Cécile Donnadieu

Goat genome assemblies, nine breeds for pangenome contribution

The paper presents high-quality genome assemblies for nine goat breeds using long-read sequencing, contributing to pangenome construction and structural variant analysis.

PolliCrop: A high-throughput computer vision pipeline for pollinator monitoring in agroecosystems

PolliCrop is a computer vision pipeline that detects and identifies flower-visiting insects on sunflower plants, showing accurate performance in predicting visitation frequencies across genotypes.

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

The paper presents new chromosome-level haplotyped genome assemblies for the Japanese quail, improving contiguity and completeness compared to previous references.

Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity

The paper constructs a cattle pangenome to identify novel non-reference unique insertions (NRUIs) and links them to economically important traits.

An extensive and unbiased genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting

The paper identifies 440 parent-of-origin expressed genes in pigs, revealing weak conservation of genomic imprinting across species and tissues.

Comprehensive detection of structural variations in long and short reads dataset of French cattle

The paper detects structural variants in French cattle using long and short-read data, identifying 25,191 deletions and 30,118 insertions across 14 breeds.

Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes

The paper constructs a bovine pangenome using long-read sequencing and identifies structural variants associated with key phenotypes in French cattle breeds.

Benchmarking long-read genome assemblers for three sequencing protocols and three agricultural species

This study benchmarks long-read genome assemblers across three agricultural species and three sequencing protocols to evaluate their performance and provide insights into optimal tool and technology combinations.

metagWGS, a comprehensive workflow to analyze metagenomic data using Illumina or PacBio HiFi reads

metagWGS is a workflow for metagenomic analysis using short or long reads, producing high-quality genome bins and comprehensive annotations.

The black honey bee genome: insights on specific structural elements and a first step towards pan-genomes

The paper presents a high-quality genome assembly for the black honey bee (Apis mellifera mellifera) and demonstrates its utility for structural variant genotyping and pan-genome analysis.

A methyl-seq tool to capture genomic imprinted loci

The paper develops a methyl-seq tool to identify genomic imprinted loci by detecting parent-of-origin methylation in 165 candidate regions.

Multi-genome comparisons reveal gain-and-loss evolution of the anti-Mullerian hormone receptor type 2 gene, an old master sex determining gene, in Percidae

The paper compares genomes across multiple fish species to study the evolutionary changes in the amhr2bY gene, a key sex-determining gene, revealing gains and losses in different Percidae species.

Massive detection of cryptic recessive genetic defects in cattle mining millions of life histories

The paper detects recessive genetic defects in cattle using genomic data and life history analysis, identifying 33 new loci linked to juvenile mortality.

The genomics of linkage drag in sunflower

This study analyzes the genomic and phenotypic impacts of wild introgressions in sunflower, finding that while some traits improve, most introgressions negatively affect yield and quality.

An ancient truncated duplication of the anti-Mullerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family

The paper identifies a truncated duplication of the amhr2 gene on the Y chromosome in Pangasiid catfishes as a conserved master sex-determining gene.

Transcriptional response to host chemical cues underpins expansion of host range in a fungal plant pathogen lineage

The paper identifies host-specific transcriptional programs in a fungal plant pathogen and shows cis-regulatory variation contributes to host range expansion.

Analysis Of Polycerate Mutants Reveals The Evolutionary Co-Option Of HOXD1 To Determine The Number And Topology Of Horns In Bovidae

The paper identifies POLYCERATE alleles in sheep and goats linked to defective HOXD1 function, showing haploinsufficiency causes horn bud splitting and highlights HOXD1's role in headgear patterning in Bovidae.

Genome sequence of the euryhaline Javafish medaka, Oryzias javanicus: a small aquarium fish model for studies on adaptation to salinity.

The paper presents a high-quality draft genome assembly of Oryzias javanicus, focusing on its adaptation to salinity.

Characterization of a Y-specific duplication/insertion of the anti-Mullerian hormone type II receptor gene based on a chromosome-scale genome assembly of yellow perch, Perca flavescens

The paper presents a chromosome-scale genome assembly of yellow perch and identifies a Y-specific duplication of the amhr2 gene as a candidate sex determination gene.