Biology subjects

Vandecasteele, C.

Publications and source records attributed to Vandecasteele, C..

11 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

Plasticity of the mutation rate and spectrum in eukaryotic marine phytoplankton

The ability to adapt shapes the future of any species or population. Adaptive potential is primarily determined by the spontaneous mutation rate {micro} and the mutation spectrum, which define the new genetic variation available to selection. Increasing evidence points to the plasticity of the mutation rate and spectrum, which vary according to environment. However, data is lacking for marine phytoplankton, an essential group for marine ecosystems as well as a major player in biogeochemical cycles. Here, we measure the plasticity of mutation rates and spectra in the chlorophyte Ostreococcus tauri by mutation accumulation experiments in 4 different conditions: low salinity, high salinity, low temperature, and high temperature. {micro}SNM is lowest under low salinity, doubles under high salinity and low temperature and quadruples under high temperature. SNM spectra become increasingly biased towards C:G[->]T:A transitions with increasing {micro}SNM. While {micro}ID does not change with the environment, the structural mutation rate {micro}SM is higher at low temperature, likely due to transposon activity. Given the rapid environmental changes associated with global climate change, mutation rates and spectra plasticity may critically influence the adaptive potential of marine primary producers.

evolutionary biology↗

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

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

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

Genomic imprinting, a mechanism resulting in parent-of-origin expression of genes through epigenetic regulation, intersects with a broad range of biological fields including evolution, molecular genetics and epigenetics and determinism of complex traits. Although next generation sequencing technologies enable nowadays to detect imprinted genes in a genome-wide manner, a wide spectrum of this phenomena is evaluated only in humans and mice. Here, we propose to map genes showing a parental expression bias in hypothalamus, muscle and placenta in piglets around birth using an extensive and unbiased strategy that relied on reciprocal crosses, genetics reconstruction of parental phases after imputation and statistical analyses discriminating parent-of-origin from allele-specific expression. We detected 440 unique genes with a weak to exclusive parental expression bias including 114 unique genes with an imbalance ratio above 25:75. About thirty imprinted genes are common to human and/or mice and an equivalent number is shared between tissues, suggesting an overall weak conservation landscape of genomic imprinting. Interestingly, we identified novel parent-of-origin expressed genes involved in neurodevelopmental (PITRM1, Pitrilysin Metallopeptidase 1) and fetal growth (FAM20B, Glycosaminoglycan Xylosylkinase and POU6F2, POU Class 6 Homeobox 2) functions. In addition, deeper analyses of specific loci likely highlighted lineage-specific imprinted genes such as a Zinc Finger Protein 300-like gene as well as specific imprinted isoforms of COPG2 (COPI Coat Complex Subunit Gamma 2), a gene showing conflicting data in the literature. Altogether, our results bring pig as the most comprehensively and exhaustively documented species for genomic imprinting after human and mice organisms. A weak conservation of this mechanism across species and tissues suggested a distinction between a small number of core imprinted genes and others parent-of-origin expressed genes that seemed subjected to evolutionary forces for acquiring their imprinting status either in a lineage-specific or tissue-specific manner.

genomics↗

bioRxiv2023

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

BackgroundThe actual honey bee reference genome, HAv3.1, was produced from a commercial line sample, thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pan-genome analyses. ResultsPacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for a re-estimation of the honey recombination rate, over-estimated in some previous studies, due to mis-assemblies resulting in spurious inversions in the older reference genomes. The sequence continuity obtained is very high and the only limit towards continuous chromosome-wide sequences seem to be due to tandem repeat arrays usually longer than 10 kb and belonging to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome, for genotyping two structural variants by a pan-genome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76 % for the two variants respectively. ConclusionsOur new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance including structural variants in GWAS. Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pan-genomes.

genomics↗

bioRxiv2023

Evidence for increased fitness of a plant pathogen conferred by epigenetic variation

Adaptation is usually explained by adaptive genetic mutations that are transmitted from parents to offspring and become fixed in the adapted population. However, more and more studies show that genetic mutation analysis alone is not sufficient to fully explain the processes of adaptive evolution and report the existence of non-genetic (or epigenetic) inheritance and its significant role in the generation of adapted phenotypes. In the present work, we tested the hypothesis of the role of DNA methylation, a form of epigenetic modification, in adaptation of the plant pathogen Ralstonia solanacearum to the host plant during an experimental evolution. Using SMRT-seq technology, we analyzed the methylomes of 31 experimentally evolved clones that were obtained after serial passages on a given host plant during 300 generations, either on susceptible or tolerant hosts. Comparison with the methylome of the ancestral clone revealed between 12 and 21 differential methylated sites (DMSs) at the GTWWAC motif in the evolved clones. Gene expression analysis of the 39 genes targeted by these DMSs revealed limited correlation between differential methylation and differential gene expression. Only one gene showed a correlation, the RSp0338 gene encoding the EpsR regulator protein. The MSRE-qPCR (Methylation Sensitive Restriction Enzyme - qPCR) technology was used as an alternative approach to assess the methylation state of the DMSs found by SMRT-seq between the ancestral and evolved clones. This approach also found the two DMSs upstream of RSp0338. Using site-directed mutagenesis, we demonstrated the contribution of these two DMSs in host adaptation. As these DMSs appeared very quickly in the experimental evolution, we hypothesize that such fast epigenetic changes can allow rapid adaptation to the plant stem environment. To our knowledge, this is the first study showing a link between epigenetic variation and evolutionary adaptation to new environment.

