Biology subjects

Lopez-Roques, C.

Publications and source records attributed to Lopez-Roques, C..

15 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

Population structure, genetic diversity and global migration of the banana Fusarium wilt pathogen, Fusarium oxysporum f. sp. cubense tropical race 4

O_LIThe current epidemic of banana Fusarium wilt is caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Foc TR4 originates in Asia and was first reported in the early 1990s, whereafter it was restricted to five Asian countries and the Northern Territory of Australia for two decades. Since 2013, the fungus was detected in the Middle East, the Indian subcontinent, Africa and Latin America. Its recent spread may be caused by the expansion of Cavendish banana production and the movement of contaminated planting materials. C_LIO_LIWhole genome sequences of 119 Foc TR4 isolates were compared based on single nucleotide polymorphisms (SNPs) to assess the population structure, genetic diversity and relation among isolates from 20 countries to reveal the evolutionary origin and likely migration. C_LIO_LIFoc TR4 is a monophyletic lineage divided into four clusters. Two of the clusters included isolates mostly from eastern Indonesia and seem to be ancestral with many rare alleles and high genetic diversity supporting this region as centre of origin. The remaining clusters were less diverse and associated with pandemic expansion. C_LIO_LIKnowledge on Foc TR4 emergence and dispersal can be used to inform more effective biosecurity and management practice. C_LI

evolutionary biology↗

bioRxiv2025

Chromosome-scale genome assembly of Xiphinema index uncovers an unparalleled epigenetic toolkit in invertebrates

Nematodes constitute the most speciose animal phylum, occupying an exceptionally broad range of biomes and encompassing free-living microbe-feeders, predators, and notorious plant or animal parasites. However, the limited availability of genome-scale resources for early-branching nematode clades has constrained our understanding of the molecular determinants underlying these multiple evolutionary adaptations. Here, we present the genome of the plant-parasitic nematode Xiphinema index, constituting the first telomere-to-telomere assembly for the order Dorylaimida, an early-branching nematode lineage. Phylogenetic analyses reveal that horizontal gene transfers (HGT) have played a pivotal role in the emergence of plant parasitism in this phylum. Remarkably, we identify the first documented case of a plant-derived HGT in a nematode genome. This gene encodes a predicted secreted parasitic effector, underscoring the diversity of evolutionary events that contributed to the parasitic arsenal. Our results suggest that, beyond bacteria and fungi, plants themselves have provided crucial genes for parasitism that may now be used by the nematodes to manipulate them. Our comparative genomic analyses across more than 70 nematode species further uncover an unprecedented epigenetic toolkit in an invertebrate genome. Indeed, X. index harbors a complete set of canonical DNA methyltransferases, a full-length ATRX chromatin remodeler, and 3D-chromatin architectural CTCF protein coding homolog. Consistent with this repertoire, we detected methylation at CpG genome-wide, which inversely correlates with gene expression and chromatin accessibility. Together, these findings reveal a vertebrate-like epigenetic machinery in an early-branching nematode and call for a fundamental reassessment of the prevailing epigenetic paradigm in nematodes and, more broadly, in animals.

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

A Chromosome-Level Assembly of the Pine Processionary Moth (Thaumetopoea pityocampa) genome

We present a chromosome-level genome assembly and annotation of the pine processionary moth, Thaumetopoea pityocampa (Lepidoptera: Notodontidae), a key forest pest that is a public health concern. The nuclear genome spans 615.9 Mb, scaffolded into 50 chromosome scale and 115 smaller scaffolds, with high completeness (BUSCO score: 98.9%) that provides a decisive improvement over the previous assembly (537 Mb; 68,292 contigs; BUSCO 83.6%). Coverage differences in resequenced males and females allowed identification of the Z chromosome and several W-linked contigs. As ex-pected from previous studies, we found that synteny was largely conserved with related Lepidoptera, although chromosomal fissions may explain the higher chromosome number of 49 autosomes com-pared to typical lepidopteran karyotypes. We also integrated into the assembly linkage map, allowing estimation of a genome-wide male recombination rate of 5.06 cM/Mb, varying from 11.6 cM/Mb to 1.98 cM/Mb from the smallest to the largest chromosomes. Repetitive elements represented 49.1% of this new assembly, dominated by LINEs (45.1% of classified repeats). Finally, gene prediction identified 12,898 gene models, among which 17 circadian rhythm genes were manually curated. Ex-pert annotation further allowed to identify 51 genes of the odorant receptor (OR) family as well as a total of 236 detoxification genes, including 78 CYPs, 56 CCEs, 30 GSTs, 23 UGTs and 49 ABCs. Overall, this assembly represents the first chromosome-level genome for a member of the Thaume-topoeinae subfamily, significantly expanding the currently limited set of genomic resources avail-able for Notodontidae. The fully annotated assembly is publicly accessible through the LepidoDB database (https://bipaa.genouest.org/is/lepidodb/) and will serve as a valuable resource for research on population genomics of this species.

genomics↗

bioRxiv2025

A new genome assembly of the pea cultivar Cameor provides resources for functional genomics and genetics

