Geometric morphometrics reveals shifts in flower shape symmetry and size following gene knockdown of CYCLOIDEA and ANTHOCYANIDIN SYNTHASE

Advances in Research on the Regulation of Floral Development by CYC-like Genes

CYCLOIDEA (CYC)-like genes belong to the TCP transcription factor family and play important roles associated with flower development. The CYC-like genes in the CYC1, CYC2, and CYC3 clades resulted from gene duplication events. The CYC2 clade includes the largest number of members that are crucial regulators of floral symmetry. To date, studies on CYC-like genes have mainly focused on plants with actinomorphic and zygomorphic flowers, including Fabaceae, Asteraceae, Scrophulariaceae, and Gesneriaceae species and the effects of CYC-like gene duplication events and diverse spatiotemporal expression patterns on flower development. The CYC-like genes generally affect petal morphological characteristics and stamen development, as well as stem and leaf growth, flower differentiation and development, and branching in most angiosperms. As the relevant research scope has expanded, studies have increasingly focused on the molecular mechanisms regulating CYC-like genes with different functions related to flower development and the phylogenetic relationships among these genes. We summarize the status of research on the CYC-like genes in angiosperms, such as the limited research conducted on CYC1 and CYC3 clade members, the necessity to functionally characterize the CYC-like genes in more plant groups, the need for investigation of the regulatory elements upstream of CYC-like genes, and exploration of the phylogenetic relationships and expression of CYC-like genes with new techniques and methods. This review provides theoretical guidance and ideas for future research on CYC-like genes.

Shape asymmetry - what's new?

Studies of shape asymmetry have become increasingly abundant as the methods of geometric morphometrics have gained widespread use. Most of these studies have focussed on fluctuating asymmetry and have largely obtained similar results as more traditional analyses of asymmetry in distance measurements, but several notable differences have also emerged. A key difference is that shape analyses provide information on the patterns, not just the amount of variation, and therefore tend to be more sensitive. Such analyses have shown that apparently symmetric structures in animals consistently show directional asymmetry for shape, but not for size. Furthermore, the long-standing prediction that phenotypic plasticity in response to environmental heterogeneity can contribute to fluctuating asymmetry has been confirmed for the first time for the shape of flower parts (but not for size). Finally, shape analyses in structures with complex symmetry, such as many flowers, can distinguish multiple types of directional asymmetry, generated by distinct direction-giving factors, which combine to the single component observable in bilaterally symmetric structures. While analyses of shape asymmetry are broadly compatible with traditional analyses of asymmetry, they incorporate more detailed morphological information, particularly for structures with complex symmetry, and therefore can reveal subtle biological effects that would otherwise not be apparent. This makes them a promising tool for a wide range of studies in the basic and applied life sciences.

Directional asymmetry and direction-giving factors: Lessons from flowers with complex symmetry

Directional asymmetry is a systematic difference between the left and right sides for structures with bilateral symmetry or a systematic differentiation among repeated parts for complex symmetry. This study explores factors that produce directional asymmetry in the flower of Iris pumila, a structure with complex symmetry that makes it possible to investigate multiple such factors simultaneously. The shapes and sizes of three types of floral organs, the falls, standards, and style branches, were quantified using the methods of geometric morphometrics. For each flower, this study recorded the compass orientations of floral organs as well as their anatomical orientations relative to the two spathes subtending each flower. To characterize directional asymmetry at the whole-flower level, differences in the average sizes and shapes according to compass orientation and relative orientation were computed, and the left-right asymmetry was also evaluated for each individual organ. No size or shape differences within flowers were found in relation to anatomical position; this may relate to the terminal position of flowers in Iris pumila, suggesting that there may be no adaxial-abaxial polarity, which is very prominent in many other taxa. There was clear directional asymmetry of shape in relation to compass orientation, presumably driven by a consistent environmental gradient such as solar irradiance. There was also clear directional asymmetry between left and right halves of every floral organ, most likely related to the arrangement of organs in the bud. These findings indicate that different factors are acting to produce directional asymmetry at different levels. In conventional analyses not recording flower orientations, these effects would be impossible to disentangle from each other and would probably be included as part of fluctuating asymmetry.