evolutionary biology↗

bioRxiv2023

A methyl-seq tool to capture genomic imprinted loci

Genomic imprinting represents an original model of epigenetic regulation resulting in a parent-of-origin expression. Despite the critical role of imprinted genes in mammalian growth, metabolism and neuronal function, there is no molecular tool specifically targeting them for a systematic evaluation. Here, we optimized and compared to bisulfite-based standard a novel methyl-seq system to capture 165 candidate regions for genomic imprinting and ultimately detect parent-of-origin methylation, the main hallmark of imprinting.

genomics↗

bioRxiv2022

Comparative genome analysis of Enterococcus cecorum reveals intercontinental spread of a lineage of clinical poultry isolates.

Enterococcus cecorum is an emerging pathogen responsible for osteomyelitis, spondylitis, and femoral head necrosis causing animal suffering, mortality, and requiring antimicrobial use in poultry. Paradoxically, E. cecorum is a common inhabitant of the intestinal microbiota of adult chickens. Despite evidence suggesting the existence of clones with pathogenic potential, the genetic and phenotypic relatedness of disease-associated isolates remains little investigated. Here, we sequenced and analyzed the genomes and characterized the phenotypes of more than 100 isolates, the majority of which were collected over the last ten years in 16 French broiler farms. Comparative genomics, genome-wide association study, and measured susceptibility to serum, biofilm forming capacity, and adhesion to chicken type II collagen were used to identify features associated with clinical isolates. We found that none of the tested phenotypes could discriminate origin of the isolates or phylogenetic group. Instead, we found that most clinical isolates are grouped phylogenetically and our analyses selected six genes that discriminate 94% of isolates associated with disease from those that are not. Analysis of the resistome and the mobilome revealed that multidrug-resistant clones of E. cecorum cluster in few clades and that integrative conjugative elements and genomic islands are the main carriers of antimicrobial resistance. This comprehensive genomic analysis shows that disease-associated clones of E. cecorum belong mainly to one phylogenetic clade. IMPORTANCEEnterococcus cecorum is an important pathogen in poultry worldwide. It causes a number of locomotor disorders and septicemia, particularly in fast-growing broilers. Animal suffering, antimicrobial use, and associated economic losses require a better understanding of disease-associated E. cecorum isolates. To address this need, we performed whole genome sequencing and analysis of a large collection of isolates responsible for outbreaks in France. By providing the first dataset on the genetic diversity and resistome of E. cecorum strains circulating in France, we pinpoint an epidemic lineage probably also circulating elsewhere and which should be targeted preferentially by preventive strategies in order to reduce the burden of E. cecorum-related diseases.

