Seed Silhouettes as Geometric Objects: New Applications of Elliptic Fourier Transform to Seed Morphology

Historically, little attention has been paid to the resemblance between seed silhouettes to geometric figures. Cardioid and derivatives, ellipses, heart curves, lemniscates, lenses, lunes, ovals, superellipses, waterdrops, and other figures can be used to describe seed shape, as well as models for quantification. Algebraic expressions representing the average silhouettes for a group of seeds are available, and their shape can be described and quantified by comparison with geometric models. Bidimensional closed-plane figures resulting from the representation of Fourier equations can be used as models for shape analysis. Elliptic Fourier Transform equations reproduce the seed silhouettes for any closed-plane curve corresponding to the contour of the image of a seed. We review the geometric properties of the silhouettes from seed images and discuss them in the context of seed development, plant taxonomy, and environmental adaptation. Silene is proposed as a model for the study of seed morphology. Three groups have been recently defined among Silene species based on the structure of their seed silhouettes, and their geometric properties are discussed. Using models based on Fourier Transform equations is useful in Silene species where the seeds are homogenous in shape but don’t adjust to described figures.Project “CLU-2019-05-IRNASA/CSIC Unit of Excellence”, funded by the Junta de Castilla y León and co-financed by the European Union (ERDF “Europe drives our growth”)

Sex-chrom, a database on plant sex chromosomes

This work has been supported by the Dirección General de Investigación Científica y Técnica (Spanish Government: CGL2016-75694-P AEI/FEDER, UE; CGL2017-84297-R), by the Generalitat de Catalunya (‘Ajuts a grups de recerca consolidats’ 2017SGR01116’), by the Czech Science Foundation (grants 16-08698S, 18-06147S and 19-03442S) and by CIJA PRESERVATION, SL. SG benefitted from a Ramón y Cajal contract (RYC-2014-16608) from the government of Spain, and SB and NS received Erasmus + grants from the European Union.Introduction Types of plant sex chromosomes, sex determination systems and their diversity Model systems in sex chromosome research Materials and Methods Information sources Data mining Database web environment and construction Results and Discussion Future directions Acknowledgements Author contribution

Genetic and epigenetic acpects of sex determination

The article concentrates on the latest knowledge concerning the role of epigenetic mechanisms in sex determination in model dioecious species Silene latifolia. Results suggest that the locus suppressing development of female organs in male plants is hypersensitive to the action of agents influencing level of DNA methylation (5-azacytidine) and histone acetylation (trichostatin A). According to the results obtained via inter-specific hybridisation and the ability of the smut Ustilago violacea to activate development of male organs in female plants, it can be deduced that there is a locus suppressing male organ development in standard female plants. Function of this locus is not influenced by the drugs mentioned above

DNA methylation and histone acetylation studies on angiosperm plant pollen

The immunohistochemical studies showed that vegetative nucleus of pollen of Lilium longiflorum is DNA-hypermethylated and histone-hypoacetylated in comparison with generative nucleus. This status could represent an adaptation for the long term survival of pollen grain. Different DNA methylation and histone acetylation patterns were observed in the ephemeric spring species Gagea lute

Seed Morphology in Silene Based on Geometric Models

Seed description in morphology is often based on adjectives such as “spherical”, “globular”, or “reniform”, but this does not provide a quantitative method. A new morphological approach based on the comparison of seed images with geometric models provides a seed description in Silene species on a quantitative basis. The novelty of the proposed method is based in the comparison of the seed images with geometric models according to a cardioid shape. The J index is a measurement that indicates the seed percentage of similarity with a cardioid or cardioid-derived figures used as models. The seeds of Silene species have high values of similarity with the cardioid and cardioid-derived models (J index superior to 90). The comparison with different figures allows species description and differentiation. The method is applied here to seeds of 21 species and models are proposed for some of them including S. diclinis, an endangered species. The method is discussed in the context of previous comparison with the measures used in traditional morphometric analysis. The similarity of seed images with geometric figures opens a new perspective for the automatized taxonomical evaluation of samples linking seed morphology to functional traits in endangered Silene species.Peer reviewe

New techniques for seed shape description in Silene species

19 páginas, 9 figuras, 7 tablasSeed shape in Silene species is often described by means of adjectives such as reniform, globose, and orbicular, but the application of seed shape for species classification requires quantification. A method for the description and quantification of seed shape consists in the comparison with geometric models. Geometric models based on mathematical equations were applied to characterize the general morphology of the seeds in 21 species of Silene. In addition to the previously described four models (M1 is the cardioid, and M2 to M4 are figures derived from it), we present four new geometric models (model 5–8). Models 5 and 6 are open cardioids that resemble M3, quite different from the flat models, M2 and M4. Models 7 and 8 were applied to those species not covered by models 2 to 6. Morphological measures were obtained to describe and characterize the dorsal view of the seeds. The analyses done on dorsal views revealed a notable morphological diversity and four groups were identified. A correlation was found between roundness of dorsal view and the geometric models based on lateral views, such that some of the groups defined by seed roundness are also characterized by the similarity to particular models. The usefulness of new morphological tools of seed morphology to taxonomy is discussedProject “CLU-2019-05-IRNASA/CSIC Unit of Excellence”, funded by the Junta de Castilla y León and co-financed by the European Union (ERDF “Europe drives our growth”).Peer reviewe

