Biology subjects

Parisod, C.

Publications and source records attributed to Parisod, C..

5 recordsLinked to original sources

bioRxiv2023

Modular transcriptional responses to environmental changes

Knowledge about the molecular underpinnings of phenotypic plasticity is still scarce and quantifying gene expression in response to abiotic and biotic factors enables to investigate transcriptional plasticity. RNAseq data on clones of the alpine plant Biscutella laevigata (Brassicaceae) subjected to control, cold, heat, drought and herbivory treatments assessed differentially expressed genes (DEGs) and transposable elements (DE-TEs) in comparison to similar experiments in Arabidopsis thaliana. Synergistic and trade-off DEGs presenting parallel and antagonistic regulation among treatments were further identified and used with networks of co-expressed DEGs to characterize transcriptional plasticity in response to environmental changes. Compared to A. thaliana, B. laevigata presented fewer DEGs that were mostly up-regulated by stronger expression shifts in response to environmental treatments. Biscutella laevigata showed constitutive expression of half of the A. thaliana DEGs. It further presented a higher proportion of synergistic DEGs, a lower number of trade-off DEGs and a transcriptome organized in environment-specific subnetworks. Several DE-TEs were identified as activated by heat and herbivory. The stress-tolerant perennial B. laevigata presents a highly modular transcriptional plasticity in response to environmental changes, contrasting with the more integrated transcriptome of A. thaliana. Significance statementLittle is known about the molecular underpinnings of phenotypic plasticity. Here, focusing on expression shifts during changes in abiotic and biotic conditions, we highlight environment-responsive genes acting synergistically or antagonistically among treatments and underlying modular transcriptional plasticity in two Brassicacea species.

plant biology↗

bioRxiv2022

Purging due to self-fertilization does not prevent accumulation of expansion load

Species range expansions are a common demographic history presenting populations with multiple evolutionary challenges. It is not yet fully understood if self-fertilization, which is often observed at species range edges, may create an evolutionary advantage against these challenges. Selfing provides reproductive reassurance to counter Allee effects and selfing may purge accumulated mutational burden due to founder events (expansion load) by further increasing homozygosity. We study how selfing impacts the accumulation of genetic load during range expansion via purging and/or speed of colonization. Using simulations, we disentangle inbreeding effects due to demography versus due to selfing and find that selfers expand faster, but still accumulate load, regardless of mating system. The severity of variants contributing to this load, however, differs across mating system: higher selfing rates purge large-effect recessive variants leaving a burden of smaller-effect alleles. We compare these predictions to the mixedmating plant Arabis alpina, using whole-genome sequences from refugial outcrossing populations versus expanded selfing populations. Empirical results indicate accumulation of expansion load along with evidence of purging in selfing populations, concordant with our simulations, and suggesting that while purging is a benefit of selfing evolving during range expansions, it is not sufficient to prevent load accumulation due to range expansion. Author SummaryThe geographic space that species occupy, i.e. the species range, is known to fluctuate over time due to changing environmental conditions. Since the most recent glaciation, many species have recolonized available habitat as the ice sheets melted, expanding their range. When populations at species range margins expand into newly available space, they suffer from an accumulation of deleterious alleles due to repeated founder effects. We study whether self-fertilization, which is considered an evolutionary deadend, can be favored under these expanding edge conditions. Selfing has two important effects: allowing for faster expansion due to reproductive assurance and purging recessive deleterious alleles by exposing them to selection as homozygotes. We use simulations to identify the impact of selfing on expanded populations and then compare these results to an empirical dataset to assess whether our predictions are met. We use the mixed-mating plant alpine rock-cress (Arabis alpina) since it has both expanded since the last glaciation and undergone a mating shift to selfing. We find that selfing does not prevent the accumulation of deleterious load, however purging does still act to remove the most severe variants, indicating that selfing provides this benefit during range expansions.

