Biology subjects

Egea-Cortines, M.

Publications and source records attributed to Egea-Cortines, M..

5 recordsLinked to original sources

bioRxiv2026

Large-scale forward genetics reveals genetically separable components of plant cell proliferative capacity

Plant cell cultures underpin regeneration, transformation and emerging applications in biotechnology and plant cell agriculture, yet the genetic determinants of proliferative performance remain poorly characterized. Here, we combined large-scale forward genetics with automated image-based phenotyping to quantify 27,648 calli representing 2,880 Arabidopsis thaliana T-DNA insertion lines. Of these, 2,456 lines produced calli smaller than the WT population mean, whereas only 190 produced larger calli, revealing a strongly asymmetric phenotypic distribution. Enhanced callus growth was not consistently associated with increased vegetative growth, indicating that these traits can be genetically uncoupled. Validation of selected high-growth mutants in suspension culture identified lines with enhanced biomass accumulation, while serial propagation revealed independent variation in sustained proliferative capacity. Thus, callus growth, whole-plant growth, short-term suspension biomass accumulation and sustained proliferation represent distinct, not necessarily coupled components of proliferative performance. These findings establish a scalable framework for identifying genetic determinants relevant to the development of improved plant cell production lines.

plant biology↗

bioRxiv2026

Secondary structure distances reveal a new dimension of protein evolution

Molecular phylogenetics based on primary sequence comparisons has been central to reconstructing protein evolution. However, structural evolution does not necessarily parallel sequence divergence, particularly in proteins combining ordered domains with intrinsically disordered regions (IDRs). Here, we introduce a quantitative secondary structure distance (S2D) metric that enables systematic comparison of protein secondary structure, including both ordered elements and IDRs. Using the MADS-box transcription factor family as a model, we show that structural divergence is domain-specific and only partially coupled to sequence-based phylogeny. Domain-resolved analyses reveal that the DNA-binding M domain remains structurally constrained, whereas the I and C domains exhibit extensive sequence divergence while retaining conserved intrinsic disorder. In contrast, the K domain contributes disproportionately to global structural variability. Integrating S2D with phylogenetic distance uncovers both convergent structural architectures among distantly related proteins and pronounced structural remodelling within closely related paralogs--patterns not evident from primary sequence comparisons alone. Residue-level analyses further demonstrate that the structural impact of mutation depends strongly on amino acid identity and does not scale directly with substitution frequency or conservation metrics. Together, these findings indicate that secondary structural evolution provides an additional dimension of protein diversification beyond sequence divergence. By integrating phylogenetic and structural distances, this framework offers a complementary approach to interpreting protein evolution, particularly in families containing mixtures of ordered domains and intrinsically disordered regions. Significance StatementEvolutionary relationships are typically inferred from primary sequence comparisons, yet structural evolution may follow different trajectories. By developing a quantitative measure of secondary structural divergence, we show that structural change within the MADS-box transcription factor family can both converge and diverge independently of sequence-based phylogeny. Intrinsically disordered regions exhibit extensive sequence divergence while retaining conserved disorder, whereas specific amino acid substitutions disproportionately reshape secondary structure. These findings demonstrate that evolutionary diversification operates through domain-specific structural modulation rather than uniform sequence divergence. Integrating structural and phylogenetic distances provides a complementary framework for interpreting protein evolution and reveals evolutionary patterns that remain hidden when relying on sequence comparisons alone.

evolutionary biology↗

bioRxiv2026

Functional Divergence of GIGANTEA paralogs in Petunia x hybrida Reveals Uncoupling of Vegetative Growth and Flowering Time