Significant improvements in sequencing technologies have allowed the development of more contiguous genome assemblies in many plant species. The pea genome is characterized by its richness in repeated elements and its long and complex centromeres. This makes its assembly challenging. In this paper, we present an improved version of the genome sequence of the French cultivar Cameor. This sequence was obtained by combining Nanopore and PacBio long-read sequencing, Hi-C contact maps and Bionano maps. The assembly of centromeres was refined using a combination of FISH and ultra-long Nanopore read analyses. Overall, Cameor_v2 genome assembly is a highly continuous pea genome assembly with small total gap size and a large contig N50. In this version, the orientation of chromosomes was revised according to internationally accepted karyotype rules. Gene annotation statistics indicated a high completeness of gene sequences, with most gene sequences with 3 and 5 UTR. This genome assembly with its associated data constitute a useful resource for pea genetics, comparative mapping and functional genomics.

genomics↗

bioRxiv2024

Unveiling the genome assembly of the polyploid and quarantine root-knot nematode, Meloidogyne enterolobii

Root-knot nematodes of the genus Meloidogyne are obligatory plant endoparasites that cause substantial economic losses to the agricultural production and impact the global food supply. These plant parasitic nematodes belong to the most widespread and devastating genus worldwide, yet few measures of control are available. The most efficient way to control root-knot nematodes (RKN) is deployment of resistance genes in plants. However, current resistance genes that control other Meloidogyne species are mostly inefficient on M. enterolobii. Consequently, M. enterolobii was listed as a European Union quarantine pest implementing regulation. To gain insight into the molecular characteristics underlying its parasitic success, exploring the genome of M. enterolobii is essential. Here, we report a high-quality genome assembly of Meloidogyne enterolobii using the high-fidelity long-read sequencing technology developed by Pacific Biosciences, combined with a gap-aware sequence transformer, DeepConsensus. The resulting genome assembly spans 273 Mbp with 556 contigs, a GC% of 30 {+/-} 0.042 and an N50 value of 2.11Mb, constituting a useful platform for comparative, population and functional genomics.

genomics↗

bioRxiv2024

Increased evolutionary rate in the Z-chromosome of Morpho butterflies and implications for speciation.

The evolution of reproductive isolation between populations shapes divergence in genome structure and content: comparing the genomes of closely-related species can thus enlighten the speciation process. Comparisons of genomes of allopatric vs. sympatric species sharing similar vs. dissimilar ecological niches allows to specifically investigate the effect of reinforcement and ecological specialization on genome evolution. In the butterfly genus Morpho, several species can be found in sympatry presenting specialisation in different microhabitats and temporal niches. Here, we sequenced, assembled and annotated the genomes of 8 Morpho species and used previously published genomes of three other Morpho species to study genomic rearrangements and signatures of positive selection. We found extensive chromosomal rearrangements in the Z chromosome compared to the autosomes, particularly among closely related sympatric species occupying similar niches, pointing at the putative role of inversions in preventing gene flow at a postzygotic level. We also detected a higher proportion of genes under positive selection on the Z-chromosome compared to the autosomes, suggesting a potential role of the Z-chromosome in driving adaptive evolution in Morpho. Finally, because of the divergence in daily activities between species, we studied the evolution of eight genes involved in the circadian clock and detected a signature of positive selection on the gene Period, located in the Z chromosome. By studying the evolution of genome structure and coding sequences, our study indicates fast evolution of the Z-chromosome, partly driven by selection, throughout this genus, highlighting the putative implication of this sexual chromosome on pre and post-zygotic isolation.

evolutionary biology↗

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

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 Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplications (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19-27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome-18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variants (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in testis than ovary. Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.

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↗

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↗

bioRxiv2022

Two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 x 10-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Cote dAzur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.

microbiology↗

bioRxiv2020

A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet (Acipenser ruthenus). Using chromosome-scale assemblies and pool-sequencing, we first identified a ~16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages (A. sturio, A. oxyrinchus vs. A. ruthenus, Huso huso), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species (A. gueldenstaedtii, A. baerii). Conservation of a female-specific sequence for a long period, representing 180 My of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives.

evolutionary biology↗

bioRxiv2018

The genomic basis of colour pattern polymorphism in the harlequin ladybird

Many animal species are comprised of discrete phenotypic forms. Understanding the genetic mechanisms generating and maintaining such phenotypic variation within species is essential to comprehending morphological diversity. A common and conspicuous example of discrete phenotypic variation in natural populations of insects is the occurrence of different colour patterns, which has motivated a rich body of ecological and genetic research1-6. The occurrence of dark, i.e. melanic, forms, displaying discrete colour patterns, is found across multiple taxa, but the underlying genomic basis remains poorly characterized. In numerous ladybird species (Coccinellidae), the spatial arrangement of black and orange patches on adult elytra varies wildly within species, forming strikingly different complex colour patterns7,8. In the harlequin ladybird Harmonia axyridis, more than 200 distinct colour forms have been described, which classic genetic studies suggest result from allelic variation at a single, unknown, locus9,10. Here, we combined whole-genome sequencing, population genomics, gene expression and functional analyses, to establish that the gene pannier controls melanic pattern polymorphism in H. axyridis. We show that pannier, which encodes an evolutionary conserved transcription factor, is necessary for the formation of melanic elements on the elytra. Allelic variation in pannier leads to protein expression in distinct domains on the elytra, and thus determines the distinct colour patterns in H. axyridis. Recombination between pannier alleles may be reduced by a highly divergent sequence of ca. 170 kb in the cis-regulatory regions of pannier with a 50 kb inversion between colour forms. This likely helps maintaining the distinct alleles found in natural populations. Thus we propose that highly variable discrete colour forms can arise in natural populations through cis-regulatory allelic variation of a single gene.

evolutionary biology↗