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Biology subjects

Oud, S.

Publications and source records attributed to Oud, S..

2 recordsLinked to original sources

Recurrent Emergence of Boundary Cell Types During Evolution of Floral Bullseye Patterns

Petal patterns play an important role in the reproductive success of flowering plants by attracting pollinators and protecting reproductive organs from environmental factors. Some transcription factors (TFs) that control pigment production and cuticle elaboration in petal epidermal cells have been identified. However, little is known about the upstream developmental processes that pre-pattern the petal surface to first establish the different domains where these regulators will later be expressed. Here, we developed a computational model of the evolution and development of petal patterns to investigate this early pre-patterning phase. We selected for gene regulatory networks (GRNs) that could divide the petal surface into proximal and distal domains to create a bullseye, a very common type of petal pattern across the angiosperms. The evolved GRNs showed robust patterning dynamics and could generate a variety of bullseye proportions. We found that the evolution of bullseye patterns was often accompanied by the spontaneous emergence of a third cell type with a unique gene expression profile at the boundary between the proximal and distal regions. These bullseye boundary cells appeared in most simulations despite not being explicitly selected for, and we validated their presence experimentally in Hibiscus trionum, a model system whose flowers display a bullseye pattern. Although boundary cell types emerged spontaneously in our simulations, they evolved more often and were more important for pattern formation when gene expression was modelled as a noisy process. This suggests that GRNs producing this emergent cell type may support reproducible bullseye formation by buffering against developmental variability. Altogether, the results from our evolutionary simulations illuminate the early steps of petal pattern formation and demonstrate that novel cell types can arise spontaneously and repeatedly from selection on other cell types when developmental robustness is considered.

systems biology↗

Ubiquitous systems drift in the evolution of development

Developmental system drift (DSD) is a process where a phenotypic trait is conserved over evolutionary time, while the genetic basis for the trait changes. DSD has been identified in models with simpler genotype-phenotype maps (GPMs), such as RNA folding, however the extent of DSD in more complex GPMs, such as developmental pattern formation, is debated. To investigate the occurrence of DSD in complex developmental GPMs, we constructed a multi-scale computational model of the evolution of gene regulatory networks (GRNs) governing plant meristem (stem cell niche) development. We found that, during adaptation, some regulatory interactions became essential for the correct expression of stem cell niche genes. These regulatory interactions were subsequently conserved for thousands of generations. Nevertheless, we observed that these deeply conserved regulatory interactions could be lost over the extended period of stabilising evolution. These losses were compensated by changes elsewhere in the GRN, which then became conserved as well. This gain and loss of regulatory interactions resulted in a continual cis-regulatory rewiring in which accumulated changes caused changes in the expression of several genes. Using two publicly available datasets we found frequent changes in conserved non-coding sequences across six evolutionarily divergent plant species, and showed that these changes do not correlate with changes in gene expression patterns, demonstrating the occurrence of DSD. These findings align with the results from our computational model, showing that DSD is pervasive in the evolution of complex developmental systems. Author SummaryA key open question in evolution of development (evo-devo) is the evolvability of complex phenotypes. Developmental system drift (DSD) contributes to evolvability by exploring different genotypes with similar phenotypic outcome, but with mutational neighbourhoods that have different, potentially adaptive, phenotypes. We investigated the potential for DSD in plant development using a computational model of developmental evolution. We found that the regulatory interactions between genes changed extensively, resulting in the continual neutral rewiring of the gene regulatory network underpinning development. Even regulatory interactions that were essential for correct development were replaced over long evolutionary time scales. Using plant genome and gene expression data from two publicly available datasets, we found high turnover of conserved non-coding sequences, which often contain regulatory sequences, occurring at both short and long time scales. This did not correlate consistently with gene expression changes in plant tissue, supporting the prevalence of DSD as predicted by our model.

systems biology↗