Publications 2022

This list includes publications for which the GenoToul Bioinformatics facility has been used (hardware infrastructure / Funding / Staff members). All Sigenae’s publications have used the GenoToul Bioinformatics hardware infrastructure.

Allaoua, M.; Bonnafé, E.; Etienne, P.; Noirot, V.; Gabarrou, J.; Castinel, A.; Pascal, G.; Darbot, V.; Treilhou, M.; Combes, S. A Carvacrol‐based Product Reduces Campylobacter Jejuni Load and Alters Microbiota Composition in the Caeca of Chickens. J of Applied Microbiology 2022, 132 (6), 4501–4516.
Mishra, B.; Ulaszewski, B.; Meger, J.; Aury, J.-M.; Bodénès, C.; Lesur-Kupin, I.; Pfenninger, M.; Da Silva, C.; Gupta, D. K.; Guichoux, E.; Heer, K.; Lalanne, C.; Labadie, K.; Opgenoorth, L.; Ploch, S.; Le Provost, G.; Salse, J.; Scotti, I.; Wötzel, S.; Plomion, C.; Burczyk, J.; Thines, M. A Chromosome-Level Genome Assembly of the European Beech (Fagus Sylvatica) Reveals Anomalies for Organelle DNA Integration, Repeat Content and Distribution of SNPs. Front. Genet. 2022, 12, 691058.
Barret, M.; Gandois, L.; Thalasso, F.; Martinez Cruz, K.; Sepulveda Jauregui, A.; Lavergne, C.; Teisserenc, R.; Aguilar, P.; Gerardo Nieto, O.; Etchebehere, C.; Martins Dellagnezze, B.; Bovio Winkler, P.; Fochesatto, G. J.; Tananaev, N.; Svenning, M. M.; Seppey, C.; Tveit, A.; Chamy, R.; Astorga España, M. S.; Mansilla, A.; Van de Putte, A.; Sweetlove, M.; Murray, A. E.; Cabrol, L. A Combined Microbial and Biogeochemical Dataset from High-Latitude Ecosystems with Respect to Methane Cycle. Sci Data 2022, 9 (1), 674.
Urvois, T.; Perrier, C.; Roques, A.; Sauné, L.; Courtin, C.; Li, Y.; Johnson, A. J.; Hulcr, J.; Auger-Rozenberg, M.-A.; Kerdelhué, C. A First Inference of the Phylogeography of the Worldwide Invader Xylosandrus Compactus. J Pest Sci 2022, 95 (3), 1217–1231.
Demars, J.; Labrune, Y.; Iannuccelli, N.; Deshayes, A.; Leroux, S.; Gilbert, H.; Aymard, P.; Benitez, F.; Riquet, J. A Genome-Wide Epistatic Network Underlies the Molecular Architecture of Continuous Color Variation of Body Extremities. Genomics 2022, 114 (3), 110361.
Dunière, L.; Renaud, J. B.; Steele, M. A.; Achard, C. S.; Forano, E.; Chaucheyras-Durand, F. A Live Yeast Supplementation to Gestating Ewes Improves Bioactive Molecule Composition in Colostrum with No Impact on Its Bacterial Composition and Beneficially Affects Immune Status of the Offspring. J Nutr Sci 2022, 11, e5.
Beaumont, M.; Lencina, C.; Painteaux, L.; Viémon-Desplanque, J.; Phornlaphat, O.; Lambert, W.; Chalvon-Demersay, T. A Mix of Functional Amino Acids and Grape Polyphenols Promotes the Growth of Piglets, Modulates the Gut Microbiota in Vivo and Regulates Epithelial Homeostasis in Intestinal Organoids. Amino Acids 2022, 54 (10), 1357–1369.
Quilbé, J.; Nouwen, N.; Pervent, M.; Guyonnet, R.; Cullimore, J.; Gressent, F.; Araújo, N. H.; Gully, D.; Klopp, C.; Giraud, E.; Arrighi, J.-F. A Mutant-Based Analysis of the Establishment of Nod-Independent Symbiosis in the Legume Aeschynomene Evenia. Plant Physiology 2022, 190 (2), 1400–1417.
