Biology subjects

Colinet, D.

Publications and source records attributed to Colinet, D..

9 recordsLinked to original sources

bioRxiv2026

Evaluating transformer-based models for structural characterization of orphan proteins

MotivationTransformer-based models (TBMs) are state-of-the-art deep learning architectures that predict protein structural features with high accuracy. Despite methodological differences, they all rely on large protein sequence datasets structured by homology, as homologous proteins typically share similar structures. However, 5-30% of eukaryotic proteomes consist of orphan proteins--sequences without detectable similarity to known families. Although they may share structural traits with characterized proteins, their lack of homology makes them and ideal dataset for evaluating TBM generalization beyond familiar sequence space. ResultsWe compared predictions from several widely used TBM architectures on an expert-curated set of orphan proteins from the Meloidogyne genus. None of these proteins has an experimentally determined structure. To assess model performance, we conducted consistency analyses, comparing predicted features with those observed in sets of known homologous proteins and across models. Multiple sequence alignment-based approaches such as AlphaFold2 performed poorly on orphan proteins, as did single-sequence or embedding-based language models including ESMFold, OmegaFold, and ProtT5. This limited performance cannot be fully attributed to intrinsic disorder, as confirmed by independent non-TBM disorder predictors. While accurate tertiary structure prediction remains out of reach, secondary structure is more reliably captured: predictors share about 70% of secondary structure elements on average, regardless of global fold similarity, and these elements are consistently identified by dedicated secondary structure tools. AvailabilityAll data and analysis scripts are available at https://doi.org/10.5281/zenodo.18788931 Contactedoardo.sarti@inria.fr

bioinformatics↗

bioRxiv2025

Identification, evolutionary history and characteristics of orphan genes in root-knot nematodes

Orphan genes, lacking detectable homologs in other species, are common across eukaryotic genomes and can arise through divergence of existing genes or de novo from non-coding regions. Here we identified and characterized orphan genes in eight root-knot nematode species (genus Meloidogyne), the most destructive plant-parasitic nematodes. For that, we used comparative genomics across 85 nematodes, ancestral sequence reconstruction, synteny analyses, and multi-omics data. We found that around 16% of Meloidogyne genes are genus-specific transcribed orphan genes, with about 20% resulting from high divergence and 18% emerging de novo, often in transposon-rich genomic regions. Transcriptomic, translatomic, and proteomic evidence confirmed expression and translation of many orphan genes, which tend to encode shorter, secreted proteins. Notably, orphan genes are preferentially expressed during the infective juvenile stage and contribute substantially to the arsenal of nematode parasitism effectors. These findings highlight orphan genes as a significant and dynamic component of Meloidogyne genomes, potentially underpinning their parasitic adaptation and success.

bioinformatics↗

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↗

bioRxiv2024

Functional carbohydrate-active enzymes acquired by horizontal gene transfer from plants in the whitefly Bemisia tabaci