evolutionary biology↗

bioRxiv2022

Variation in the rate lateral gene transfers accumulate in a grass lineage

Lateral gene transfer (LGT) has been reported in multiple eukaryotes. This process seems particularly widespread in the grass family, although we know very little about the underlying dynamics and how it impacts gene content variation within a species. Alloteropsis semialata is a tropical grass, and multiple LGT were detected in a reference genome assembled from an Australian individual. As part of this study we assemble three additional de novo genomes for A. semialata and one for its sister species Alloteropsis angusta. In total we detect 168 LGT across the five reference genomes. Using whole-genome resequencing data for a further 40 individuals we establish the distribution of these transfers and map their origin along the species phylogeny. This shows that many LGTs were acquired relatively recently, with numerous secondary losses. Exponential decay models indicate that the rate of LGT acquisitions varied significantly among lineages [6-28 per Ma], with a high rate of subsequent LGT losses [11-24% per Ma] that largely exceeds that of native loci [0.02-0.8% per Ma]. This high turnover creates large intraspecific structural variants, with a preponderance of LGT occurring as accessory genes in the Alloteropsis pangenome. The acquired genes represent unparalleled genetic novelties, having independently evolved for tens of millions of years before they were transferred. Ultimately, the rapid LGT turnover generates standing variation that can fuel local adaptation.

evolutionary biology↗

bioRxiv2019

Plant defense resistance in natural enemies of a specialist insect herbivore

Plants defend themselves against herbivores through the production of toxic and deterrent metabolites. Adapted herbivores can tolerate and sequester these metabolites, allowing them to feed on defended plants and become toxic to their own enemies. Can herbivore natural enemies overcome sequestered plant defense metabolites to prey on adapted herbivores? To address this question, we studied how entomopathogenic nematodes cope with benzoxazinoid defense metabolites that are produced by grasses and sequestered by a specialist maize herbivore, the western corn rootworm. We find that nematodes from US maize fields in regions in which the western corn rootworm was present over the last 50 years are behaviorally and metabolically resistant to sequestered benzoxazinoids and more infective towards the western corn rootworm than nematodes from other parts of the world. Exposure of a benzoxazinoid-susceptible nematode strain to the western corn rootworm for five generations results in higher behavioral and metabolic resistance and benzoxazinoid-dependent infectivity towards the western corn rootworm. Thus, herbivores that are exposed to a plant defense sequestering herbivore can evolve both behavioral and metabolic resistance to plant defense metabolites, and these traits are associated with higher infectivity towards a defense sequestering herbivore. We conclude that plant defense metabolites that are transferred through adapted herbivores may result in the evolution of resistance in herbivore natural enemies. Our study also identifies plant defense resistance as a novel target for the improvement of biological control agents.

plant biology↗

bioRxiv2019

Hybridization preceded radiation in diploid wheats

Evolutionary relationships among the Aegilops-Triticum relatives of cultivated wheats have been difficult to resolve owing to incomplete lineage sorting and reticulate evolution. Recent studies have suggested that the wheat D-genome lineage (progenitor of Ae. tauschii) originated through homoploid hybridization between the A-genome lineage (progenitor of Triticum s.str.) and the B-genome lineage (progenitor of Ae. speltoides). Scenarios of reticulation have been debated, calling for adequate phylogenetic analyses based on comprehensive sampling. To reconstruct the evolution of Aegilops-Triticum diploids, we here combined high-throughput sequencing of 38 nuclear low-copy loci of multiple accessions of all 13 species with inferences of the species phylogeny using the full-parameterized MCMC_SEQ method. Phylogenies recovered a monophyletic Aegilops-Triticum lineage that began diversifying ~6.5 Ma ago and gave rise to four sublineages, i.e. the A- (2 species), B- (1 species), D- (9 species) and T- (Ae. mutica) genome lineage. Full-parameterized phylogenies as well as patterns of tree dilation and tree compression supported a hybrid origin of the D-genome lineage from A and B ~4.1 Ma ago, and did not indicate additional hybridization events. This comprehensive and dated phylogeny of wheat relatives indicates that the origin of the hybrid D-genome was followed by intense diversification into almost all diploid as well as allopolyploid wild wheats.

evolutionary biology↗