Biology subjects

Klopp, C.

Publications and source records attributed to Klopp, C..

At least 19 recordsLinked to original sources

bioRxiv2026

High-quality genome assembly of several Noccaea caerulescens accessions reveals gene expansion events associated with metal adaptation and hyperaccumulation

Since the beginning of the 20th century, the growth of the world's population and industrial development have led to increased soil pollution with metals, which poses a threat to the environment and human health. In this context, plants that are adapted to metalliferous soils and hyperaccumulate metals offer an opportunity to develop phytotechnologies for remediating metal-polluted soils. However, the molecular mechanisms by which plants tolerate and hyperaccumulate metals are not yet fully understood, which limits the improvement of these technologies. The metal hyperaccumulator species Noccaea caerulescens, belonging to the Brassicaceae family, is being developed as a genetic model to decipher these mechanisms. In this study, we have significantly improved the genome assembly of the N. caerulescens Cira accession and have produced high-quality assemblies for five additional accessions originating from different soil types and genetic groups. We used these high-quality assemblies to identify gene copy number variation associated with the metal hyperaccumulation trait in the Noccaea genus. Our analysis revealed that gene copy number variation affects a wide variety of biological functions in Noccaea, including genes that encode metal transporters belonging to the HMA, NRAMP and ZIP families. Notably, duplications affecting the magnesium transporter MGR2 suggest that the adaptation to ultramafic soils may be an ancestral trait in Noccaea. Finally, the association of transposable elements with gene duplications suggests that transposon activity may have played an important role in the evolution of metal hyperaccumulation in this genus.

plant biology↗

bioRxiv2026

Cromosomal genomes assemblies of twelve sheep breeds

The sheep research community benefits from a genome assembly that has been refined over the last 15 years. However, the rich diversity of sheep breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, twelve breeds were selected to represent (mostly French) sheep genetic diversity: Basco-Bearnaise, Black Belly, Blanche du Massif Central, Corse, Ile de France, Lacaune, Manech Tete Noire, Noire du Velay, Ouessant, Rambouillet, Vendeen, Soay. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. The reads were used to generate de novo assemblies and were aligned onto the public reference to call structural variants. PacBio HiFi and parental Illumina reads were used to assemble phased haplotypes of the Lacaune breed. For the other breeds, PacBio raw (CLR) or ONT reads were generated. Our work demonstrates the feasibility of assembling genomes with a reasonable amount of data and appropriate software packages, delivering one high-quality assembly and 11 standard sheep assemblies that pave the way for pangenome construction and structural variant functional studies.

genomics↗

bioRxiv2026

Goat genome assemblies, nine breeds for pangenome contribution

The goat research community benefits from one of the most comprehensive livestock genome assemblies, ARS1. However, the rich diversity of goat breeds suggests that a single individual genome is not enough to represent the species full genomic content. Third-generation sequencing technologies have recently made it possible to generate very high quality assemblies that should enable to elucidate unique and/or complex phenotype determinisms depending on genetic structural variations. In the SeqOccin project, nine goat breeds were selected to represent French goat genetic diversity: Alpine, Boer, Creole, Fosses, Poitevine, Provencale, Pyreneenne, Rove and Saanen. High-molecular-weight DNA was extracted from blood samples and subjected to long read whole-genome sequencing. There reads were used to generate de novo assemblies and were aligned onto the public reference to call structural variants. PacBio HiFi and parental Illumina reads were used to assemble phased haplotypes of the Alpine breed. For the other breeds, PacBio raw (CLR) or ONT reads were generated. Our work demonstrates the feasibility of assembling genomes with a reasonable amount of data and appropriate software packages, delivering one high-quality assembly and 8 standard goat assemblies that pave the way for pangenome construction and structural variant functional studies.

genomics↗

bioRxiv2026

Chromosome-scale assembly of the Cupressus sempervirens genome unravels new insights into the evolutionary history of conifers