Comparative analysis of a plant pseudoautosomal region (PAR) in <it>Silene latifolia</it> with the corresponding <it>S. vulgaris</it> autosome

<p>Abstract</p> <p>Background</p> <p>The sex chromosomes of <it>Silene latifolia</it> are heteromorphic as in mammals, with females being homogametic (XX) and males heterogametic (XY). While recombination occurs along the entire X chromosome in females, recombination between the X and Y chromosomes in males is restricted to the pseudoautosomal region (PAR). In the few mammals so far studied, PARs are often characterized by elevated recombination and mutation rates and high GC content compared with the rest of the genome. However, PARs have not been studied in plants until now. In this paper we report the construction of a BAC library for <it>S. latifolia</it> and the first analysis of a > 100 kb fragment of a <it>S. latifolia</it> PAR that we compare to the homologous autosomal region in the closely related gynodioecious species <it>S. vulgaris</it>.</p> <p>Results</p> <p>Six new sex-linked genes were identified in the <it>S. latifolia</it> PAR, together with numerous transposable elements. The same genes were found on the <it>S. vulgaris</it> autosomal segment, with no enlargement of the predicted coding sequences in <it>S. latifolia</it>. Intergenic regions were on average 1.6 times longer in <it>S. latifolia</it> than in <it>S. vulgaris</it>, mainly as a consequence of the insertion of transposable elements. The GC content did not differ significantly between the PAR region in <it>S. latifolia</it> and the corresponding autosomal region in <it>S. vulgaris</it>.</p> <p>Conclusions</p> <p>Our results demonstrate the usefulness of the BAC library developed here for the analysis of plant sex chromosomes and indicate that the PAR in the evolutionarily young <it>S. latifolia</it> sex chromosomes has diverged from the corresponding autosomal region in the gynodioecious <it>S. vulgaris</it> mainly with respect to the insertion of transposable elements. Gene order between the PAR and autosomal region investigated is conserved, and the PAR does not have the high GC content observed in evolutionarily much older mammalian sex chromosomes.</p

New Geometric Models for Shape Quantification of the Dorsal View in Seeds of Silene Species

The description of shape in Silene seeds is based on adjectives coined by naturalists in the 19th century. The expressions reniform, dorso plana, and dorso canaliculata were applied in reference to lateral or dorsal views of seeds, but the characters described can be submitted now to an analytical description by quantitative methods, allowing shape quantification and the comparison between species or populations. A quantitative morphological analysis is based on the comparison with geometric models that adjust to the shape of seeds. Morphological analysis of the dorsal view of Silene seeds based on geometric models is applied here to 26 seed populations belonging to 12 species. According to their dorsal views, the seeds are classified as convex and non-convex. New geometric models are presented for both types, including figures such as super-ellipses and modified ellipses. The values of J index (percent of similarity of a seed image with the model) are obtained in representative seed samples from diverse populations and species. The quantitative description of seed shape based on the comparison with geometric models allows the study of variation in shape between species and in populations, as well as the identification of seeds in Silene species. The method is of application to other plant species.Project “CLU-2019-05-IRNASA/CSIC Unit of Excellence”, funded by the Junta de Castilla y León and co-financed by the European Union (ERDF “Europe drives our growth”)

Comparative analysis of a plant pseudoautosomal region (PAR) in Silene latifolia with the corresponding S-vulgaris autosome

Background The sex chromosomes of Silene latifolia are heteromorphic as in mammals, with females being homogametic (XX) and males heterogametic (XY). While recombination occurs along the entire X chromosome in females, recombination between the X and Y chromosomes in males is restricted to the pseudoautosomal region (PAR). In the few mammals so far studied, PARs are often characterized by elevated recombination and mutation rates and high GC content compared with the rest of the genome. However, PARs have not been studied in plants until now. In this paper we report the construction of a BAC library for S. latifolia and the first analysis of a > 100 kb fragment of a S. latifolia PAR that we compare to the homologous autosomal region in the closely related gynodioecious species S. vulgaris. Results Six new sex-linked genes were identified in the S. latifolia PAR, together with numerous transposable elements. The same genes were found on the S. vulgaris autosomal segment, with no enlargement of the predicted coding sequences in S. latifolia. Intergenic regions were on average 1.6 times longer in S. latifolia than in S. vulgaris, mainly as a consequence of the insertion of transposable elements. The GC content did not differ significantly between the PAR region in S. latifolia and the corresponding autosomal region in S. vulgaris. Conclusions Our results demonstrate the usefulness of the BAC library developed here for the analysis of plant sex chromosomes and indicate that the PAR in the evolutionarily young S. latifolia sex chromosomes has diverged from the corresponding autosomal region in the gynodioecious S. vulgaris mainly with respect to the insertion of transposable elements. Gene order between the PAR and autosomal region investigated is conserved, and the PAR does not have the high GC content observed in evolutionarily much older mammalian sex chromosomes