Carbohydrate-active enzymes (CAZymes) involved in the degradation of plant cell walls and/or the assimilation of plant carbohydrates for energy uptake are widely distributed in microorganisms. In contrast, they are less frequent in animals, although there are exceptions, including examples of CAZymes acquired by horizontal gene transfer (HGT) from bacteria or fungi in several of phytophagous arthropods and plant-parasitic nematodes. Although the whitefly Bemisia tabaci is a major agricultural pest, knowledge of HGT-acquired CAZymes in this phloem-feeding insect of the Hemiptera order (subfamily Aleyrodinae) is still lacking. We performed a comprehensive and accurate detection of HGT candidates in B. tabaci and identified 136 HGT events, 14 of which corresponding to CAZymes. The B. tabaci HGT-acquired CAZymes were not only of bacterial or fungal origin, but some were also acquired from plants. Biochemical analysis revealed that members of the glycoside hydrolase families 17 (GH17) and 152 (GH152) acquired from plants are functional beta-glucanases with different substrate specificities, suggesting distinct roles. These two CAZymes are the first characterized GH17 and GH152 glucanases in an animal. We identified a lower number of HGT events in the related Aleyrodinae Trialeurodes vaporariorum, with only three HGT-acquired CAZymes, including a GH152 glucanase, with phylogenetic analysis suggesting a unique HGT event in the ancestor of the Aleyrodinae. Another GH152 CAZyme, most likely independently acquired from plants, was also identified in two plant cell-feeding insects of the Thysanoptera order, highlighting the importance of plant-acquired CAZymes in the biology of piercing-sucking insects. Significance statementCarbohydrate-active enzymes (CAZymes) are crucial for sugar metabolism. Those involved in plant cell wall degradation are usually absent from animal genomes. In this study, we explored CAZyme repertoires in the genomes of several insects: the phloem-feeding whitefly Bemisia tabaci, a major agricultural pest, and the related greenhouse whitefly Trialeurodes vaporariorum, as well as two Thysanoptera species that feed on plant cell contents. We identified several cases of CAZymes acquired from plant via horizontal gene transfer in the genome of these insects. Notably, we showed that two B. tabaci CAZymes of plant origin function as glucanases with distinct substrate specificities, potentially helping the insect to overcome plant defenses. Overall, these findings enhance our understanding of how the ability to feed on plants evolved in insects.

evolutionary biology↗

bioRxiv2024

Nitrate reductase activity is required in Medicago truncatula-Sinorhizobium meliloti nitrogen-fixing symbiosis

Nitrate reductase (NR) is a key enzyme in higher land plants, catalyzing the rate-limiting reduction of nitrate to nitrite in the nitrate assimilation pathway. Phylogenetic analysis of NR protein sequences indicates that duplication events responsible for the existence of two NR branches, corresponding to NR1 and NR2 genes, occurred after the divergence of the different orders within the Rosids clade. A third NR sequence branch, named NR3-type, emerged in the inverted repeat-lacking clade of the Fabales order. An intriguing feature of the NR3-type sequences is the absence of conserved phosphorylation sites in the two hinge regions, in contrast to all other NRs. To investigate the respective roles of MtNR1, MtNR2 and MtNR3 in M. truncatula, three single Tnt1 retrotransposon-tagged nr mutants and one nr1/nr2 double mutant were analyzed on plants growing either on nitrate, or during the nodulation process. Overall, the absence of phenotypes observed in M. truncatula single mutants suggests a significant functional redundancy between the different NRs in M. truncatula. The most striking outcome of this work is the almost complete impairment of nodulation capacity observed in the nr1/nr2 double mutant, demonstrating that NR activity is required for the functioning of the N2-fixing symbiosis.

plant biology↗

bioRxiv2023

Convergent origin and accelerated evolution of vesicle-associated RhoGAP proteins in two unrelated parasitoid wasps

Animal venoms and other protein-based secretions that perform a variety of functions, from predation to defense, are highly complex cocktails of bioactive compounds. Gene duplication, accompanied by modification of the expression and/or function of one of the duplicates under the action of positive selection, followed by further duplication to produce multigene families of toxins is a well-documented process in venomous animals. This evolutionary model has been less described in parasitoid wasps, which use maternal fluids, including venom, to protect their eggs from encapsulation by the host immune system. Here, we evidence the convergent recruitment and accelerated evolution of two multigene families of RhoGAPs presumably involved in virulence in two unrelated parasitoid wasp species, Leptopilina boulardi (Figitidae) and Venturia canescens (Icheumonidae). In both species, these RhoGAPs are associated with vesicles that act as transport systems to deliver virulence factors, but are produced in different tissues: the venom gland in Leptopilina sp. and the ovarian calyx in V. canescens. We show that the gene encoding the cellular RacGAP1 is at the origin of the virulent RhoGAP families found in Leptopilina sp. and V. canescens. We also show that both RhoGAP families have undergone evolution under positive selection and that almost all of these RhoGAPs lost their GAP activity and GTPase binding ability due to substitutions in key amino acids. These results suggest an accelerated evolution and functional diversification of these vesicle-associated RhoGAPs in the two phylogenetically distant parasitoid species. The potential new function(s) and the exact mechanism of action of these proteins in host cells remain to be elucidated.

