Biology subjects

Diblasi, C.

Publications and source records attributed to Diblasi, C..

7 recordsLinked to original sources

bioRxiv2025

Large-scale eQTL analyses in Atlantic salmon reveal persistent dosage compensation 100 million years after genome duplication.

Whole-genome duplication (WGD) through autopolyploidization has played a role in genome evolution across eukaryotes. A major consequence of WGD is the rewiring of gene regulatory networks, partly driven by selection on dosage balance. In multicellular organisms, evidence for dosage balance selection has relied on comparative patterns of duplicate gene retention and expression, with few studies directly examining regulatory architecture after WGD. Here, we analysed a large-scale eQTL dataset from Atlantic salmon (Salmo salar), which experienced a WGD 100 million years ago. We found that trans-regulatory connections were enriched between duplicated regions, indicating long-term conservation of ancestral interchromosomal regulatory interactions. Overall, 230 duplicated genes (5%) shared eQTLs, suggesting conserved regulatory control. Moreover, 16 gene pairs showed compensatory expression effects mediated by a common regulator, consistent with predictions of the dosage balance hypothesis. These gene pairs were significantly enriched in recently rediploidized regions. Our results indicate long-term maintenance of dosage balance after WGD. TeaserGenetic regulation in Atlantic salmon shows that duplicated genes can remain dosage-balanced across 100 million years of evolution.

evolutionary biology↗

bioRxiv2025

Impaired trap closure in the counting-deficient Venus flytrap mutant DYSCALCULIA is caused by cell wall biomechanics

Living in nutrient-poor environments, the carnivorous Venus flytrap Dionaea muscipula captures animal prey to compensate for this deficiency. Stimulation of trigger hairs located on the inner trap surface elicits an action potential (AP). While two consecutive APs result in fast trap closure in wildtype (WT) plants, sustained AP generation by the insect struggling to escape the trap leads to jasmonic acid (JA) biosynthesis, formation of the digestive "stomach", and release of enzymes needed to decompose the victim. The Dionaea muscipula DYSCALCULIA (DYSC) mutant is able to fire touch-induced APs, but unlike WT plants, it does not snap-close its traps after two consecutive APs. Moreover, DYSC plants fail to properly initiate the JA pathway in response to mechanostimulation and even wounding, a well-known JA-dependent process conserved among plants. As demonstrated in previous studies, this DYSC mutant defect is associated with impaired decoding of mechanostimulation (i.e. touch) -induced Ca2+ signals. External JA application to the trap, however, restores slow trap closure and digestive gland function in DYSC, while rapid trap closure is JA-independent and cannot be rescued by exogenous JA application. Higher frequency mechanostimulation and thus more APs, however, revealed that DYSC is still able to close its traps, albeit much slower than WT plants. To reveal the molecular underpinnings of DYSCs delayed trap movement, we generated a chromosome-scale Dionaea genome assembly and profiled gene expression. The refined transcriptomic analysis uncovered widespread misregulation of cell wall-related genes in DYSC, implicating altered cell wall plasticity in the sluggish mutant. Cell indentation studies by atomic force microscopy revealed a strictly localized and strikingly enhanced stiffening of the cell wall for DYSC that may hinder rapid trap closure and snap buckling. Together, these genomic, transcriptomic, and biophysical data identify cell wall elasticity as a key constraint on voltage and Ca2+ dependent trap kinetics. This finding documents the interrelationship between mechanosensing and Ca2+ signaling in the ultrafast capture organ of the Venus flytrap.

plant biology↗

bioRxiv2025

Metatranscriptomic Insights into Microbial Dynamics Prior to Disease Onset in Atlantic Salmon Aquaculture

Poly(A)-selected RNA-seq datasets are routinely generated in aquaculture research, yet the microbial information contained in unmapped reads is seldom explored due to the low abundance of nonhost transcripts and concerns about contamination. In this study, we repurposed Atlantic salmon gill RNA-seq data to assess whether meaningful microbial signals can be recovered using a contamination-aware and compositionally appropriate framework. Unmapped reads were analyzed with a custom Kraken2 database composed exclusively of complete, circularized salmon-associated bacterial genomes together with all available Atlantic salmon assemblies and the human genome. Although microbial sequences represented only a small fraction of total reads, 21 genera were detectable across samples. Genus-level profiles, Jaccard-based ordination, and ANCOM-BC analyses consistently revealed clear differences between tanks, whereas no associations were observed for sex or survival status. Three species exhibited significant tank-specific effects, indicating that environmental factors contributed the strongest detectable structure in the data. The limited microbial diversity recovered here reflects the expected constraints of poly(A)-enriched libraries, yet the results demonstrate that unmapped reads from host-derived RNA-seq can still provide informative environmental signatures when analyzed with curated reference databases and compositional statistical approaches. This strategy offers a practical means to extract exploratory microbiome information from existing transcriptomic datasets.