The symmetry spectrum in a hybridising, tropical group of rhododendrons

Many diverse plant clades possess bilaterally symmetrical flowers and specialised pollination syndromes, suggesting that these traits may promote diversification. We examined the evolution of diverse floral morphologies in a species-rich tropical radiation of Rhododendron. We used restriction-site associated DNA sequencing on 114 taxa from Rhododendron sect. Schistanthe to reconstruct phylogenetic relationships and examine hybridisation. We then captured and quantified floral variation using geometric morphometric analyses, which we interpreted in a phylogenetic context. We uncovered phylogenetic conflict and uncertainty caused by introgression within and between clades. Morphometric analyses revealed flower symmetry to be a morphological continuum without clear transitions between radial and bilateral symmetry. Tropical Rhododendron species that began diversifying into New Guinea c. 6 million years ago expanded into novel floral morphological space. Our results showed that the evolution of tropical Rhododendron is characterised by recent speciation, recurrent hybridisation and the origin of floral novelty. Floral variation evolved via changes to multiple components of the corolla that are only recognised in geometric morphometrics with both front and side views of flowers.

Duplication and expression patterns of CYCLOIDEA-like genes in Campanulaceae

Background

CYCLOIDEA (CYC)-like transcription factors pattern floral symmetry in most angiosperms. In core eudicots, two duplications led to three clades of CYC-like genes: CYC1, CYC2, and CYC3, with orthologs of the CYC2 clade restricting expression dorsally in bilaterally symmetrical flowers. Limited data from CYC3 suggest that they also play a role in flower symmetry in some asterids. We examine the evolution of these genes in Campanulaceae, a group that contains broad transitions between radial and bilateral floral symmetry and 180° resupination (turning upside-down by twisting pedicle).

Results

We identify here all three paralogous CYC-like clades across Campanulaceae. Similar to other core eudicots, we show that CamCYC2 duplicated near the time of the divergence of the bilaterally symmetrical and resupinate Lobelioideae. However, in non-resupinate, bilaterally symmetrical Cyphioideae, CamCYC2 appears to have been lost and CamCYC3 duplicated, suggesting a novel genetic basis for bilateral symmetry in Cyphioideae. We additionally, utilized qRT-PCR to examine the correlation between CYC-like gene expression and shifts in flower morphology in four species of Lobelioideae. As expected, CamCYC2 gene expression was dorsoventrally restricted in bilateral symmetrical flowers. However, because Lobelioideae have resupinate flowers, both CamCYC2A and CamCYC2B are highly expressed in the finally positioned ventral petal lobes, corresponding to the adaxial side of the flower relative to meristem orientation.

Conclusions

Our sequences across Campanulaceae of all three of these paralogous groups suggests that radially symmetrical Campanuloideae duplicated CYC1, Lobelioideae duplicated CYC2 and lost CYC3 early in their divergence, and that Cyphioideae lost CYC2 and duplicated CYC3. This suggests a dynamic pattern of duplication and loss of major floral patterning genes in this group and highlights the first case of a loss of CYC2 in a bilaterally symmetrical group. We illustrate here that CYC expression is conserved along the dorsoventral axis of the flower even as it turns upside-down, suggesting that at least late CYC expression is not regulated by extrinsic factors such as gravity. We additionally show that while the pattern of dorsoventral expression of each paralog remains the same, CamCYC2A is more dominant in species with shorter relative finally positioned dorsal lobes, and CamCYC2B is more dominant in species with long dorsal lobes.

A CYC-RAD-DIV-DRIF interaction likely pre-dates the origin of floral monosymmetry in Lamiales

BACKGROUND

An outstanding question in evolutionary biology is how genetic interactions defining novel traits evolve. They may evolve either by de novo assembly of previously non-interacting genes or by en bloc co-option of interactions from other functions. We tested these hypotheses in the context of a novel phenotype-Lamiales flower monosymmetry-defined by a developmental program that relies on regulatory interaction among CYCLOIDEA, RADIALIS, DIVARICATA, and DRIF gene products. In Antirrhinum majus (snapdragon), representing Lamiales, we tested whether components of this program likely function beyond their previously known role in petal and stamen development. In Solanum lycopersicum (tomato), representing Solanales which diverged from Lamiales before the origin of Lamiales floral monosymmetry, we additionally tested for regulatory interactions in this program.