Wen, M.; Pan, Q.; Jouanno, E.; Montfort, J.; Zahm, M.; Cabau, C.; Klopp, C.; Iampietro, C.; Roques, C.; Bouchez, O.; Castinel, A.; Donnadieu, C.; Parrinello, H.; Poncet, C.; Belmonte, E.; Gautier, V.; Avarre, J.; Dugue, R.; Gustiano, R.; Hà, T. T. T.; Campet, M.; Sriphairoj, K.; Ribolli, J.; de Almeida, F. L.; Desvignes, T.; Postlethwait, J. H.; Bucao, C. F.; Robinson‐Rechavi, M.; Bobe, J.; Herpin, A.; Guiguen, Y. An Ancient Truncated Duplication of the Anti‐Müllerian Hormone Receptor Type 2 Gene Is a Potential Conserved Master Sex Determinant in the Pangasiidae Catfish Family. Molecular Ecology Resources 2022, 22 (6), 2411–2428.
Bouchiba, Y.; Esque, J.; Cottret, L.; Maréchaux, M.; Gaston, M.; Gasciolli, V.; Keller, J.; Nouwen, N.; Gully, D.; Arrighi, J.; Gough, C.; Lefebvre, B.; Barbe, S.; Bono, J. An Integrated Approach Reveals How Lipo‐chitooligosaccharides Interact with the Lysin Motif Receptor‐like Kinase MtLYR3. Protein Science 2022, 31 (6).
Mariette, J.; Blanchard, O.; Berné, O.; Aumont, O.; Carrey, J.; Ligozat, A.; Lellouch, E.; Roche, P.-E.; Guennebaud, G.; Thanwerdas, J.; Bardou, P.; Salin, G.; Maigne, E.; Servan, S.; Ben-Ari, T. An Open-Source Tool to Assess the Carbon Footprint of Research. Environ. Res.: Infrastruct. Sustain. 2022, 2 (3), 035008.
Payton, L.; Noirot, C.; Last, K. S.; Grigor, J.; Hüppe, L.; Conway, D. V. P.; Dannemeyer, M.; Suin, A.; Meyer, B. Annual Transcriptome of a Key Zooplankton Species, the Copepod Calanus Finmarchicus. Ecology and Evolution 2022, 12 (2).
Simon, M.; Durand, S.; Ricou, A.; Vrielynck, N.; Mayjonade, B.; Gouzy, J.; Boyer, R.; Roux, F.; Camilleri, C.; Budar, F. APOK3 , a Pollen Killer Antidote in Arabidopsis Thaliana. Genetics 2022, 221 (4), iyac089.
Orozco-Arias, S.; Candamil-Cortes, M. S.; Jaimes, P. A.; Valencia-Castrillon, E.; Tabares-Soto, R.; Isaza, G.; Guyot, R. Automatic Curation of LTR Retrotransposon Libraries from Plant Genomes through Machine Learning. Journal of Integrative Bioinformatics 2022, 19 (3), 20210036.
Koutsovoulos, G. D.; Granjeon Noriot, S.; Bailly-Bechet, M.; Danchin, E. G. J.; Rancurel, C. AvP: A Software Package for Automatic Phylogenetic Detection of Candidate Horizontal Gene Transfers. PLoS Comput Biol 2022, 18 (11), e1010686.
Battaglia-Brunet, F.; Naveau, A.; Cary, L.; Bueno, M.; Briais, J.; Charron, M.; Joulian, C.; Thouin, H. Biogeochemical Behaviour of Geogenic As in a Confined Aquifer of the Sologne Region, France. Chemosphere 2022, 304, 135252.
Pichot, C.; Djari, A.; Tran, J.; Verdenaud, M.; Marande, W.; Huneau, C.; Gautier, V.; Latrasse, D.; Arribat, S.; Sommard, V.; Troadec, C.; Poncet, C.; Bendahmane, M.; Szecsi, J.; Dogimont, C.; Salse, J.; Benhamed, M.; Zouine, M.; Boualem, A.; Bendahmane, A. Cantaloupe Melon Genome Reveals 3D Chromatin Features and Structural Relationship with the Ancestral Cucurbitaceae Karyotype. iScience 2022, 25 (1), 103696.
