Biology subjects

Coen, E.

Publications and source records attributed to Coen, E..

9 recordsLinked to original sources

bioRxiv2025

Antirrhinum flower shape: unravelling gene expression across developmental axes and boundaries

O_LIZygomorphic flowers in Antirrhinum majus arise from coordinated patterning along the dorsoventral and proximal-distal axes, but the transcriptional programs that pattern these axes to generate the complex corolla morphology remain poorly understood. C_LIO_LIWe performed comparative transcriptomic analyses of dorsal and ventral petals across developmental stages, combined with expression profiling in floral symmetry mutants, to identify genes potentially associated with dorsal identity (AmCYC-dependent) and ventral identity (AmDIV-dependent), and to map their spatial dynamics along the proximal-distal axis. Axis-specific and boundary-localized expression patterns were validated by in situ hybridisation. C_LIO_LIWe identified dorsal-specific candidate targets of AmCYC and ventral-specific genes regulated by AmDIV, including factors with regionally restricted expression along the proximal-distal axis. We further found that a conserved NGATHA-LIKE1-BRASSINAZOLE-RESISTANT 1-miR164 module, known for primordia growth regulation in Arabidopsis, has been co-opted in Antirrhinum to act as a potential spatiotemporal regulator of AmCUP, a target of AmDIV, thereby contributing to the complex shape of the Antirrhinum flower. C_LIO_LIOur results provide new insight into the gene regulatory landscape underlying zygomorphic flower development and highlight specific regulatory modules that may coordinate axis patterning with boundary establishment in the corolla. This work establishes a framework for further understanding how developmental gene networks shape a complex corolla morphology and offers new targets for functional and evolutionary investigation of floral diversity. C_LI

plant biology↗

bioRxiv2025

Tissue-wide cues are sensed at the cellular level to coordinate microtubule orientations in plants

Plant morphogenesis depends on tissue-wide coordination of cortical microtubule orientations. This coordination is thought to depend on microtubules responding to mechanical stress orientations. Here we test this stress-sensing hypothesis by quantifying microtubule behaviours on different faces and edges of growing leaf cells. We show that microtubules orientations exhibit both cell-geometric and tissue biases. Stress sensing can account for tissue biases but not microtubule trajectories and densities. An alternative hypothesis is suggested by two edge behaviours: generation of microtubules within cell edges and a filter that prevents microtubules entering side faces at shallow angles. Incorporating these features into a combinatorial model in which cell face identities modulate microtubule behaviours, accounts for tissue coordination and observed dynamics. Thus, instead of orientations being sensed at the microtubule level, they are sensed at the cellular level through changes in statistical behaviours at cell faces and edges, coordinated across a tissue through cell polarity.

plant biology↗

bioRxiv2025

Synthetic pectin-cellulose nanofiber capsule provides minimal model capturing mechanics of a regenerating plant cell wall

Plant primary cell walls are dynamic supramolecular assemblies composed of layered cellulose, hemicellulose and pectin, progressively built through synthesis and secretion. However, the specific architectural features and structural components sufficient to endow the mechanical properties of the wall remain unclear. Here, we construct a minimal synthetic spherical shell and compare its structural and mechanical properties to those of a plant single-cell system. To eliminate complexities from intercellular connectivity and developmental history, we exploit the ability of plant protoplasts to regenerate cell walls de novo. Compression tests of regenerating protoplasts between parallel plates reveal that wall stiffness increases with wall thickening over time. Despite differences in assembly pathways, architecture, and composition, the synthetic shell exhibits a similar thickness-dependent modulus and similar material stiffness. The synthetic shell, composed of pectin and cellulose layers, mirrors the mechanical behavior of regenerating primary cell walls, suggesting that these components are sufficient to confer key viscoelastic properties in the limit of small deformations. Given the complexity of natural plant cell walls, the synthetic analogue offers a controllable platform to dissect the mechanical contributions of individual wall components.

plant biology↗

bioRxiv2025

Genome-wide cline analysis identifies new locus contributing to a barrier to gene flow across an Antirrhinum hybrid zone

Identification of the genomic regions that contribute to reproductive isolation and how they interact is a major goal of evolutionary genetics. Much effort has focused on locating candidate genes and potential barrier loci by scanning genomes for regions of excess differentiation (FST). An alternative, and perhaps more robust approach, would be to scan for genomic regions exhibiting steep clines in allele frequency across a hybrid zone. Here we develop this approach and apply it to genomic data from across a hybrid zone between varieties of Antirrhinum majus subspecies majus with different flower colour patterns (A. m. m var. pseudomajus and A. m. m var. striatum). Most steep clines are clustered in seven genomic regions, only four of which were present from FST scans between all pair-wise comparisons. Six of these regions carry previously identified loci that influence flower colour in the hybrid zone. The seventh region harbours a novel locus, RUBIA, modifying magenta intensity. Clines at RUBIA approached towards fixation on magenta side of the hybrid zone, whilst remaining polymorphic on the yellow side. This polymorphism on the yellow side may reflect a smaller phenotypic effect of RUBIA in yellow compared to magenta genetic backgrounds. Our findings illustrate how whole-genome cline scans in hybrid zones can robustly detect genomic regions contributing to phenotypic differences and highlight how different reproductive barrier loci interact across the genome.

evolutionary biology↗

bioRxiv2025

Shaping of developmental gradients through selection on multiple loci in Antirrhinum