evolutionary biology↗

bioRxiv2020

Parasitic success and venom composition evolve upon specialization of parasitoid wasps to different host species

AO_SCPLOWBSTRACTC_SCPLOWFemale endoparasitoid wasps usually inject venom into hosts to suppress their immune response and ensure offspring development. However, the parasitoids ability to evolve towards increased success on a given host simultaneously with the evolution of the composition of its venom has never been demonstrated. Here, we designed an experimental evolution to address this question. We crossed two parasitoid lines of Leptopilina boulardi differing both in parasitic success on different Drosophila hosts and venom composition. F2 descendants were reared on three different Drosophila species for nine generations. We tested for evolution of parasitic success over the generations and for the capacity of parasitoids selected on a given host to succeed on another host. We also tested whether the venom composition - based on a statistical analysis of the variation in intensity of the venom protein bands on SDS-PAGE 1D - evolved in response to different host species. Results showed a specialization of the parasitoids on their selection host and a rapid and differential evolution of the venom composition according to the host. Overall, data suggest a high potential for parasitoids to adapt to a new host, which may have important consequences in the field as well in the context of biological control.

evolutionary biology↗

bioRxiv2019

Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

BackgroundParasitoid wasps have fascinating life cycles and play an important role in trophic networks, yet little is known about their genome content and function. Parasitoids that infect aphids are an important group with the potential for biocontrol, and infecting aphids requires overcoming both aphid defenses and their defensive endosymbionts. ResultsWe present the de novo genome assemblies, detailed annotation, and comparative analysis of two closely related parasitoid wasps that target pest aphids: Aphidius ervi and Lysiphlebus fabarum (Hymenoptera: Braconidae: Aphidiinae). The genomes are small (139 and 141 Mbp), highly syntenic, and the most AT-rich reported thus far for any arthropod (GC content: 25.8% and 23.8%). This nucleotide bias is accompanied by skewed codon usage, and is stronger in genes with adult-biased expression. AT-richness may be the consequence of reduced genome size, a near absence of DNA methylation, and age-specific energy demands. We identify expansions of F-box/Leucine-rich-repeat proteins, suggesting that diversification in this gene family may be associated with their broad host range or with countering defenses from aphids endosymbionts. The absence of some immune genes (Toll and Imd pathways) resembles similar losses in their aphid hosts, highlighting the potential impact of symbiosis on both aphids and their parasitoids. ConclusionsThese findings are of fundamental interest for insect evolution and beyond. This will provide a strong foundation for further functional studies including coevolution with respect to their hosts, the basis of successful infection, and biocontrol. Both genomes are available at https://bipaa.genouest.org.

genomics↗

bioRxiv2019

Rapid and differential evolution of the venom composition of a parasitoid wasp depending on the host strain

Parasitoid wasps rely primarily on venom to suppress the immune response and regulate the physiology of their host. Intraspecific variability of venom protein composition has been documented in some species, but its evolutionary potential is poorly understood. We performed an experimental evolution initiated with crosses of two lines of Leptopilina boulardi of different venom composition to generate variability and create new combinations of venom factors. The offspring were maintained for 10 generations on two strains of Drosophila melanogaster differing in resistance / susceptibility to the parasitoid lines. The venom composition of individuals was characterized by a semi-automatic analysis of 1D SDS-PAGE protein profiles whose accuracy was checked by Western blot analysis of well-characterized venom proteins. Results evidenced a rapid and differential evolution of the venom composition on both hosts and showed that the proteins beneficial on one host can be costly on the other. Overall, we demonstrated the capacity of rapid evolution of the venom composition in parasitoid wasps, important regulators of arthropod populations, suggesting a potential for adaptation to new hosts. Our approach also proved relevant in identifying, among the diversity of venom proteins, those possibly involved in parasitism success and whose role deserves to be deepened.\n\nKey ContributionThe venom protein composition of parasitoid wasps can evolve rapidly and differently depending on the host strain. Studying this evolution can help identify new venom proteins possibly involved in parasitism success on a given host.

evolutionary biology↗