the hermaphrodite flower of angiosperms. The Mostly Male (MM) theory predicts that, of genes expressed primarily in male versus female gymnosperm cones, an excess of male orthologs will be expressed in flowers, excluding ovules, while Out Of Male (OOM) and Out Of Female (OOF) theories predict no such excess.

Results

In this paper, we tested these predictions by comparing the transcriptomes of three gymnosperms (Ginkgo biloba, Welwitschia mirabilis and Zamia fisheri) and two angiosperms (Arabidopsis thaliana and Oryza sativa), using EST data. We found that the proportion of orthologous genes expressed in the reproductive organs of the gymnosperms and in the angiosperms flower is significantly higher than the proportion of orthologous genes expressed in the reproductive organs of the gymnosperms and in the angiosperms vegetative tissues, which shows that the approach is correct. However, we detected no significant differences between the proportion of gymnosperm orthologous genes expressed in the male cone and in the angiosperms flower and the proportion of gymnosperm orthologous genes expressed in the female cone and in the angiosperms flower.

Conclusions

These results do not support the MM theory prediction of an excess of male gymnosperm genes expressed in the hermaphrodite flower of the angiosperms and seem to support the OOM/OOF theories. However, other explanations can be given for the 1:1 ratio that we found. More abundant and more specific (namely carpel and ovule) expression data should be produced in order to further test these theories.

The evolution of seeds

The evolution of the seed represents a remarkable life-history transition for photosynthetic organisms. Here, we review the recent literature and historical understanding of how and why seeds evolved. Answering the 'how' question involves a detailed understanding of the developmental morphology and anatomy of seeds, as well as the genetic programs that determine seed size. We complement this with a special emphasis on the evolution of dormancy, the characteristic of seeds that allows for long 'distance' time travel. Answering the 'why' question involves proposed hypotheses of how natural selection has operated to favor the seed life-history phenomenon. The recent flurry of research describing the comparative biology of seeds is discussed. The review will be divided into sections dealing with: (1) the development and anatomy of seeds; (2) the endosperm; (3) dormancy; (4) early seed-like structures and the transition to seeds; and (5) the evolution of seed size (mass). In many cases, a special distinction is made between angiosperm and gymnosperm seeds. Finally, we make some recommendations for future research in seed biology.

The naked and the dead: the ABCs of gymnosperm reproduction and the origin of the angiosperm flower

20 years after establishment of the ABC model many of the molecular mechanisms underlying development of the angiosperm flower are relatively well understood. Central players in the gene regulatory network controlling flower development are SQUA-like, DEF/GLO-like, AG-like and AGL6/SEP1-like MIKC-type MADS-domain transcription factors. These provide class A, class B, class C and the more recently defined class E floral homeotic functions, respectively. There is evidence that the floral homeotic proteins recognize the DNA of target genes in an organ-specific way as multimeric protein complexes, thus constituting 'floral quartets'. In contrast to the detailed insights into flower development, how the flower originated during evolution has remained enigmatic. However, while orthologues of all classes of floral homeotic genes appear to be absent from all non-seed plants, DEF/GLO-like, AG-like, and AGL6-like genes have been found in diverse extant gymnosperms, the closest relatives of the angiosperms. While SQUA-like and SEP1-like MADS-box genes appear to be absent from extant gymnosperms, reconstruction of MADS-box gene phylogeny surprisingly suggests that the most recent common ancestor of gymnosperms and angiosperms possessed representatives of both genes, but that these have been lost in the lineage that led to extant gymnosperms. Expression studies and genetic complementation experiments indicate that both angiosperm and gymnosperm AG-like and DEF/GLO-like genes have conserved functions in the specification of reproductive organs and in distinguishing male from female organs, respectively. Based on these findings novel models about the molecular basis of flower origin, involving changes in the expression patterns of DEF/GLO-like or AGL6/SEP1/SQUA-like genes in reproductive structures, were developed. While in angiosperms SEP1-like proteins play an important role in floral quartet formation, preliminary evidence suggests that gymnosperm DEF/GLO-like and AG-like proteins alone can already form floral quartet-like complexes, further corroborating the view that the formation of floral quartet-like complexes predated flower origin during evolution.