Conifers, which comprise nearly two-thirds of extant gymnosperm species, are ecologically and economically important but remain genomically understudied because of their exceptionally large, repeat-rich genomes. Here, we report a chromosome-level assembly of the haploid genome of Cupressus sempervirens generated using PacBio HiFi reads and scaffolded with optical and genetic maps. The 10 Gb assembly shows exceptional contiguity for a conifer genome (contig N50 = 29.8 Mb) and was organized into 11 pseudomolecules. Iso-Seq-supported annotation identified 42,980 protein-coding genes. Repetitive elements account for over 80% of the genome, with LTR retrotransposons alone representing 52.5%. Transposable elements (TE) are pervasive in both intergenic and genic regions and have a major impact on gene architecture: TE insertions within introns generate ultra-long introns, often exceeding 100 kb, and drive gene size expansion. Analyses of LTR retrotransposon dynamics indicate that genome enlargement in C. sempervirens was driven not by recent transpositional bursts, but by the long-term accumulation and incomplete removal of ancient LTR retrotransposons. Consistent with this pattern, paleogenomic reconstruction across representative gymnosperms found no evidence of whole-genome duplication in the Cupressus lineage. This reference genome provides a valuable resource for studying conifer genome evolution, gene structure, and traits of agronomic and ecological interest, including cypress pollinosis.

genomics↗

bioRxiv2026

A gapless telomere-to-telomere reference genome of Ostreococcus tauri RCC4221 with expanded annotation of medium-sized ncRNAs

Marine photosynthetic microbes contribute substantially to global primary production, yet many algal lineages still lack reference genomes with the continuity and annotation quality required for fine-scale structural, regulatory and comparative analyses. Ostreococcus tauri, one of the smallest known free-living photosynthetic eukaryotes, has been a model marine picoeukaryote for over two decades. Despite successive improvements to its historical reference genome, previous assemblies retained hundreds of gaps and incomplete genes, hampering high-resolution genomic analyses. Here, we present O. tauri RCC4221 genome version 2026, a telomere-to-telomere assembly of all 20 chromosomes spanning 13.34 Mb with no gaps. This assembly combines PacBio long-read sequencing, Illumina short-read polishing, correction of unresolved regions guided by independent Nanopore-based assemblies. The updated reference supports a curated annotation comprising 7,683 protein-coding genes, 48 tRNA genes, 3 rRNA operons, 116 medium-sized noncoding RNAs, one signal recognition particle RNA and 138 small nucleolar RNAs. It also improves gene-model integrity and recovers candidate coding loci absent from the 2014 reference. Structural analyses resolved the organization of the two atypical low-GC chromosome 2 and 19 that contain duplicated regions that were collapsed or misrepresented in previous assemblies. Finally, bisulfite sequencing and PacBio SMRT sequencing revealed a dual DNA methylation landscape, with CG-context cytosine methylation concentrated in gene bodies and N6-methyladenosine (m6A) enriched at the start codon. The updated O. tauri 2026 assembly provides a complete and curated reference resource for chromosome biology, comparative genomics, epigenomics and RNA biology in a model marine picoeukaryote.

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↗

bioRxiv2026

Pan1c : a pipeline to easily build chromosome-level pangenome graphs

The advances of sequencing technologies and the availability of high-quality genome assemblies for many genotypes per species, give the opportunity to improve sequence alignment rate and quality, and the variant calling accuracy by including all genomic variations in a graph reference, called a pangenome graph. Because the process of building and analysing a pangenome graph is still complex, with related software packages under development, there is an important need for releasing user-friendly pipelines for this emerging research area. Pan1C is a pipeline based on a chromosome-by-chromosome graph construction strategy. It integrates two complementary strate-gies for building pangenomes and produces informative metric plots and graphics using a large set of tools. By benchmarking Pan1C on human, fungal, and wheat assemblies, which span a wide range of genome sizes and complexities, we showed the interest of Pan1C for assembly and graph validation as well as for performing primary analyses.

bioinformatics↗

bioRxiv2026

Ancestral Genome Reconstruction.

AGR, for Ancestral Genome Reconstruction, is an automatic publicly available and open-source pipeline to infer paleogenomes from modern species genome comparisons exploiting the concept of inter-species chromosomal synteny relationships hierarchical clustering that can be used to unveil how ancestral genomes, genes, sequences and functions have been shaped during million years of present-day plant evolution.

genomics↗

bioRxiv2026

Genetic differentiation between two locations along an ocean/river gradient captures the signature of intragenerational selection in the European eel (Anguilla anguilla)

