Biology subjects

Degalez, F.

Publications and source records attributed to Degalez, F..

7 recordsLinked to original sources

bioRxiv2026

A single-nucleus atlas of the adult laying hen liver reveals metabolic specialization and improved cellular resolution through enhanced genome annotation

The liver of laying hens plays a central role in metabolism and reproduction, supporting the synthesis of egg yolk precursors under strong hormonal regulation. Despite its physiological importance, a high-resolution cellular reference of the adult chicken liver is still lacking. Here, we generated a single-nucleus RNA sequencing atlas of the adult laying hen liver from eight individuals, providing a comprehensive view of its cellular composition and transcriptional landscape. Using this framework, we identified major hepatic cell populations, including hepatocytes, endothelial cells, cholangiocytes, hepatic stellate cells, and diverse immune cell types, revealing a broadly conserved vertebrate liver architecture. However, hepatocyte zonation, a key feature of mammalian liver organization, was not observed, consistent with the absence of hepatocyte zonation reported in birds. Importantly, we demonstrate that the use of an enriched genome annotation, incorporating additional protein-coding and long non-coding RNA models, substantially improves transcript detection and enhances cell-type resolution in single-nucleus datasets. This improved resolution allows more accurate marker-based assignment of hepatocyte subpopulations and refines the interpretation of hepatic cellular heterogeneity. Within hepatocytes, we uncovered transcriptionally distinct subpopulations associated with lipid metabolism and reproductive function, including estrogen-responsive programs involving cytochrome P450 genes such as CYP2C23A and CYP2C23B. In parallel, we characterized a complex immune compartment composed of resident macrophages and adaptive immune cells, highlighting the dual metabolic and immunological roles of the avian liver. Overall, this atlas provides a high-resolution reference for avian liver biology and demonstrates that improved genome annotation enhances the resolution and interpretation of cellular heterogeneity in single-cell transcriptomic studies.

genomics↗

bioRxiv2026

New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)

The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.

genomics↗

bioRxiv2025

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation

Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic data of individuals with European ancestry, introducing potential biases that remain uncharacterized. Here, we generate over 800 million full-length reads with long-read RNA-seq in 43 lymphoblastoid cell line samples from eight genetically-diverse human populations and build a cross-ancestry gene annotation. We show that transcripts from non-European samples are underrepresented in reference gene annotations, leading to systematic biases in allele-specific transcript usage analyses. Furthermore, we show that personal genome assemblies enhance transcript discovery compared to the generic GRCh38 reference assembly, even though genomic regions unique to each individual are heavily depleted of genes. These findings underscore the urgent need for a more inclusive gene annotation framework that accurately represents global transcriptome diversity.

genomics↗

bioRxiv2024

Cross-species orthology detection of long non-coding RNAs (lncRNA) through 13 species using genomic and functional annotations.

Long non-coding RNAs (lncRNAs), defined by a length of over 200 nucleotides and limited protein-coding potential, have emerged as key regulators of gene expression. However, their evolutionary conservation and functional roles remain largely unexplored. Comparative genomics, particularly through sequence conservation analysis, offers a promising approach to infer lncRNA functions. Traditional methods focusing on protein-coding genes (PCGs) fall short due to the rapid evolutionary divergence of lncRNA sequences. To address this, a workflow combining syntenic methods and motif analysis via the Mercator- Pecan genome alignment was developed and applied across 13 vertebrate species, from zebrafish to various amniotes and birds. Further analyses to infer functionality revealed co-expression patterns through 17 shared tissues between human and chicken but also functional short-motif enrichment across the 13 species using the LncLOOM tool, exemplified by the human OTX2-AS1 and its counterparts in other species. The study expanded the catalog of conserved lncRNAs, providing insights into their evolutionary conservation and information related to potential functions. The workflow presented serves as a robust tool for investigating lncRNA conservation across species, supporting future research in molecular biology to elucidate the roles of these enigmatic transcripts.

genomics↗

bioRxiv2024

Variant calling and genotyping accuracy of ddRAD-seq: comparison with 20X WGS in layers