Reproductive short-shoots of Ginkgo biloba: A quantitative analysis of the disposition of axillary structures

Ginkgo biloba, the only living representative in an otherwise extinct clade, is of pivotal importance to understanding seed plant phylogeny. Although G. biloba and its fossil relatives have been studied for over two centuries, there are both gaps and contradictions in the information available. We present data documenting the distributions of strobili and consider what an understanding of the disposition of strobili along short-shoots in Ginkgo adds to knowledge of the evolution of reproductive structures in seed plants in general. The megasporangiate strobili are found at and around the boundary between bracts and foliage leaves, while the expanse of microsporangiate strobili centers on the fifth bract back from that boundary. Quantitative analysis of the locations of the strobili along the short-shoot finds that increases in numbers of strobili are the result of recruitment of adjacent axils into morphogenetic activity. Gaps in the series of strobili are exceedingly rare. Further, while increased numbers of megasporangiate strobili arise from the symmetrical addition of axils into the fertile zone, increased numbers of microsporangiate strobili arise from a distinctly asymmetrical, basipetally biased, addition of axillary positions. This accurate morphological framework should orient molecular genetic studies that probe gymnosperm development itself or that consider gymnosperms as the proximate sources of gene expression redeployed in the origin of the angiosperm flower.

The analysis of entire gene promoters by surface plasmon resonance

We demonstrate that the biophysical technique of surface plasmon resonance (SPR) analysis, which has previously been used to measure transcription factor binding to short DNA molecules, can also be used to characterize interactions involving entire gene promoters. This discovery has two main implications that relate, respectively, to novel qualitative and quantitative uses of the SPR technique. Firstly, SPR analysis can be used qualitatively to test the capacity of any transcription factor to interact physically with its putative target genes. This application should prove particularly useful for the confirmation of predicted transcriptional interactions in model species, and for comparative studies of non-model species in which transcriptional interactions are not amenable to study by other methods. Secondly, SPR may be used quantitatively to characterize interactions between transcription factors and gene promoters containing multiple cis-acting sites. This application should prove useful for the detailed dissection of promoter function in known target genes. The qualitative and quantitative applications of the SPR analysis of whole promoters combine to make this a uniquely powerful technique, which should prove particularly useful in systems biology, evolutionary developmental biology and various branches of applied biology.

Green Life Through Time The Biology and Evolution of Fossil Plants. 2nd ed. Academic (Elsevier), Burlington, MA, 2009. 1252 pp. $125, £62.99, €91.95. ISBN 9780123739728

An expansion and update of Taylor and Taylor's classic 1993 book, this lavishly illustrated volume offers a comprehensive survey of fossil plants and fungi.

Auxin-dependent patterning and gamete specification in the Arabidopsis female gametophyte

The female reproductive unit of flowering plants, the haploid female gametophyte, is highly reduced relative to other land plants. We show that patterning of the Arabidopsis female gametophyte depends on an asymmetric distribution of the hormone auxin during its syncitial development. Furthermore, this auxin gradient is correlated with location-specific auxin biosynthesis, rather than auxin efflux that directs patterning in the diploid sporophytic tissues comprising the rest of the plant. Manipulation of auxin responses or synthesis induces switching of gametic and nongametic cell identities and specialized nonreproductive cells to exhibit attributes presumptively lost during angiosperm evolution. These findings may account for the unique egg cell specification characteristic of angiosperms and the formation of seeds with single diploid embryos while containing endosperm that can have variable numbers of parental haploid genomes.

Ants sow the seeds of global diversification in flowering plants

Background

The extraordinary diversification of angiosperm plants in the Cretaceous and Tertiary periods has produced an estimated 250,000–300,000 living angiosperm species and has fundamentally altered terrestrial ecosystems. Interactions with animals as pollinators or seed dispersers have long been suspected as drivers of angiosperm diversification, yet empirical examples remain sparse or inconclusive. Seed dispersal by ants (myrmecochory) may drive diversification as it can reduce extinction by providing selective advantages to plants and can increase speciation by enhancing geographical isolation by extremely limited dispersal distances.

Methodology/Principal Findings

Using the most comprehensive sister-group comparison to date, we tested the hypothesis that myrmecochory leads to higher diversification rates in angiosperm plants. As predicted, diversification rates were substantially higher in ant-dispersed plants than in their non-myrmecochorous relatives. Data from 101 angiosperm lineages in 241 genera from all continents except Antarctica revealed that ant-dispersed lineages contained on average more than twice as many species as did their non-myrmecochorous sister groups. Contrasts in species diversity between sister groups demonstrated that diversification rates did not depend on seed dispersal mode in the sister group and were higher in myrmecochorous lineages in most biogeographic regions.

Conclusions/Significance

Myrmecochory, which has evolved independently at least 100 times in angiosperms and is estimated to be present in at least 77 families and 11 000 species, is a key evolutionary innovation and a globally important driver of plant diversity. Myrmecochory provides the best example to date for a consistent effect of any mutualism on large-scale diversification.

