bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.09.27.615352

CAYSS: package for automatic Cytometry Analysis of Yeast Spore Segregation

Raffoux, X.·Falque, M.
View original source ↗Export metadata ↓

Abstract

Meiotic recombination is a powerful source of haplotypic diversity, and thus plays an important role in the dynamics of short-term adaptation. However, high-throughput quantitative measurement of recombination parameters is challenging because of the large size of offspring to be genotyped. One of the most efficient approaches for large-scale recombination measurement is to study the segregation of fluorescent markers in gametes. Applying this to yeast spores by flow cytometry has already been proved to be highly efficient, but manual analyses of density distributions of signal intensities is time-consuming and produces non-perfectly reproducible results. Such analyses are required to identify events corresponding to spores and to assign each of them to a genotypic class depending on their fluorescence intensity. The CAYSS package automatically reproduces the manual process that weve been developing to analyze yeast recombination for years, including Maximum-Likelihood estimation of fluorescence extinction (Raffoux et al. 2018a). When comparing the results of manual vs CAYSS automatic analyses of the same cytometry data, recombination rates and interference were on average very similar, with less than 3% differences on average and strong correlations (R2>0.9). In conclusion, as compared to manual analysis, CAYSS allows to save a lot of human time and produces totally reproducible results. The CAYSS software is freely available under GPL license from https://forgemia.inra.fr/gqe-base/cayss/-/releases. The package is also provided as Supplementary Material 1 and a tutorial may be found as Supplementary Material 2. TAKE AWAYThe CAYSS R package measures recombination rate and crossover interference from flow cytometry data of isolated yeast spores segregating for fluorescent markers. The analysis is fully automatic and reproducible. It includes spore identification from FSC and SSC data, genotype determination from fluorescence intensities, and Maximum Likelihood estimation of recombination parameters.

Source connections

Explore related subjects

geneticsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Raffoux, X., Falque, M.. 2024-09-30. CAYSS: package for automatic Cytometry Analysis of Yeast Spore Segregation. https://doi.org/10.1101/2024.09.27.615352

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Large language model-based bibliometric evaluation of population descriptors in human genetics

As the use of population descriptors such as race, ethnicity, and ancestry have become increasingly common in modern genetics research, there have been growing calls to critically examine their use. Most notably, in 2023, the National Academies of Science, Engineering, and Medicine (NASEM) published a report titled Using Population Descriptors in Genetics and Genomics Research: A New Framework for an Evolving Field, which included eight specific and actionable recommendations for researchers to implement the ethical and accurate use of population descriptors in genetic research. Here, we use the 2023 NASEM report as a benchmark to analyze the use of population descriptors in genome-wide association studies (GWAS). We develop a general toolkit for large language model-based bibliometrics, operationalize the report's recommendations into an evaluation framework, and apply this framework to evaluate all 4,007 papers from the GWAS Catalog published between 2007 and 2025 with full text available on PubMedCentral. We find significant improvements in adherence to NASEM report recommendations over time. However, most improvements predate the publication of the NASEM report itself, suggesting the report functioned primarily as a synthesis of existing best practices rather than a catalyst for change. We conclude by highlighting opportunities for growth in the field of human genetics.

genetics↗
bioRxiv2026

Mitigating biases of rescaling in forward-in-time population genetic simulations

Forward-in-time population genetic simulations are widely used in evolutionary analyses, but simulating large populations and long genomic regions remains computationally demanding. To reduce this cost, parameter rescaling is widely employed, in which the original evolutionary process is approximated by one with a smaller population size and fewer generations. Recently, several studies using the SLiM simulator have raised concerns about the accuracy of this rescaling approach. In this study, we show that many of the biases reported in these studies can be mitigated by using a different simulation algorithm. These results reveal that the accuracy of parameter rescaling depends on how well the simulation algorithm preserves diffusion-limit properties under rescaling.

genetics↗
bioRxiv2026

OPA1 controls mitochondrial dysfunction-driven liver fibrosis in MASLD

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

genetics↗