AO_SCPLOWBSTRACTC_SCPLOWMigration events can act as strong selective filters by spatially sorting individuals according to their migration ability, behaviour, and associated functional traits. The European eel, a panmictic and threatened fish, presents various estuarine migration patterns at juvenile stage (glass eel), ranging from sedentarization in brackish/saltwater of the estuary (non-migrant phenotype) to upstream colonisation of freshwater ecosystems (migrant phenotype). We hypothesize that migration propensity is partly genetically determined in glass eel, and that migration-related genotypes are spatially sorted during estuarine migration. To test these hypotheses, we first collected six pools of individuals over three years at two extreme sites along a gradient from ocean to Adour River tidal limit (Ocean vs. Upstream). Secondly, we collected additional glass eels and phenotypically sorted migrant vs. non-migrant individuals using an experimental device mimicking alternating tidal currents, producing two other pools. Whole genome pool sequencing and analysis of these eight pools generated 18.99 106 SNP variants. Controlling for linked selection through a local score approach, we found five best outlier SNPs with a significant genetic differentiation between Ocean vs. Upstream sites (average FST = 0.21) compared to the pangenomic estimate (FST = 0.0086). These five SNPs were all found in the same gene (gpb2), involved in interferon-mediated antiviral immune responses. We also found 28 best outlier SNPs with a significant genetic differentiation between migrant vs. non-migrant phenotypes (average FST = 0.51). They were located in genes mainly involved in neuronal development, cell migration and tissue remodelling, transcriptional regulation, and metabolic or stress-related processes. Our results support that variation in eel migration propensity is partly genetically determined and that, while panmixia maintains high level of genetic diversity, spatial sorting could promote intra-generational genetic divergence between habitats of European eels. However, the absence of shared genes among the best outliers between in-situ and experimental contrasts suggests a complex and context-dependent genetic control of migration.

evolutionary biology↗

bioRxiv2026

Integrating Structural Variants into Sequence-Based GWAS Using a Pangenome and Imputation Framework in French Dairy Cattle

BackgroundStructural variants (SVs) are most effectively identified using long-read (LR) sequenc-ing. However, such data remain scarce, and sequenced samples often lack associated phenotypic information. To overcome this limitation, we integrated pangenome-based (variation graph-based) and imputation approaches to enable large-scale SV association studies in the three main French dairy cattle breeds. ResultsA variation graph was constructed using 69,892 deletions, 89,900 insertions, and 17,402 duplications detected in 176 LR samples. We subsequently genotyped 939 samples for each SV in the panel by realigning their short read (SR) sequences to the graph. Validation analyses showed high genotype concordance rates for deletions (0.79) and insertions (0.79); however, concordance for duplications was low (0.14), leading to their exclusion from further analyses. The retained SVs were combined with single nucleotide variants (SNVs) to build a sequence-level imputation reference panel. Using SNP genotyping array data, we imputed SVs and SNVs for 11,902 Holstein, 3,753 Montbeliarde, and 3,053 Normande bulls. After quality control, more than 14 million SNVs and 40 thousand SVs were retained for within-breed genome-wide association studies (GWAS) us-ing daughter yield deviations for stature and four milk production and composition traits. The GWAS results reveled genetic architectures consistent with previous findings and identified 40 genome-wide significant associations between structural variant and key phenotypes. Conditional analyses showed that ten of these SVs as strong candidates associated with milk fat and protein contents, as well as stature. ConclusionsBy integrating LR, SR, and SNP genotyping data within a unified pangenome and imputation framework, we demonstrate a scalable strategy to systematically interrogate the contribution of SVs to complex traits. The resulting genetic architectures were highly consistent with previous findings, validating both the robustness and transferability of our approach. Our findings highlight the added value of integrating SVs into routine genomic analyses and provide a scalable framework for incorporating SVs into genomic selection in dairy cattle.