Courbin, V.; Riller, Q.; Amegnizin, J.-L.; Gricourt, G.; Demontant, V.; Fihman, V.; Angebault, C.; Mahevas, M.; Gaube, G.; Coutte, L.; Pawlotsky, J.-M.; Lepeule, R.; Rodriguez, C.; Woerther, P.-L. Case Report: Cerebral Nocardiosis Caused by Nocardia Cyriacigeorgica Detected by Metagenomics in an Apparently Immunocompetent Patient. Front. Immunol. 2022, 13, 719124.
Changey, F.; Nunan, N.; Herrmann, A. M.; Lerch, T. Z. Catching Change in Microbial Diversity Indicators under Different Soil Organic Matter Managements: Higher Taxonomic Resolution, Better Discrimination? Ecological Indicators 2022, 139, 108897.
Côte, J.; Jacquin, L.; Veyssière, C.; Manzi, S.; Etienne, R.; Perrault, A.; Cambon, M. C.; Jean, S.; White, J. Changes in Fish Skin Microbiota along Gradients of Eutrophication in Human-Altered Rivers. FEMS Microbiology Ecology 2022, 98 (1), fiac006.
Wen, M.; Pan, Q.; Larson, W.; Eché, C.; Guiguen, Y. Characterization of the Sex Determining Region of Channel Catfish (Ictalurus Punctatus) and Development of a Sex-Genotyping Test. Gene 2023, 850, 146933.
Brucato, N.; André, M.; Hudjashov, G.; Mondal, M.; Cox, M. P.; Leavesley, M.; Ricaut, F.-X. Chronology of Natural Selection in Oceanian Genomes. iScience 2022, 25 (7), 104583.
Eljebbawi, A.; Savelli, B.; Libourel, C.; Estevez, J. M.; Dunand, C. Class III Peroxidases in Response to Multiple Abiotic Stresses in Arabidopsis Thaliana Pyrenean Populations. IJMS 2022, 23 (7), 3960.
Lesturgie, P.; Planes, S.; Mona, S. Coalescence Times, Life History Traits and Conservation Concerns: An Example from Four Coastal Shark Species from the Indo‐Pacific. Molecular Ecology Resources 2022, 22 (2), 554–566.
Malkócs, T.; Viricel, A.; Becquet, V.; Evin, L.; Dubillot, E.; Pante, E. Complex Mitogenomic Rearrangements within the Pectinidae (Mollusca: Bivalvia). BMC Ecol Evo 2022, 22 (1), 29.
Wragg, D.; Eynard, S. E.; Basso, B.; Canale‐Tabet, K.; Labarthe, E.; Bouchez, O.; Bienefeld, K.; Bieńkowska, M.; Costa, C.; Gregorc, A.; Kryger, P.; Parejo, M.; Pinto, M. A.; Bidanel, J.; Servin, B.; Le Conte, Y.; Vignal, A. Complex Population Structure and Haplotype Patterns in the Western European Honey Bee from Sequencing a Large Panel of Haploid Drones. Molecular Ecology Resources 2022, 22 (8), 3068–3086.
Orozco-Arias, S.; Candamil, M. S.; Jaimes, P. A.; Cristancho, M.; Tabares-Soto, R.; Guyot, R. Composition and Diversity of LTR Retrotransposons in the Coffee Leaf Rust Genome (Hemileia Vastatrix). Agronomy 2022, 12 (7), 1665.
Kalachova, T.; Jindřichová, B.; Burketová, L.; Monard, C.; Blouin, M.; Jacquiod, S.; Ruelland, E.; Puga-Freitas, R. Controlled Natural Selection of Soil Microbiome through Plant-Soil Feedback Confers Resistance to a Foliar Pathogen. Plant Soil 2022.
Chevignon, G.; Dotto-Maurel, A.; Serpin, D.; Chollet, B.; Arzul, I. De Novo Transcriptome Assembly and Analysis of the Flat Oyster Pathogenic Protozoa Bonamia Ostreae. Front. Cell. Infect. Microbiol. 2022, 12, 921136.
Beaumont, M.; Mussard, E.; Barilly, C.; Lencina, C.; Gress, L.; Painteaux, L.; Gabinaud, B.; Cauquil, L.; Aymard, P.; Canlet, C.; Paës, C.; Knudsen, C.; Combes, S. Developmental Stage, Solid Food Introduction, and Suckling Cessation Differentially Influence the Comaturation of the Gut Microbiota and Intestinal Epithelium in Rabbits. The Journal of Nutrition 2022, 152 (3), 723–736.