RESULTS

We found that RADIALIS, DIVARICATA, and DRIF are expressed in snapdragon ovaries and developing fruit, similar to their homologs during tomato fruit development. In addition, we found that a tomato CYCLOIDEA ortholog positively regulates a tomato RADIALIS ortholog.

CONCLUSION

Our results provide preliminary support to the hypothesis that the developmental program defining floral monosymmetry in Lamiales was co-opted en bloc from a function in carpel development. This expands our understanding of novel trait evolution facilitated by co-option of existing regulatory interactions.

Evolution of flower allometry and pigmentation in Mammillaria haageana (Cactaceae)

BACKGROUND

A puzzle in evolution is the understanding of how the environment might drive subtle phenotypic variation, and whether this variation is adaptive. Under the neutral evolutionary theory, subtle phenotypes are almost neutral with little adaptive value. To test this idea, we studied the infraspecific variation in flower shape and color in Mammillaria haageana, a species with a wide geographical distribution and phenotypic variation, which populations are often recognized as infraspecific taxa.

RESULTS

We collected samples from wild populations, kept them in the greenhouse for at least one reproductive year, and collected newly formed flowers. Our first objective was to characterize tepal natural variation in M. haageana through geometric morphometric and multivariate pigmentation analyses. We used landmark-based morphometrics to quantify the trends of shape variation and tepal color-patterns in 20 M. haageana accessions, belonging to five subspecies, plus 8 M. albilanata accessions for comparison as the sister species. We obtained eight geometric morphometric traits for tepal shape and color-patterns. We found broad variation in these traits between accessions belonging to the same subspecies, without taxonomic congruence with those infraspecific units. Also the phenetic cluster analysis showed different grouping patterns among accessions. When we correlated these phenotypes to the environment, we also found that solar radiation might explain the variation in tepal shape and color, suggesting that subtle variation in flower phenotypes might be adaptive. Finally we present anatomical sections in M. haageana subsp. san-angelensis to propose some of the underlying tepal structural features that may give rise to tepal variation.

CONCLUSIONS

Our geometric morphometric approach of flower shape and color allowed us to identify the main trends of variation in each accession and putative subspecies, but also allowed us to correlate these variation to the environment, and propose anatomical mechanisms underlying this diversity of flower phenotypes.

Capturing variation in floral shape: a virtual3D based morphospace for Pelargonium

Background

Variation in floral shapes has long fascinated biologists and its modelling enables testing of evolutionary hypotheses. Recent comparative studies that explore floral shape have largely ignored 3D floral shape. We propose quantifying floral shape by using geometric morphometrics on a virtual3D model reconstructed from 2D photographical data and demonstrate its performance in capturing shape variation.

Methods

This approach offers unique benefits to complement established imaging techniques (i) by enabling adequate coverage of the potential morphospace of large and diverse flowering-plant clades; (ii) by circumventing asynchronicity in anthesis of different floral parts; and (iii) by incorporating variation in copy number of floral organs within structures. We demonstrate our approach by analysing 90 florally-diverse species of the Southern African genus Pelargonium (Geraniaceae). We quantify Pelargonium floral shapes using 117 landmarks and show similarities in reconstructed morphospaces for nectar tube, corolla (2D datasets), and a combined virtual3D dataset.

Results

Our results indicate that Pelargonium species differ in floral shape, which can also vary extensively within a species. PCA results of the reconstructed virtual3D floral models are highly congruent with the separate 2D morphospaces, indicating it is an accurate, virtual, representation of floral shape. Through our approach, we find that adding the third dimension to the data is crucial to accurately interpret the manner of, as well as levels of, shape variation in flowers.