genomics↗

bioRxiv2025

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

BackgroundThe current cattle reference genome, derived from a single Hereford cow, does not capture the full spectrum of genetic diversity present within the species. Moreover, detecting structural variations (SVs [≥] 50 nucleotides long) remains challenging using only standard approaches of either short or long-read sequence approaches against a linear reference genome. Recent advances in long-read sequencing technologies and graph-based assembly now enable the construction of breed-specific pangenomes, revealing previously uncharacterized genomic regions that may contribute to important agricultural traits. ResultsIn this study we constructed a cattle pangenome graph using 16 high-quality haplotype-resolved genome assemblies originating from nine breeds representing the diversity of French cattle populations, and including Yak (Bos grunniens) as a close outgroup species. Using a trio-based strategy combined with complementary sequencing technologies and bioinformatics methods, we identified and characterized 101,219 structural variations. Of these, 33,634 were classified as non-reference unique insertions (NRUIs), adding several megabases of novel genomic sequences absent from the current Hereford reference genome. Analysis of the distribution of these NRUIs revealed significant genome-wide enrichment within QTL regions associated with milk production and morphological traits, suggesting their contribution to the genetic basis of economically relevant phenotypes. Furthermore, their functional annotation highlighted two NRUIs located within the intronic regions of ARMH3 and EPHA5, both specific to the Normande breed and significantly associated with milk production and morphological traits, respectively. ConclusionsOur findings demonstrate the value of pangenome approaches to uncover functionally relevant SVs, particularly NRUIs, that are systematically not in the current reference genome. By linking these variants to economically important traits, our work underscores the need to incorporate breed diversity into future genomic analyses and reference-building efforts in cattle.

genetics↗

bioRxiv2025

Peripheral tissues of deep-sea mussels exhibit autonomous circadian timing via an atypical mechanism

While biological rhythms are crucial to life, the deep sea has long been considered an arrhythmic exception. However, at hydrothermal vents - devoid of diel cues yet shaped by tides - the mussel Bathymodiolus azoricus shows both tidal and, unexpectedly, circadian rhythms at -1700 m. Whether endogenous clock(s) drive these cycles remained unanswered. Here, we report endogenous circadian rhythms in B. azoricus cell cultures under constant conditions: isolated cells displayed a circadian oscillator despite tidal-dominant rhythms in situ. Reporter assays using genomic regions upstream of the mussels per gene and containing E-box motifs indicate that a functional transcription-translation feedback loop (TTFL) underpins circadian timing even in the deep sea. In contrast to conventional models, however, BazPeriod lacks autonomous repressive activity but modulates BazCry2. As BazPeriod itself oscillates tidally, it may explain how a single endogenous clock yields both tidal and diel rhythms. The work also spotlights the highly time-sensitive biology of vastly unexplored deep-sea biology.

molecular biology↗

bioRxiv2025

Gain and loss of gene function shaped the nickel hyperaccumulation trait in Noccaea caerulescens

Nickel hyperaccumulation is an extreme adaptation to ultramafic soils observed in more than 500 plant species. However, our understanding of the molecular mechanisms underlying the evolution of this trait remains limited. To shed light on these mechanisms, we have generated a high-quality genome assembly of the metal hyperaccumulator Noccaea caerulescens. We then used this genome as reference to conduct comparative intraspecific and interspecific transcriptomic analyses using various accessions of N. caerulescens and the non-accumulating relative Microthlaspi perfoliatum, to identify genes associated with nickel hyperaccumulation. Our results suggest a correlation between nickel hyperaccumulation and a decrease in the expression of genes involved in defense responses and the regulation of membrane trafficking. Surprisingly, these analyses did not reveal a significant enrichment of genes involved in the regulation of metal homeostasis. However, we found that the expression levels of selected metal transporters, namely NcHMA3, NcHMA4 and NcIREG2, is consistently elevated in N. caerulescens accessions hyperaccumulating nickel. Furthermore, our analyses identified frameshift mutations in NcIRT1 associated with the loss of nickel hyperaccumulation in a few accessions. We further showed that the expression of a functional NcIRT1 in roots of the La Calamine accession increases nickel accumulation in shoots. Our results demonstrate that NcIRT1 participate in nickel hyperaccumulation in N. caerulescens. They also suggest that nickel hyperaccumulation is an ancient trait in N. caerulescens that has evolved from the high and constitutive expression of few metal transporters including NcIREG2 and that the trait was subsequently lost in a few accessions due to mutations in NcIRT1.