Development depends on precise shaping of molecular gradients, but how natural selection acts to establish precision is unknown. Here we analyse genes that control differences in the gradient of yellow flower colour between two varieties of snapdragon (Antirrhinum). We show that these differences depend, in part, on cis regulatory variation in the pigment biosynthetic gene, FLAVIA (FLA). FLA interacts multiplicatively with three other loci, one of which is a trans-acting regulator of FLA, to further shape the yellow gradient. All the loci exhibit clines at a hybrid zone, with widths that correlate with phenotypic effect, showing how selection can hone gradient shape with remarkable precision by acting on cis and trans variation at multiple loci.

evolutionary biology↗

bioRxiv2025

Genomic tree scans identify loci underlying adaptive peaks in Antirrhinum

A key question in evolutionary biology is how barriers to gene flow operate and arise between populations, leading to speciation. Barriers are typically identified by comparing populations distinguished by phenotype, geographical location and/or environment. However, such prior classifications may bias recovery towards features obvious to the human eye, influencing mechanistic interpretations. Here we develop a method blind to prior classifications. We apply it to 18 Antirrhinum populations occupying habitats from coastal to alpine. By scanning the genome for regions with deeply rooted similar trees, we identify a single multi-locus partition, comprising less than 0.5% of the genome. It derives from eight genes, three newly identified here, which interact to generate complementary pollinator guides, likely corresponding to two adaptive peaks in a fitness landscape. Hybrid genotypes fall in a fitness valley, allowing the partition to be maintained through hybrid incompatibility and creating steep clines in allele frequency at a hybrid zone. Another partition derives from a single locus linked to a gene controlling plant height. The locus exhibits a shallow cline in allele frequency across an eco-geographic barrier and may be eco-adaptive. Our results suggest that two ancestral subspecies underwent extensive gene flow except at a few barrier loci, showing how both hybrid incompatibility and eco-adaptation can operate to maintain diversity.

evolutionary biology↗

bioRxiv2023

Genetic control of cell layer interactions in plants via tissue mechanics

Plant development depends on coordination of growth between different cell layers. Coordination may be mediated by molecular signalling or mechanical connectivity between cells, but evidence for genetic control via direct mechanics has been lacking. We show that a brassinosteroid-deficient dwarf mutant of the aquatic plant Utricularia gibba has twisted internal tissue, likely caused by a mechanical constraint from a slow-growing epidermis creating tissue stresses. This conclusion is supported by showing that inhibition of brassinosteroid action in an Arabidopsis mutant compromised for cell adhesion, enhances epidermal crack formation, an indicator of increased tissue tension. Thus, genes driving brassinosteroid synthesis can promote growth of internal tissue by reducing mechanical epidermal constraint, showing that tissue mechanics plays a key role in coordinating growth between cell layers. One-Sentence SummaryInternal twists in a mutant carnivorous plant reveal how genes control growth via tissue mechanics.

plant biology↗

bioRxiv2022

New genomic resources provide insights into the recent evolutionary adaptation of Antirrhinum lineage and multiomics investigation of S-locus

The multi-allelic S-locus, containing a pistil S-RNase and dozens of S-locus F-box (SLF), underlies genetic control of self-incompatibility (SI) in Antirrhinum hispanicum. The genus Antirrhinum, harboring such a SI system has been used as a model to study self-incompatibility extensively. However, there have been limited studies on the genomic organization of the S-locus supergene due to a lack of high-quality genomic data. Here, we present the chromosome-level reference and haplotype-resolved genome assemblies of a self-incompatible Antirrhinum hispanicum line, AhS7S8. Alongside with the draft genome of Misopates orontium, comparative genomics reveals that A.hispanicum diverged from its self-compatible cousin 12.3 million years ago (Mya). Expanded gene families enriched in distinct functional terms implied different evolutionary trajectories of outcrossing and selfing species. For the first time, two complete A.hispanicum S-haplotypes spanning [~]1.2Mb and containing 32 SLFs were reconstructed, while most of the SLFs derived from retroelement-mediated proximal or tandem duplication approximately 122 Mya. Moreover, we detected a candidate cis-transcription factor associated with regulating SLFs expression, and two miRNAs may control the expression of this transcription factor. Inter-specific S-locus and intra-specific S-haplotype comparisons revealed the dynamic nature and polymorphism of the S-locus supergene mediated by continuous gene duplication, segmental translocation or loss, and TE-involved transposition events. Our data provides an excellent resource for future research on the evolutionary studies on S-RNase-based self-incompatibility system.

genomics↗

bioRxiv2018

Genome structure and evolution of Antirrhnum majus L.

Snapdragon (Antirrhinum majus L.), a member of Plantaginaceae, is an important model for plant genetics and molecular studies on plant growth and development, transposon biology and self-incompatibility. Here we report a high-quality genome assembly of A. majus cultivated JI7 (A. majus cv.JI7) of a 510 Mb with 37,714 annotated protein-coding genes. The scaffolds covering 97.12% of the assembled genome were anchored on 8 chromosomes. Comparative and evolutionary analyses revealed that Plantaginaceae and Solanaceae diverged from their most recent ancestor around 62 million years ago (MYA). We also revealed the genetic architectures associated with complex traits such as flower asymmetry and self-incompatibility including a unique TCP duplication around 46-49 MYA and a near complete{psi} S-locus of ca.2 Mb. The genome sequence obtained in this study not only provides the first genome sequenced from Plantaginaceae but also bring the popular plant model system of Antirrhinum into a genomic age.

genomics↗