Des Marais, D. | bioRxiv Science

bioRxiv2021

Evolution and functional dynamics of dehydrins in model Brachypodium grasses

Dehydration proteins (dehydrins, DHNs) confer tolerance to water-stress deficit to plants, thus playing a fundamental role in plant response and adaptation to water-deprivation stressful environments. We have performed a comparative genomics and evolutionary study of DHN genes in four model Brachypodium grass species, and a drought-induced functional analysis in 32 ecotypes of the flagship species B. distachyon, to gain insight into the origins and dynamics of these proteins and the correlated drought-mediated phenotypic responses in ecotypes showing different hydric requirements. Genomic sequence analysis detected 10 types of dehydrin genes (Bdhn) across the Brachypodium species, totalling 47 genes. Domain and conserved motif contents of peptides encoded by Bdhn genes revealed eight protein architectures, YS{phi}K2 being the most common architecture. Bdhn genes were spread across several chromosomes and more frequent in syntenic chromosomes 3 and 4 of B. distachyon, 4 and 5 of B. stacei and 4 of B. sylvaticum. Tandem and segmental duplication events were detected for four Bdhn genes. Selection analysis indicated that all the Bdhn genes were constrained by purifying selection. Three upstream cis-regulatory motifs (BES1, MYB124, ZAT) were consistently detected in several Bdhn genes. Functional analysis in 32 natural accessions of B. distachyon demonstrated that only four Bdhn genes (Bdhn1, Bdhn2, Bdhn3, Bdhn7) were expressed in mature leaves and that all of them were significantly more highly expressed in plants under drought conditions. These genes corresponded to wheat orthologs that were also significantly more expressed under drought stress. Brachypodium dehydrin expression was significantly correlated with drought-response phenotypic traits (plant biomass, leaf carbon and proline contents and WUE increases, leaf water and nitrogen content changes) being more pronounced in drought-tolerant ecotypes. Bdhn expression, associated phenotypic trait changes and climate niche variation did not show significant phylogenetic signal when tested in the B. distachyon genealogical-species tree. By contrast, some of them showed low or marginal significant phylogenetic signal when tested in the B. distachyon Bdhn tree, suggesting that Bdhn gene evolution is partially related to adaptation to drought in this species. Our results demonstrate that dehydrin composition and regulation is a key factor determining the acquisition of water-stress tolerance in grasses.

genetics↗

bioRxiv2021

Temporal correlations robustly reveal regulatory coherence uponenvironmental perturbation

Environment can alter the degree of phenotypic variation and covariation, potentially influencing evolutionary trajectories. However, environment-driven changes in phenotypic variation remain understudied. In an effort to exploit the abundance of RNASequencing data now available, an increasing number of ecological studies rely on population-level correlation to characterize the plastic response of the entire transcriptome and to identify environmentally responsive molecular pathways. These studies are fundamentally interested in identifying groups of genes that respond in concert to environmental shifts. We show that population-level differential co-expression exhibits biases when capturing changes of regulatory activity and strength in rice plants responding to elevated temperature. One possible cause of this bias is regulatory saturation, the observation that detectable co-variance between a regulator and its target may be low as their transcript abundances are induced. This phenomenon appears to be particularly acute for rapid-onset environmental stressors. However, our results suggest that temporal correlations may be a reliable means to detect transient regulatory activity following rapid onset environmental perturbations such as temperature stress. Such temporal bias is likely to confound the studies of phenotypic integration, where high-order organismal traits are hypothesized to be more integrated with strong correlation under stressful conditions, while recent transcriptome studies exhibited weaker coexpression between genes under stressful conditions. Collectively, our results point to the need to account for the nuances of molecular interactions and the possibly confounding effects that these can introduce into conventional approaches to study transcriptome datasets.

systems biology↗