Pecrix, Y.; Sallet, E.; Moreau, S.; Bouchez, O.; Carrere, S.; Gouzy, J.; Jardinaud, M.-F.; Gamas, P. DNA Demethylation and Hypermethylation Are Both Required for Late Nodule Development in Medicago. Nat. Plants 2022, 8 (7), 741–749.
Azzouzi, N.; Guillory, A.-S.; Chaudieu, G.; Galibert, F. Dog Olfactory Receptor Gene Expression Profiling Using Samples Derived from Nasal Epithelium Brushing. Canine Med Genet 2022, 9 (1), 7.
Paës, C.; Gidenne, T.; Bébin, K.; Duperray, J.; Gohier, C.; Guené-Grand, E.; Rebours, G.; Barilly, C.; Gabinaud, B.; Cauquil, L.; Castinel, A.; Pascal, G.; Darbot, V.; Aymard, P.; Debrusse, A.-M.; Beaumont, M.; Combes, S. Early Introduction of Plant Polysaccharides Drives the Establishment of Rabbit Gut Bacterial Ecosystems and the Acquisition of Microbial Functions. mSystems 2022, 7 (3), e00243-22.
Lesturgie, P.; Lainé, H.; Suwalski, A.; Chifflet-Belle, P.; Maisano Delser, P.; Clua, E.; Jaquemet, S.; Magalon, H.; Mona, S. Ecological and Biogeographic Features Shaped the Complex Evolutionary History of an Iconic Apex Predator (Galeocerdo Cuvier). BMC Ecol Evo 2022, 22 (1), 147.
Hu, J.; Vandenkoornhuyse, P.; Khalfallah, F.; Causse‐Védrines, R.; Mony, C. Ecological Corridors Homogenize Plant Root Endospheric Mycobiota. New Phytologist 2022, nph.18606.
Malsa, J.; Courtot, É.; Boisseau, M.; Dumont, B.; Gombault, P.; Kuzmina, T. A.; Basiaga, M.; Lluch, J.; Annonay, G.; Dhorne-Pollet, S.; Mach, N.; Sutra, J.-F.; Wimel, L.; Dubois, C.; Guégnard, F.; Serreau, D.; Lespine, A.; Sallé, G.; Fleurance, G. Effect of Sainfoin ( Onobrychis Viciifolia ) on Cyathostomin Eggs Excretion, Larval Development, Larval Community Structure and Efficacy of Ivermectin Treatment in Horses. Parasitology 2022, 149 (11), 1439–1449.
Gaudino, M.; Chiapponi, C.; Moreno, A.; Zohari, S.; O’Donovan, T.; Quinless, E.; Sausy, A.; Oliva, J.; Salem, E.; Fusade-Boyer, M.; Meyer, G.; Hübschen, J. M.; Saegerman, C.; Ducatez, M. F.; Snoeck, C. J. Evolutionary and Temporal Dynamics of Emerging Influenza D Virus in Europe (2009–22). Virus Evolution 2022, 8 (2), veac081.
Villain, P.; Catchpole, R.; Forterre, P.; Oberto, J.; da Cunha, V.; Basta, T. Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea. Molecular Biology and Evolution 2022, 39 (8), msac155.
Brouard, C.; Mariette, J.; Flamary, R.; Vialaneix, N. Feature Selection for Kernel Methods in Systems Biology. NAR Genomics and Bioinformatics 2022, 4 (1), lqac014.
Pedro, N.; Brucato, N.; Cavadas, B.; Lisant, V.; Camacho, R.; Kinipi, C.; Leavesley, M.; Pereira, L.; Ricaut, F. First Insight into Oral Microbiome Diversity in Papua New Guineans Reveals a Specific Regional Signature. Molecular Ecology 2022, mec.16702.
Fruleux, A.; Duclercq, J.; Dubois, F.; Decocq, G. First Report of Ectomycorrhizae in Prunus Serotina in the Exotic Range. Plant Soil 2022.