Ancestral xerophobia: a hypothesis on the whole plant ecophysiology of early angiosperms

Today, angiosperms are fundamental players in the diversity and biogeochemical functioning of the planet. Yet despite the omnipresence of angiosperms in today's ecosystems, the basic evolutionary understanding of how the earliest angiosperms functioned remains unknown. Here we synthesize ecophysiological, paleobotanical, paleoecological, and phylogenetic lines of evidence about early angiosperms and their environments. In doing so, we arrive at a hypothesis that early angiosperms evolved in evermoist tropical terrestrial habitats, where three of their emblematic innovations - including net-veined leaves, xylem vessels, and flowers - found ecophysiological advantages. However, the adaptation of early angiosperm ecophysiology to wet habitats did not initially promote massive diversification and ecological dominance. Instead, wet habitats were permissive for the ecological roothold of the clade, a critical phase of early diversification that entailed experimentation with a range of functional innovations in the leaves, wood, and flowers. Later, our results suggest that some of these innovations were co-opted gradually for new roles in the evolution of greater productivity and drought tolerance, which are characteristics seen across the vast majority of derived and ecologically dominant angiosperms today.

Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolution

Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to poor sampling in the Turonian-Santonian interval. Stegosauria shows a significant negative correlation with flowering plants and a significant positive correlation with the nonflowering cycadophytes (cycads, Bennettitales). This interesting pattern is worthy of further investigation, and it reflects the decline of both stegosaurs and cycadophytes during the Early Cretaceous.

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.

Transmitting tissue architecture in basal-relictual angiosperms: Implications for transmitting tissue origins

Carpel transmitting tissue is a major floral innovation that is essential for angiosperm success. It facilitates the rapid adhesion, hydration, and growth of the male gametophyte to the female gametophyte. As well, it functions as a molecular screen to promote male gametophytic competition and species-specific recognition and compatibility. Here, we characterize the transmitting tissue extracellular matrix (ECM) and pollen tube growth in basal-relictual angiosperms and test the hypothesis that a freely flowing ECM (wet stigma) was ancestral to a cuticle-bound ECM (dry stigma). We demonstrate that the most recent common ancestor of extant angiosperms produced an ECM that was structurally and functionally equivalent to a dry stigma. Dry stigmas are composed of a cuticle and primary wall that contains compounds that facilitate the adhesion and growth of the male gametophyte. These compounds include methyl-esterified homogalacturonans, arabinogalactan-proteins, and lipids. We propose that transmitting tissue evolved in concert with an increase in cuticle permeability that resulted from modifications in the biosynthesis and secretion of fatty acids needed for cuticle construction. Increased cuticle permeability exposed the male gametophyte to pre-existing molecules that enabled rapid male gametophyte adhesion, hydration, and growth as well as species-specific recognition and compatibility.

Nonflowers near the base of extant angiosperms? Spatiotemporal arrangement of organs in reproductive units of Hydatellaceae and its bearing on the origin of the flower

Reproductive units (RUs) of Trithuria, the sole genus of the early-divergent angiosperm family Hydatellaceae, are compared with flowers of their close relatives in Cabombaceae (Nymphaeales). Trithuria RUs combine features of flowers and inflorescences. They differ from typical flowers in possessing an "inside-out" morphology, with carpels surrounding stamens; furthermore, carpels develop centrifugally, in contrast to centripetal or simultaneous development in typical flowers. Trithuria RUs could be interpreted as pseudanthia of two or more cymose partial inflorescences enclosed within an involucre, but the bractlike involucral phyllomes do not subtend partial inflorescences and hence collectively resemble a typical perianth. Teratological forms of T. submersa indicate a tendency to fasciation and demonstrate that the inside-out structure-the primary feature that separates RUs of Hydatellaceae from more orthodox angiosperm flowers-can be at least partially modified, thus producing a morphology that is closer to an orthodox flower. The Trithuria RU could be described as a "nonflower", i.e., a structure that contains typical angiosperm carpels and stamens but does not allow recognition of a typical angiosperm flower. The term nonflower could combine cases of secondary loss of flower identity and cases of a prefloral condition, similar to those that gave rise to the angiosperm flower. Nonhomology among some angiosperm flowers could be due to iterative shifts between nonfloral construction and flower/inflorescence organization of reproductive organs. Potential testing of these hypotheses using evolutionary-developmental genetics is explored using preliminary data from immunolocalization of the floral meristem identity gene LEAFY in T. submersa, which indicated protein expression at different hierarchical levels.