microbiology↗

bioRxiv2024

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

Aquaculture has a considerably shorter history compared to the domestication of plants and animals. Among aquatic species, those that have undergone whole genome duplication events (WGD) seem particularly successful. This suggests that genetic redundancy from WGD is important for domestication, possibly similar to plant domestication. Atlantic salmon (Salmo salar), which has experienced a lineage-specific WGD, has undergone rapid domestication through intensive breeding since the 1960s. Here, we examined the genomic responses to the domestication of Atlantic salmon, including the impacts of WGD, by comparing the whole genome sequence data of aquaculture and wild populations from two lineages: the Eastern and Western Atlantic (Western Norway and North America). Our analysis revealed shared selective sweeps on identical SNPs in major histocompatibility complex (MHC) genes across distinct aquaculture populations compared to their wild counterparts. This SNP level parallelism suggests that a combination of long-term balancing selection and recent human-induced selection has significantly shaped the evolutionary trajectory of MHC genes. In addition, we observed selective sweeps on gene pairs in the homeologous regions originating from WGD, highlighting WGDs role in maintaining genomic variation and potentially reducing pleiotropy through sub-functionalization. This unique type of "parallel" selection contributes to adapting to the intensive artificial conditions of aquaculture. These findings provide valuable insights into the genetic mechanisms of domestication and adaptive responses in Atlantic salmon, suggesting that the salmonid whole genome duplication has underpinned their successful rapid domestication. Our research emphasizes the importance of maintaining genetic diversity to support sustainable aquaculture practices.

genomics↗

bioRxiv2023

MiniRead: a simple and inexpensive do-it-yourself device for multiple analyses of micro-organism growth kinetics

Fitness in micro-organisms can be proxied by growth parameters on different media and/or temperatures. This is achieved done by measuring optical density at 600 nm using a spectrophotometer, which measures the effect of absorbance and side scattering due to turbidity of cells suspensions. However, when growth kinetics must be monitored in many 96-well plates at the same time, buying several 96-channels spectrophotometers is often beyond budgets. The MiniRead device presented here is a simple and inexpensive do-it-yourself 96-well temperature-controlled turbidimeter designed to measure the interception of white light via absorption or side scattering through liquid culture medium. Turbidity is automatically recorded in each well at regular time intervals for up to several days or weeks. Output tabulated text files are recorded into a micro-SD memory card to be easily transferred to a computer. We propose also an R package which allows (1) to compute the non-linear calibration curves required to convert raw readings into cell concentration values, and (2) to analyze growth kinetics output files to automatically estimate growth parameters such as lag time, maximum growth rate, or cell concentration at the plateau. The MiniRead project is freely available under GPL license from https://forgemia.inra.fr/gqe-base/MiniRead. The project includes (1): user manual (Supplementary Material 1), firmware, list of electronic components and printed circuit board manufacturing files for the MiniRead device, and (2) a release containing the MiniRead R package for calibration and data analysis (Supplementary Material 2) with its tutorial (Supplementary Material 3). Detailed device building instructions are available at https://moulon.inrae.fr/materiel_labo/miniread/.

microbiology↗

bioRxiv2023

Co-segregation of recombinant chromatids maintains genome-wide heterozygosity in an asexual nematode

In asexual animals, female meiosis is modified to produce diploid oocytes. Associated with recombination, this is expected to lead to a rapid loss of heterozygosity, with adverse effects on fitness. Many asexuals, however, have a heterozygous genome, the underlying mechanisms being most often unknown. Cytological and population genomic analyses in the nematode Mesorhabditis belari revealed another case of recombining asexual being highly heterozygous genome-wide. We demonstrated that heterozygosity is maintained because the recombinant chromatids of each chromosome pair co-segregate during the unique meiotic division. A theoretical model confirmed that this segregation bias is necessary to account for the observed pattern and likely to evolve under a wide range of conditions. Our study uncovers a new type of cell division involving Directed Chromatid Assortment. One sentence summaryGenome wide heterozygosity in the asexual nematode Mesorhabditis belari is achieved by directed assortment of recombinant chromatids during female meiosis

evolutionary biology↗

bioRxiv2023

Functional and regulatory diversification of circadian rhythm period genes during the evolution of vertebrates

The Period genes (Per) play essential roles in modulating the molecular circadian clock timing in a broad range of species, which regulates the physiological and cellular through the transcription-translation feedback loop. While the Period gene paralogs are widely observed among vertebrates, the evolutionary history and the functional diversification of Per genes across vertebrates are not well known. In this study, we comprehensively investigated the evolution of Per genes, including de novo binding motif discovery by comparative genomics. We also determined the lineage-specific transcriptome landscape across tissues and developmental stages and phenotypic effects in public RNA-seq data sets of model species. We observed multiple lineage-specific gain and loss events of Per genes, though no simple association was observed between ecological factors and Per gene numbers in each species. Among salmonid fish species, the per3 gene has been lost in the majority, whereas those retaining the per3 gene exhibit not a signature of relaxed selective constraint but rather a signature of intensified selection. We also determined the signature of adaptive diversification of the CRY-binding region in Per1 and Per3, which modulates the circadian rhythm. We also discovered putative regulatory sequences, which are lineage-specific, suggesting that these cis-regulatory elements may have evolved rapidly and divergently across different lineages. Collectively, our findings revealed the evolution of Per genes and their fine-tuned contribution to the plastic and precise regulation of circadian rhythms in various vertebrate taxa. SignificanceThe Period (Per) genes play essential roles in the circadian rhythm in animals. In this study, we comprehensively investigated the evolutionary diversification of the three types of Period genes in vertebrates. As a result, we observed a rapid evolution and sub-functionalization of these genes, especially adaptive diversification signatures in the protein-binding region, which plays a crucial role in regulating circadian rhythms. This underscores the fine-tuned contribution of Per genes in the biological clocks precision and adaptability across various vertebrate taxa.

evolutionary biology↗