Robic, A.; Cerutti, C.; Demars, J.; Kühn, C. From the Comparative Study of a CircRNA Originating from an Mammalian ATXN2L Intron to Understanding the Genesis of Intron Lariat-Derived CircRNAs. Biochimica et Biophysica Acta (BBA) – Gene Regulatory Mechanisms 2022, 1865 (4), 194815.
Dupin, J.; Hong-Wa, C.; Pillon, Y.; Besnard, G. From the Mediterranean to the Pacific: Re-Circumscription towards Notelaea s.l. and Historical Biogeography of a Generic Complex in Oleinae (Oleaceae). Botanical Journal of the Linnean Society 2022, 200 (3), 360–377.
Vidal-Dupiol, J.; Harscouet, E.; Shefy, D.; Toulza, E.; Rey, O.; Allienne, J.-F.; Mitta, G.; Rinkevich, B. Frontloading of Stress Response Genes Enhances Robustness to Environmental Change in Chimeric Corals. BMC Biol 2022, 20 (1), 167.
Le Provost, G.; Brachi, B.; Lesur, I.; Lalanne, C.; Labadie, K.; Aury, J.-M.; Da Silva, C.; Postolache, D.; Leroy, T.; Plomion, C. Gene Expression and Genetic Divergence in Oak Species Highlight Adaptive Genes to Soil Water Constraints. Plant Physiology 2022, 190 (4), 2466–2483.
Brener-Raffalli, K.; Vidal-Dupiol, J.; Adjeroud, M.; Rey, O.; Romans, P.; Bonhomme, F.; Pratlong, M.; Haguenauer, A.; Pillot, R.; Feuillassier, L.; Claereboudt, M.; Magalon, H.; Gélin, P.; Pontarotti, P.; Aurelle, D.; Mitta, G.; Toulza, E. Gene Expression Plasticity and Frontloading Promote Thermotolerance in Pocillopora Corals. Peer Community Journal 2022, 2, e13.
Pomiès, L.; Brouard, C.; Duruflé, H.; Maigné, É.; Carré, C.; Gody, L.; Trösser, F.; Katsirelos, G.; Mangin, B.; Langlade, N. B.; de Givry, S. Gene Regulatory Network Inference Methodology for Genomic and Transcriptomic Data Acquired in Genetically Related Heterozygote Individuals. Bioinformatics 2022, 38 (17), 4127–4134.
Fuchs, S.; Babin, L.; Andraos, E.; Bessiere, C.; Willier, S.; Schulte, J. H.; Gaspin, C.; Meggetto, F. Generation of Full-Length Circular RNA Libraries for Oxford Nanopore Long-Read Sequencing. PLoS ONE 2022, 17 (9), e0273253.
Mohammadpanah, M.; Ayatollahi Mehrgardi, A.; Gilbert, H.; Larzul, C.; Mercat, M.-J.; Esmailizadeh, A.; Momen, M.; Tusell, L. Genic and Non-Genic SNP Contributions to Additive and Dominance Genetic Effects in Purebred and Crossbred Pig Traits. Sci Rep 2022, 12 (1), 3795.
García-Galán, A.; Baranowski, E.; Hygonenq, M.-C.; Walch, M.; Croville, G.; Citti, C.; De la Fe, C.; Nouvel, L.-X. Genome Mosaicism in Field Strains of Mycoplasma Bovis as Footprints of In-Host Horizontal Chromosomal Transfer. Appl Environ Microbiol 2022, 88 (1), e01661-21.
Mesbah-Uddin, M.; Guldbrandtsen, B.; Capitan, A.; Lund, M. S.; Boichard, D.; Sahana, G. Genome-Wide Association Study with Imputed Whole-Genome Sequence Variants Including Large Deletions for Female Fertility in 3 Nordic Dairy Cattle Breeds. Journal of Dairy Science 2022, 105 (2), 1298–1313.
Saleh, D.; Chen, J.; Leplé, J.; Leroy, T.; Truffaut, L.; Dencausse, B.; Lalanne, C.; Labadie, K.; Lesur, I.; Bert, D.; Lagane, F.; Morneau, F.; Aury, J.; Plomion, C.; Lascoux, M.; Kremer, A. Genome‐wide Evolutionary Response of European Oaks during the Anthropocene. Evolution Letters 2022, 6 (1), 4–20.