Whole Genome Sequencing (WGS) remains a costly or unsuitable method for routine genotyping of laying hens methods, thus alternatives have been developed. Among these, reduced representation sequencing approaches can offer both sequencing quality and cost-effectiveness by reducing the genomic regions covered by sequencing. The aim of this study was to evaluate the ability of double digested Restriction site Associated DNA sequencing (ddRAD-seq) to identify and genotype SNPs in laying hens, by comparison with a presumed reliable WGS approach. Firstly, the sensitivity and precision of variant calling and the genotyping reliability of ddRADseq were determined. Next, the SNP Call Rate (CRSNP) and mean depth of sequencing per SNP (DPSNP) were compared between both methods. Finally, the effect of multiple combinations of thresholds for these parameters on genotyping reliability and amount of remaining SNPs in ddRAD-seq was studied. In raw form, the ddRAD-seq identified 349,497 SNPs evenly distributed on the genome with a CRSNP of 0.55, a DPSNP of 11X and a mean genotyping reliability rate per SNP of 80%. Considering genomic regions covered by expected enzymatic fragments (EFs), the sensitivity of the ddRAD-seq was estimated at 32.4% and its precision at 96.4%. The low CRSNP and DPSNP values were explained by the detection of SNPs outside the EFs theoretically generated by the ddRAD-seq protocol. Indeed, SNPs outside the EFs had significantly lower CRSNP (0.25) and DPSNP (1X) values than SNPs within the EFs (0.7 and 17X, resp.). The study demonstrated the relationship between CRSNP, DPSNP, genotyping reliability and the number of SNPs retained, to provide a decision-support tool for defining filtration thresholds. Severe quality control over ddRAD-seq data allowed to retain a minimum of 40% of the SNPs with a CcR of 98%. Then, ddRAD-seq was defined as a suitable method for variant calling and genotyping in layers.

genomics↗

bioRxiv2023

Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.

Gene atlases for livestock are steadily improving thanks to new genome assemblies and new expression data improving the gene annotation. However, gene content varies across databases due to differences in RNA sequencing data and bioinformatics pipelines, especially for long non-coding RNAs (lncRNAs) which have higher tissue and developmental specificity and are harder to consistently identify compared to protein coding genes (PCGs). As done previously in 2020 for chicken assemblies galgal5 and GRCg6a, we provide a new gene atlas, lncRNA-enriched, for the latest GRCg7b chicken assembly, integrating "NCBI RefSeq", "EMBL-EBI Ensembl/GENCODE" reference annotations and other resources such as FAANG and NONCODE. As a result, the number of PCGs increases from 18,022 (RefSeq) and 17,007 (Ensembl) to 24,102, and that of lncRNAs from 5,789 (RefSeq) and 11,944 (Ensembl) to 44,428. Using 1,400 public RNA-seq transcriptome representing 47 tissues, we provided expression evidence for 35,257 (79%) lncRNAs and 22,468 (93%) PCGs, supporting the relevance of this atlas. Further characterization including tissue-specificity, sex-differential expression and gene configurations are provided. We also identifiend conserved miRNA-hosting genes with human counterparts, suggesting common function. The annotated atlas is available at www.fragencode.org/lnchickenatlas.html.

genomics↗

bioRxiv2023

The ChickenGTEx pilot analysis: a reference of regulatory variants across 28 chicken tissues

Chicken is a valuable model for understanding fundamental biology, vertebrate evolution and diseases, as well as a major source of nutrient-dense and lean-protein-enriched food globally. Although it is the first non-mammalian amniote genome to be sequenced, the chicken genome still lacks a systematic characterization of functional impacts of genetic variants. Here, through integrating 7,015 RNA-Seq and 2,869 whole-genome sequence data, the Chicken Genotype- Tissue Expression (ChickenGTEx) project presents the pilot reference of regulatory variants in 28 chicken tissue transcriptomes, including millions of regulatory effects on primary expression (including protein-coding genes, lncRNA and exon) and post-transcriptional modifications (alternative splicing and 3 untranslated region alternative polyadenylation). We explored the tissue-sharing and context-specificity of these regulatory variants, their underlying molecular mechanisms of action, and their utility in interpreting adaptation and genome-wide associations of 108 chicken complex traits. Finally, we illustrated shared and lineage-specific features of gene regulation between chickens and mammals, and demonstrated how the ChickenGTEx resource can further assist with translating genetic findings across species. One-Sentence SummaryThe ChickenGTEx provides a multi-tissue reference of regulatory variants for chicken genetics and genomics, functional genomics, precision breeding, veterinary medicine, vertebrate evolution and even human biomedicine.

genetics↗