Biology subjects

Prost-Boxoen, L.

Publications and source records attributed to Prost-Boxoen, L..

3 recordsLinked to original sources

bioRxiv2024

Expanding the toolkit for ploidy manipulation in Chlamydomonas reinhardtii

SummaryO_LIWhole genome duplications, widely observed in plant lineages, have significant evolutionary and ecological impacts. Yet, our current understanding of the direct implications of ploidy shifts on short- and long-term plant evolution remains fragmentary, necessitating further investigations across multiple ploidy levels. C_LIO_LIChlamydomonas reinhardtii, a haploid green alga, is a valuable model organism with profound potential to study the impact of ploidy increase on the longer-term in a laboratory environment. This is partly due to the ability to successfully increase the ploidy level. C_LIO_LIWe developed a strategy to engineer ploidy in Chlamydomonas reinhardtii using a collection of non-interfering antibiotic selectable markers. This approach allows to induce higher ploidy levels in Chlamydomonas reinhardtii and is applicable to field isolates, which expands beyond specific auxotroph laboratory strains and broadens the genetic diversity of parental haploid strains that can be crossed. We implement flow cytometry for precise measurement of the genome size of strains of different ploidy. C_LIO_LIWe demonstrate the creation of diploids, triploids and tetraploids by engineering North American field isolates, broadening the application of synthetic biology principles in Chlamydomonas reinhardtii. C_LIO_LIOur study greatly facilitates the application of Chlamydomonas reinhardtii to study polyploidy, both in fundamental and applied settings. C_LI

synthetic biology↗

bioRxiv2024

Asymmetric genome merging leads to gene expression novelty through nucleo-cytoplasmic disruptions and transcriptomic shock in Chlamydomonas triploids

Genome merging is a common phenomenon in many organisms, causing a wide range of consequences on phenotype, adaptation, and gene expression, among other effects, yet its broader implications are not well understood. Two consequences of genome merging on gene expression remain poorly understood: dosage effects and evolution of expression. In this study, we employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection (LNS) experiment. Utilizing fitness assays, qPCR, and RNA-Seq, we assessed the immediate consequences of genome merging and subsequent evolution over time. Our findings reveal substantial alterations in gene expression, protein homeostasis (proteostasis) and cytonuclear stoichiometry. Notably, gene expression exhibited expression level dominance and transgressivity (i.e., expression level higher or lower than either parent). Ongoing expression level dominance and a pattern of "functional dominance" from the haploid parent was observed, alongside remarkable stability in expression patterns across generations. Despite major nucleo-cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems.

evolutionary biology↗

bioRxiv2024

HybridExpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors

Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex non-additive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. Here, we introduce HybridExpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). HybridExpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of HybridExpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. HybridExpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. HybridExpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).

bioinformatics↗