plant biology↗

bioRxiv2025

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

Structural variants (SVs) correspond to different types of genomic variants larger than 50 bp. Many findings suggest the use of long rather than short reads to improve the accuracy of SV detection. Here, we present the results of an in-depth analysis for detection of SVs, mainly large insertions and deletions, in 14 French bovine breeds, based on whole-genome data comprising 176 long-read and 571 short-read samples, with 154 individuals having both long- and short-read data available. We first investigated possible biases on the performances of well-known SV detection tools, namely CUTESV, PBSV, and SNIFFLES, using long reads from different technologies, including PacBio HiFi, Oxford ONT, and PacBio CLR. We subsequently highlighted the abilities of tools for detecting SVs (DELLY, LUMPY, and MANTA) and for genotyping known SVs (GRAPHTYPER, SVTYPER, PARAGRAPH, and VG toolkit) using short-read data. We then show how the incremental composition of samples in the reference panel affected the SV genotyping for six validation individuals sequenced in short reads. We then searched for the optimal parameters and created the final SV reference panel consisting of 25,191 deletions and 30,118 insertions. Finally, we emphasized the landscape of the genotyped SVs segregating across 571 short-read individuals of 14 breeds.

genomics↗

bioRxiv2025

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

BackgroundThe current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represent a limit when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of short or long-read sequence mapping to the current bovine genome assembly. ResultsIn this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Using a combination of complementary approaches, we explored the pangenome graph and identified 2.563 Gb of sequences common to all samples, and cumulated 0.295 Gb of variable sequences. Notably, we discovered 0.159 Gb of novel sequences not present in the current Hereford reference genome assembly. Our analysis also revealed 109,275 SVs, of which 84,612 were bi-allelic, including 21,840 insertions and 21,340 deletions. Genome-wide association studies using SNPs and a panel of 221 SVs, shared between the pangenome and the EuroGMD chip, revealed several well-known QTLs across the genome for the Holstein, Montbeliarde and Normande breeds. Among those, a QTL on chromosome 11 presents an SV with a highly significant effect on stature in the Holstein breed. This SV is a 6.2 kb deletion affecting the 5UTR, first exon and part of first intron of MATN3 gene, suggesting a potential regulatory and coding effect. ConclusionsOur study provides new insights into the genetic diversity of 14 French dairy and beef breeds and highlights the utility of pangenome graphs in capturing structural variation. The identified SV associated with stature highlights the importance of integrating SVs into GWAS for a more comprehensive understanding of complex traits.

genetics↗

bioRxiv2025

Improving hifiasm haplotypes for autopolyploid genome assemblies using constraint programming

Actual versions of hifiasm often produce unbalanced haplotype contigs for autopolyploid genome assemblies. Adding a contraint on the distribution of proteins among haplotypes improves haplotype sizes and busco scores balances. Four species were used to benchmark this approach against hifiasm raw results. The script can be downloaded from https://github.com/chklopp/Separate_haplotypes_with_toulbar2.

bioinformatics↗

bioRxiv2025

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

Today, long read technologies make it possible to produce telomere-to-telomere genome assemblies. These assemblies permit more accurate whole genome analyses, including on repeated regions. The genome assembly process can chain several steps such as read correction, contigs assembly, contig polishing, scaffolding and gap filling, among others. Each step usually requires at least one software package, and input sequences. For the end user, it is not necessarily clear which combination of tools, together with read types, will work best for a given genome. In this work, we will focus on contig production, which is a central and complex task of the assembly process. It aims at producing the longest, errorless, sequences, called contigs, from reads. While it is possible to produce contigs from short reads, long reads are now widely preferred, since they produce much longer contigs. In this work, we evaluate several contig producing software packages (usually named assemblers), on long reads generated by two sequencers using three protocols, for three eukaryotic, complex species with different characteristics. Our aim is twofold. First, we would like to give readers insight on the impact of sequencing technology and assembler combinations, in order to help them make their choice for a given genome. Second, we would like to present different assembly metrics and provide a critical view on their interpretation.

bioinformatics↗

bioRxiv2024

Draft genome and transcriptomic sequence data of three invasive insect species

Cydalima perspectalis (the box tree moth), Leptoglossus occidentalis (the western conifer seed bug), and Tecia solanivora (the Guatemalan tuber moth) are three economically harmful invasive insect species. This study presents their genomic and transcriptomic sequences, generated through whole- genome sequencing, RNA-seq transcriptomic data, and Hi-C sequencing. The resulting genome assemblies exhibit good quality, providing valuable insights into these species. The genome sizes are 500.4 Mb for C. perspectalis, 1.74 Gb for L. occidentalis, and 623.3 Mb for T. solanivora. These datasets are available in the NCBI Sequence Read Archive (BioProject PRJNA1140410) and serve as essential resources for population genomics studies and the development of effective pest management strategies, addressing significant gaps in the understanding of invasive insect species.

genomics↗