Christophe Klopp

The paper integrates long-read, short-read, and SNP data using a pangenome and imputation framework to identify structural variants associated with stature and milk traits in dairy cattle.

This study improves genome assemblies of Noccaea caerulescens accessions and identifies gene copy number variations linked to metal hyperaccumulation and adaptation.

The paper assembles high-quality genomes for twelve sheep breeds using long-read sequencing and phased haplotyping, enabling pangenome construction and structural variant analysis.

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

The paper presents a chromosome-level genome assembly of Cupressus sempervirens, revealing insights into conifer genome evolution and the role of transposable elements.

The paper presents a gapless, telomere-to-telomere genome assembly of Ostreococcus tauri RCC4221 with improved annotation of noncoding RNAs and epigenomic features.

Pan1C is a pipeline that builds chromosome-level pangenome graphs, improving alignment and variant calling by integrating multiple strategies and benchmarked across different species.

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

This paper introduces AGR, a pipeline to infer paleogenomes from modern species by using inter-species chromosomal synteny and hierarchical clustering.

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

The paper identifies genetic markers associated with migration behavior in European eels by comparing genetic differentiation between ocean and river sites, and between migrant and non-migrant phenotypes.

This study identifies genetic changes in Noccaea caerulescens that correlate with nickel hyperaccumulation, showing that NcIRT1 mutations can cause loss of the trait.

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.

This study identifies an endogenous circadian clock in deep-sea mussels that generates both tidal and circadian rhythms through an atypical mechanism.

This paper identifies a gene duplication-derived RLCK in Aeschynomene legumes that mediates Nod-independent rhizobial symbiosis, distinct from arbuscular mycorrhizal interactions.

The paper builds a reference genome for Cylicocyclus nassatus, estimates its genetic diversity across regions, and identifies genetic candidates for pyrantel resistance.

This paper provides genome and transcriptomic sequences of three invasive insect species, offering resources for population genomics and pest management.

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

The paper improves hifiasm haplotype contigs for autopolyploid genomes by adding protein distribution constraints, enhancing balance and BUSCO scores.

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.

This study identifies ancient Wnt-dependent habenular asymmetries in sharks, suggesting a conserved developmental mechanism across jawed vertebrates.

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.

The paper identifies a candidate sex determination locus in the European green toad, involving structural variation in the bod1l gene and a Y-specific non-coding RNA.

The paper creates an enriched gene atlas for the GRCg7b chicken assembly, increasing the number of annotated lncRNAs and PCGs and providing functional annotations across 47 tissues.

The paper identifies novel enzymes from rumen microbiomes that break down plant cell walls using a high-throughput metagenomic approach.

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.

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

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

This study investigates the distinct roles of maternally-inherited mRNAs and proteins in fish egg development, showing they contribute to neurodevelopment and immune protection respectively.

RADSex is a computational workflow for analyzing RAD-Seq data to identify sex determination systems, uncovering new sex-specific markers in fish species.