genomics↗

bioRxiv2021

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are mostly unknown but can rely on the ability to release phytohormones, degrade plant cell-wall polysaccharides and produce specialised metabolites. Here we sequenced the genome of the rhizospheric and plant defence-stimulating strain Streptomyces sp. AgN23. We found out that it belongs to the soil and plant root dwelling S. violaceusniger clade. The genome annotation of AgN23 revealed the ability of the bacterium to synthesise auxin, a major regulator of plant development, to degrade plant cell wall with a large repertoire of carbohydrate degrading enzymes and to produce antimicrobials (rustmicin, mediomycin, niphimycin, nigericin) and plant bioactive compounds (nigericin, echosides, elaiophylin) through a set of biosynthetic gene clusters. We also found that these genomic features are well-conserved among members of the S. violaceusniger clade. In addition, AgN23 display original events of biosynthetic gene clusters acquisitions and losses which may account for its beneficial effect on plants. Taken together, our work supports the hypothesis that hydrolytic enzymes and specialised metabolites repertoires underpin the interaction of bacteria belonging to the S. violaceusniger clade with plant roots within the rhizosphere. Impact statementStreptomycetes are filamentous Gram-positive bacteria universally found around and within host plant tissues. These actinobacteria have been extensively investigated for their tremendous ability to produce diverse specialised metabolites (e.g., antibiotics). By contrast their impact on host plant physiology is widely neglected. Whether specific lineage of Streptomyces colonise host plant and what are the underlying molecular mechanisms is poorly documented. Here we report a chromosome-scale assembly of AgN23 genome, a Streptomyces sp. strain previously characterised for its ability to activate the plant immune system. This reference sequence enabled us to position AgN23 in the S. violaceusniger clade from which several representatives have been isolated worldwide from the rhizosphere of unrelated plants. Comparative genomic studies suggest that S. violaceusniger spp. produce a prominent CAZyome with expansion of plant cell wall degrading enzymes families and a conserved specialised metabolism acting on host plant physiology and its rhizospheric microbiota. These genomic features may underly S. violaceusniger spp. adaptation to the rhizopsheric niche. Data summaryThe raw reads sequences of AgN23 genome are available at NCBI on the Sequence Read Archive portal for PacBio and MiSeq data (SRR13990229 and SRR14028548 respectively). The Genome assembly is available on the NCBI nucleotide portal under the accession NZ_CP007153.1. This genome sequence was uploaded on the MicroScope platform for genome annotation and analysis (https://mage.genoscope.cns.fr/microscope/home/index.php) [1]. The RNA-seq raw reads are archived in the NCBI Bioproject PRJNA745930. The following eight supplementary tables are included in the online version of this article. Supplementary Information 1: Genomes used in this study. The accession number used from the NCBI portal, name, size, number of contigs as well as the level of completeness of the assembly are indicated. Supplementary Information 2: List of the single copy core genes used by autoMLST to build the phylogenetic tree in Figure 1. O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/465742v2_fig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@e15f3org.highwire.dtl.DTLVardef@c34218org.highwire.dtl.DTLVardef@1286956org.highwire.dtl.DTLVardef@1bb5b3_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Multi-locus sequence typing assigned AgN23 to the S. violaceusniger clade. Phylogenetic tree based on the multiple alignment of 85 single-copy homologous genes selected from genomic sequences with AutoMLST. The green node highlights the isolates considered to be from the same species (ANI>95%). The black node highlights the clade formed by isolates with ANI>90% as compared to AgN23. The black squares highlights the eight strains that were used for the BGC conservation study. The green logo indicates plant-isolated strains. Frankia alni ACN14a was used as outgroup, bootstrap=100. C_FIG Supplementary information 3: Annotation of AgN23 full chromosome. For each gene the frame of translation, sequence length and position on the chromosome are indicated. All genes were annotated according to the Microscope platform, see materials and methods. In addition, the expression for each gene is reported in transcripts per million (TPM) based on the the RNA-seq data from three biological replicates. Supplementary Information 4: Genomes having a Mash-based estimated ANI (Average Nucleotide Identity) superior or egal to 80% according to autoMLST. Supplementary Information 5: Prediction of the CAZyme encoding genes using HMMER dbCAN2. The genes are sorted according their CAZy families. For each gene, the begin position on the chromosome, the CAZy category, the annotation, the expression level in transcripts per million (TPM) and the predicted targets of the putative enzymes are described. Supplementary Information 6: Gene identified by antiSMASH in the region containing a biosynthetic gene cluster. Expression levels in transcripts per million (TPM) are indicated for each gene. Annotated central bioynthetic genes are indicated as Y. Those are the ones used for the calculation of mean BGC expression in Table 2. O_TBL View this table: org.highwire.dtl.DTLVardef@1362f24org.highwire.dtl.DTLVardef@50f792org.highwire.dtl.DTLVardef@1ad9681org.highwire.dtl.DTLVardef@1742e96org.highwire.dtl.DTLVardef@9e9b6c_HPS_FORMAT_FIGEXP M_TBL O_FLOATNOTable 2:C_FLOATNO O_TABLECAPTIONantiSMASH annotation of AgN23 chromosomal regions coding for Biosynthetic Gene Clusters. The functional category of each BGCs was determined by antiSMASH. The BGC type, best hit in the MIBiG database as its percentage of similarity to the query are indicated along with the bacterial strain from whom the cluster was described. The expression level of each BGCs was determined by doing the mean of the expression level in Transcripts Per Million (TPM) of the core biosynthetic genes of each BGC from the RNA-seq data (n=3). C_TABLECAPTION C_TBL Supplementary Information 7: Annotation of AgN23 genes putatively involved in biosynthetic pathways for Auxins related phytohomones. Expression levels in transcripts per million (TPM) are indicated for each gene. The genes were detected by blasting reference KEGG sequences for each KEGG ONTOLOGY against AgN23 genes. A cut off of 70% identity and 40% coverage was applied to detect positive hits. These biosynthetic pathways and the KEGG ONTOLOGY are indicated in column F and G. Supplementary Information 8: Inspection of BiG-FAM hits with AgN23 BGCs to identify homologous BGCs found outside the S. violaceusniger clade. BiG-FAM distance higher than 900 were excluded from the analysis. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

genomics↗

bioRxiv2021

Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity

DNA methylation plays an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they also provide a defence against foreign DNA. Little is known regarding the methylome of the mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, single molecule real-time (SMRT) and bisulphite sequencing combined with whole-genome analysis identified 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems in Mycoplasma agalactiae, a ruminant pathogen and a model organism. All systems had a homolog in at least one phylogenetically distinct Mycoplasma spp. Our study also revealed that several superimposed genetic events may participate in the M. agalactiae dynamic epigenome landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers.

microbiology↗