The circadian clock gene GIGANTEA (GI) coordinates vegetative growth and floral transition in plants, yet the roles of its paralogs in Solanaceae remain unclear. In Petunia x hybrida, the GI locus is duplicated as PhGI1 and PhGI2. We investigated whether this duplication uncouples vegetative growth from flowering time. Using RNA interference and CRISPR/Cas9 mutagenesis, we dissected the function of PhGI2. RNAi silencing of PhGI2 produced complex phenotypes, including enhanced vegetative growth, early floral abortion, and delayed flowering, raising questions about cosuppression effects. To resolve this, we generated three independent CRISPR alleles of PhGI2. These mutants exhibited extreme late flowering without changes in vegetative architecture or scent emission, demonstrating that PhGI2 specifically controls floral transition. Expression analyses revealed that PhGI2 is required to maintain rhythmicity and amplitude of PhGI1 and core clock genes, including PhTOC1 and PhLHY. Our findings uncover subfunctionalization of GI paralogs. Whilst PhGI1 represses vegetative growth and influences floral development, PhGI2 promotes flowering and coordinates circadian transcription. This genetic separation of vegetative growth and flowering time provides a framework for manipulating crop architecture and phenology. HighlightDuplication of GIGANTEA in petunia uncouples vegetative growth from flowering time through paralog subfunctionalization

plant biology↗

bioRxiv2020

Automatic classification of constitutive and non-constitutive metabolites with gcProfileMakeR

Data analysis in non-targeted metabolomics is extremely time consuming. Genetic factors and environmental cues affect the composition and quantity of present metabolites i.e. the constitutive and non-constitutive metabolites. We developed gcProfileMakeR, an R package that uses standard output files from GC-MS for automatic data analysis using CAS numbers. gcProfileMakeR produces three outputs: a core or constitutive metabolome, a second list of compounds with high quality matches that is non-constitutive and a third set of compounds with low quality matching to MS libraries. As a proof of concept, we defined the floral scent emission of Antirrhinum majus using wild type plants, the floral identity mutants deficiens and compacta as well as RNAi lines of AmLHY. Loss of petal identity was accompanied by appearance of aldehydes typical of green leaf volatile profiles. Decreased levels of AmLHY caused a major increase in volatile complexity, and activated the synthesis of benzyl acetate, absent in WT. Furthermore, some volatiles emitted in a gated fashion in WT such as methyl 3,5-dimethoxybezoate or linalool became constitutive. Using sixteen volatiles of the constitutive profile, all genotypes were classified by Machine Learning with 0% error. gcProfileMakeR may thus help define core and pan-metabolomes. It enhances the quality of data reported in metabolomic profiles as text outputs rely on CAS numbers. This is especially important for FAIR data implementation. One sentence summarygcProfileMakeR allows the automatic annotation of the core metabolome and non-constitutive metabolites, increasing speed and accuracy of non-targeted metabolomics.

bioinformatics↗

bioRxiv2019

Molecular and transcriptional structure of the petal and leaf circadian clock in Petunia hybrida

The plant circadian clock coordinates environmental signals with internal processes. We characterized the genomic and transcriptomic structure of the Petunia hybrida W115 clock in leaves and petals. We found three levels of evolutionary differences. First, PSEUDO-RESPONSE REGULATORS PhPRR5a, PhPRR5b, PhPRR7a, PhPRR7b, and GIGANTEA PhGI1 and PhGI2, differed in gene structure including exon number and deletions including the CCT domain of the PRR family. Second, leaves showed preferential day expression while petals tended to display night expression. Under continuous dark, most genes were delayed in leaves and petals. Importantly, photoperiod sensitivity of gene expression was tissue specific as TIMING OF CAB EXPRESSION PhNTOC1 was affected in leaves but not in petals, and PhPRR5b, PhPRR7b and the ZEITLUPE ortholog CHANEL, PhCHL, were modified in petals but not leaves. Third, we identified a strong transcriptional noise at different times of the day, and high robustness at dawn in leaves and dusk in petals, coinciding with the coordination of photosynthesis and scent emission. Our results indicate multilayered evolution of the Petunia clock including gene structure, number of genes and transcription patterns. The major transcriptional reprogramming of the clock in petals, with night expression may be involved in controlling scent emission in the dark.\n\nHighlightThe petunia leaf circadian clock shows maxima during the day while petal clock does it during the night. Reaction to dark is organ specific.

plant biology↗