Bellec, L.; Le Du-Carré, J.; Almeras, F.; Durand, L.; Cambon-Bonavita, M.-A.; Danion, M.; Morin, T. Glyphosate-Based Herbicide Exposure: Effects on Gill Microbiota of Rainbow Trout ( Oncorhynchus Mykiss ) and the Aquatic Bacterial Ecosystem. FEMS Microbiology Ecology 2022, 98 (8), fiac076.
Evariste, L.; Mouchet, F.; Pinelli, E.; Flahaut, E.; Gauthier, L.; Barret, M. Gut Microbiota Impairment Following Graphene Oxide Exposure Is Associated to Physiological Alterations in Xenopus Laevis Tadpoles. Science of The Total Environment 2023, 857, 159515.
Garcia-Baccino, C. A.; Pineda-Quiroga, C.; Astruc, J. M.; Ugarte, E.; Legarra, A. High Genetic Correlation for Milk Yield across Manech and Latxa Dairy Sheep from France and Spain. JDS Communications 2022, 3 (4), 260–264.
Fiteni, E.; Durand, K.; Gimenez, S.; Meagher, R. L.; Legeai, F.; Kergoat, G. J.; Nègre, N.; d’Alençon, E.; Nam, K. Host-Plant Adaptation as a Driver of Incipient Speciation in the Fall Armyworm (Spodoptera Frugiperda). BMC Ecol Evo 2022, 22 (1), 133.
Bertucci, A.; Hoede, C.; Dassié, E.; Gourves, P.-Y.; Suin, A.; Le Menach, K.; Budzinski, H.; Daverat, F. Impact of Environmental Micropollutants and Diet Composition on the Gut Microbiota of Wild European Eels (Anguilla Anguilla). Environmental Pollution 2022, 314, 120207.
Valette, N.; Legout, A.; Goodell, B.; Alfredsen, G.; Auer, L.; Gelhaye, E.; Derrien, D. Impact of Norway Spruce Pre-Degradation Stages Induced by Gloeophyllum Trabeum on Fungal and Bacterial Communities. Fungal Ecology 2023, 61, 101188.
Darriaut, R.; Tran, J.; Martins, G.; Ollat, N.; Masneuf-Pomarède, I.; Lauvergeat, V. In Grapevine Decline, Microbiomes Are Affected Differently in Symptomatic and Asymptomatic Soils. Applied Soil Ecology 2023, 183, 104767.
Orozco-Arias, S.; Humberto Lopez-Murillo, L.; Candamil-Cortés, M. S.; Arias, M.; Jaimes, P. A.; Rossi Paschoal, A.; Tabares-Soto, R.; Isaza, G.; Guyot, R. Inpactor2: A Software Based on Deep Learning to Identify and Classify LTR-Retrotransposons in Plant Genomes. Briefings in Bioinformatics 2022, bbac511.
Bartha, L.; Mandáková, T.; Kovařík, A.; Bulzu, P.; Rodde, N.; Mahelka, V.; Lysak, M. A.; Fustier, M.; Šafář, J.; Cápal, P.; Keresztes, L.; Banciu, H. L. Intact Ribosomal DNA Arrays of Potentilla Origin Detected in Erythronium Nucleus Suggest Recent Eudicot‐to‐monocot Horizontal Transfer. New Phytologist 2022, 235 (3), 1246–1259.
Cohen, H.; Hoede, C.; Scharte, F.; Coluzzi, C.; Cohen, E.; Shomer, I.; Mallet, L.; Holbert, S.; Serre, R. F.; Schiex, T.; Virlogeux-Payant, I.; Grassl, G. A.; Hensel, M.; Chiapello, H.; Gal-Mor, O. Intracellular Salmonella Paratyphi A Is Motile and Differs in the Expression of Flagella-Chemotaxis, SPI-1 and Carbon Utilization Pathways in Comparison to Intracellular S. Typhimurium. PLoS Pathog 2022, 18 (4), e1010425.
Pavinato, V. A. C.; De Mita, S.; Marin, J.-M.; de Navascués, M. Joint Inference of Adaptive and Demographic History from Temporal Population Genomic Data. Peer Community Journal 2022, 2, e78.