Gynodioecy in the common spindle tree (Euonymus europaeus L.) involves differences in the asymmetry of corolla shapes between sexually differentiated flowers

Gynodioecy is typically associated with a smaller perianth size in purely pistillate flowers than in hermaphrodite flowers. However, it is unclear whether this size differentiation is associated with any differences in flower shape between the two sexual groups. A geometric morphometric analysis of the symmetry of tetrameric corolla shapes was used in the study of Euonymus europaeus L., Darwin’s classical system of floral sexual differentiation. I investigated whether there are any shape differences between the female and bisexual flowers, with respect to both purely symmetric variation involving coordinated shape changes of the four petals and asymmetry among petals within flowers. The corolla shapes of the female and bisexual flowers and the variability among flowers within each sexual group were very similar in the purely symmetric components of shape variation. However, the female flowers were significantly more asymmetric with respect to both the lateral and transversal asymmetry of their corolla shapes. This is the first study to apply geometric morphometrics in the analysis of morphological patterns in a sexually differentiated gynodioecious plant system. The results showed that subtle shape differences in corolla asymmetry differ between the sexual groups and indicate diverging developmental or selection signals between the sexes.

A Step-by-Step Guide for Geometric Morphometrics of Floral Symmetry

This paper provides a step-by-step guide for the morphological analysis of corolla and the decomposition of corolla shape variation into its symmetric and asymmetric components. The shape and symmetric organisation of corolla are key traits in the developmental and evolutionary biology of flowering plants. The various spatial layout of petals can exhibit bilateral symmetry, rotational symmetry or more complex combination of symmetry types. Here, I describe a general landmark-based geometric morphometric framework for the full statistical shape analysis of corolla and exemplify its use with four fully worked out case studies including tissue treatment, imaging, landmark data collection, file formatting, and statistical analyses: (i) bilateral symmetry (Fedia graciliflora), (ii) two perpendicular axes of bilateral symmetry (Erysimum mediohispanicum), (iii) rotational symmetry (Vinca minor), and (iv) combined bilateral and rotational symmetry (Trillium undulatum). The necessary tools for such analyses are not implemented in standard morphometric software and they are therefore provided here as functions running in the R environment. Principal Component Analysis is used to separate symmetric and asymmetric components of variation, respectively, quantifying variation among and within individuals. For bilaterally symmetric flowers, only one component of left-right asymmetric variation is extracted, while flowers with more complex symmetric layout have components of asymmetric variation associated with each symmetry operator implied (e.g., left-right asymmetry and adaxial-abaxial asymmetry). Fundamental information on the genetic, developmental, and environmental determinants of shape variation can be inferred from this decomposition (e.g., directional asymmetry, fluctuating asymmetry) and further exploited to document patterns of canalization, developmental stability, developmental modularity and morphological integration. Even if symmetry and asymmetry are not the primary interest of a study on corolla shape variation, statistical and anatomical arguments support the use of the framework advocated. This didactic protocol will help both morphometricians and non-morphometricians to further understand the role of symmetry in the development, variation and adaptive evolution of flowers.

Arabidopsis phenotyping through geometric morphometrics

Background

Recently, great technical progress has been achieved in the field of plant phenotyping. High-throughput platforms and the development of improved algorithms for rosette image segmentation make it possible to extract shape and size parameters for genetic, physiological, and environmental studies on a large scale. The development of low-cost phenotyping platforms and freeware resources make it possible to widely expand phenotypic analysis tools for Arabidopsis. However, objective descriptors of shape parameters that could be used independently of the platform and segmentation software used are still lacking, and shape descriptions still rely on ad hoc or even contradictory descriptors, which could make comparisons difficult and perhaps inaccurate. Modern geometric morphometrics is a family of methods in quantitative biology proposed to be the main source of data and analytical tools in the emerging field of phenomics studies. Based on the location of landmarks (corresponding points) over imaged specimens and by combining geometry, multivariate analysis, and powerful statistical techniques, these tools offer the possibility to reproducibly and accurately account for shape variations among groups and measure them in shape distance units.

Results

Here, a particular scheme of landmark placement on Arabidopsis rosette images is proposed to study shape variation in viral infection processes. Shape differences between controls and infected plants are quantified throughout the infectious process and visualized. Quantitative comparisons between two unrelated ssRNA+ viruses are shown, and reproducibility issues are assessed.

Conclusions

Combined with the newest automated platforms and plant segmentation procedures, geometric morphometric tools could boost phenotypic features extraction and processing in an objective, reproducible manner.