Biology subjects

Raimondeau, P.

Publications and source records attributed to Raimondeau, P..

5 recordsLinked to original sources

bioRxiv2026

Divergence in wilt tolerance across the range of Mimulus guttatus in the absence of stomatal regulation

Whether phenotypes and environments predict performance under stress is central to ecology and evolution and can reveal species' vulnerability to global change. We sampled Mimulus guttatus range-wide to test whether reproductive, morphological, and physiological traits predict drought responses. Surprisingly, we find that stomatal response, a key mediator of water balance, did not change as drought intensified. Climate, however, predicted survival after turgor loss: plants from regions with large daily relative to seasonal temperature ranges survived wilting longer. Stress responses also depended on life history: where summers are dry, perennials withstood lower water potentials, whereas annuals increased leaf cooling as they wilted. Known trait associations were not fixed: although many baseline traits tracked climate, none predicted drought responses. Drought performance therefore cannot be inferred from traits measured under well-watered conditions. Lacking stomatal regulation, riparian drought escapers like M. guttatus may be vulnerable if shorter growing seasons bring drought before reproduction.

plant biology↗

bioRxiv2025

Regulatory features determine the evolutionary fate of laterally acquired genes in plants

Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. However, the factors that influence the integration and long-term retention of transferred genes remain poorly understood. The pangenome of the grass Alloteropsis has a high turnover of laterally acquired genes, and here we combine expression, methylation and genomic data to identify factors promoting their long-term persistence. Most transferred genes appear to be degenerating, showing lower expression levels and/or greater sequence truncation compared to their vertically inherited homologs. These degenerating genes also show significantly higher levels of DNA methylation, potentially indicating transcriptional silencing. The likelihood of a transferred gene being retained will be influenced by how easily it can be expressed in the recipient genome. In Alloteropsis, putatively functional laterally acquired genes had expression levels significantly more similar to their donor xenolog than to their vertically inherited homolog. This pattern suggests that transferred genes may carry cis-regulatory elements encoded on the fragment of DNA that moves between species, facilitating their expression in the new genomic context. Evolutionary novelty may also increase the likelihood that selection retains a transferred gene. However, only a significant difference in expression level, not sequence divergence, between donor and recipient orthologs is associated with successful lateral gene transfer. Overall, our results show that most transferred genes degrade over time. However, those capable of regulating their own expression are more likely to persist and contribute to long-term evolutionary innovation. Significance StatementLateral gene transfer (LGT) can introduce novel traits into plant genomes, yet most transferred genes are only transient residents and are degenerating, with reduced expression, truncation, and elevated DNA methylation. However, a minority persist and are more likely to resemble their donor counterparts in expression, suggesting co-transfer of cis-regulatory elements. These findings indicate that regulatory compatibility is key to their long-term survival.

evolutionary biology↗

bioRxiv2024

A high-quality genome of the mass-blooming desert plant Cistanthe longiscapa and its photosynthetic behavior related to drought and life history

O_LICrassulacean acid metabolism (CAM) photosynthesis has independently evolved many times in arid-adapted plant lineages. Cistanthe longiscapa (Montiaceae), a desert mass-blooming annual, can upregulate CAM facultatively upon stress such as drought. Few studies, however, consider life history stages when measuring CAM activity or its facultative onset. C_LIO_LITo test the effect of drought and flowering on photosynthetic activity, we assayed Cistanthe individuals in fully-watered and drought conditions, as well as fully-watered individuals at pre-flowering and flowering life stages. We assembled and annotated a chromosome-scale genome of C. longiscapa and compared it with the genome of Portulaca amilis and analyzed differential gene expression. C_LIO_LIResults show significantly upregulated CAM in drought conditions as compared to fully-watered conditions; furthermore, flowering individuals showed slightly higher CAM activity as compared to pre-flowering plants, even when fully-watered. Differential gene expression analyses provide preliminary support for the possible co-regulation of CAM expression and reproduction. C_LIO_LIWe emphasize the potentially missed significance of life history in the CAM literature, and consider how the CAM biochemical module could become co-opted into other plant behaviors and responses, such as the shift to reproduction or flowering in annuals. C_LI

plant 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↗

bioRxiv2020

Phylogenetic relatedness, co-occurrence, and rhizomes increase lateral gene transfer among grasses

O_LILateral gene transfer (LGT) has been documented in a broad range of prokaryotes and eukaryotes, and it can promote adaptation. LGT of functional nuclear genes has been reported among some plants, but systematic studies are needed to assess the frequency and facilitators of LGT in the group. C_LIO_LIWe scan the genomes of a diverse set of 17 grass species that span more than 50 million years of divergence and include major crops to identify grass-to-grass protein-coding LGT. C_LIO_LIWe identify LGT in 13 species, with significant variation in the amount each received. Rhizomatous species acquired statistically more genes, probably because this growth habit boosts opportunities for transfer into the germline. In addition, the amount of LGT increases with phylogenetic relatedness, which might reflect genomic compatibility amongst close relatives facilitating successful transfers. However, genetic exchanges among highly divergent species with overlapping distributions also occur, pointing to an additional role of biogeography. C_LIO_LIOverall, we show that LGT is a widespread phenomenon in grasses, which has moved functional genes across the entire grass family into domesticated and wild species alike. The dynamics of successful LGT appears to be dependent on both opportunity (co-occurrence and rhizomes) and compatibility (phylogenetic distance). C_LI

evolutionary biology↗