Hévin, N. M. ‐C.; Hansen, S.; Addison, P.; Benoit, L.; Kergoat, G. J.; Haran, J. Late Cenozoic Environmental Changes Drove the Diversification of a Weevil Genus Endemic to the Cape Floristic Region. Zoologica Scripta 2022, 51 (6), 724–740.
Douchet, P.; Boissier, J.; Mulero, S.; Ferté, H.; Doberva, M.; Allienne, J.; Toulza, E.; Bethune, K.; Rey, O. Make Visible the Invisible: Optimized Development of an Environmental DNA Metabarcoding Tool for the Characterization of Trematode Parasitic Communities. Environmental DNA 2022, 4 (3), 627–641.
Mazenc, A.; Mervant, L.; Maslo, C.; Lencina, C.; Bézirard, V.; Levêque, M.; Ahn, I.; Alquier-Bacquié, V.; Naud, N.; Héliès-Toussaint, C.; Debrauwer, L.; Chevolleau, S.; Guéraud, F.; Pierre, F. H. F.; Théodorou, V.; Olier, M. Maternal Heme-Enriched Diet Promotes a Gut pro-Oxidative Status Associated with Microbiota Alteration, Gut Leakiness and Glucose Intolerance in Mice Offspring. Redox Biology 2022, 53, 102333.
Berthomieu, R.; Pérez-Bernal, M. F.; Santa-Catalina, G.; Desmond-Le Quéméner, E.; Bernet, N.; Trably, E. Mechanisms Underlying Clostridium Pasteurianum’s Metabolic Shift When Grown with Geobacter Sulfurreducens. Appl Microbiol Biotechnol 2022, 106 (2), 865–876.
Leclaire, S.; Pineaux, M.; Blanchard, P.; White, J.; Hatch, S. A. Microbiota Composition and Diversity of Multiple Body Sites Vary According to Reproductive Performance in a Seabird. Molecular Ecology 2022, mec.16398.
Nezamabadi, S.; Ghadiri, M.; Delenne, J.-Y.; Radjai, F. Modelling the Compaction of Plastic Particle Packings. Comp. Part. Mech. 2022, 9 (1), 45–52.
Le Provost, G.; Gerardin, T.; Plomion, C.; Brendel, O. Molecular Plasticity to Soil Water Deficit Differs between Sessile Oak ( Quercus Petraea (Matt.) Liebl.) High- and Low-Water Use Efficiency Genotypes. Tree Physiology 2022, 42 (12), 2546–2562.
Brondani, M.; Plassard, C.; Ramstein, E.; Cousson, A.; Hedde, M.; Bernard, L.; Trap, J. Morpho-Anatomical Traits Explain the Effects of Bacterial-Feeding Nematodes on Soil Bacterial Community Composition and Plant Growth and Nutrition. Geoderma 2022, 425, 116068.
Nieberding, C. M.; Beldade, P.; Baumlé, V.; San Martin, G.; Arun, A.; Lognay, G.; Montagné, N.; Bastin-Héline, L.; Jacquin-Joly, E.; Noirot, C.; Klopp, C.; Visser, B. Mosaic Evolution of Molecular Pathways for Sex Pheromone Communication in a Butterfly. Genes 2022, 13 (8), 1372.
Benites, L. F.; Stephens, T. G.; Bhattacharya, D. Multiple Waves of Viral Invasions in Symbiodiniaceae Algal Genomes. Virus Evolution 2022, 8 (2), veac101.
Vittecoq, M.; Brazier, L.; Elguero, E.; Bravo, I. G.; Renaud, N.; Manzano‐Marín, A.; Prugnolle, F.; Godreuil, S.; Blanchon, T.; Roux, F.; Durand, P.; Renaud, F.; Thomas, F. Multiresistant Enterobacteriaceae in Yellow‐legged Gull Chicks in Their First Weeks of Life. Ecology and Evolution 2022, 12 (6).
Vaiman, A.; Fritz, S.; Beauvallet, C.; Boussaha, M.; Grohs, C.; Daniel-Carlier, N.; Relun, A.; Boichard, D.; Vilotte, J.-L.; Duchesne, A. Mutation of the MYH3 Gene Causes Recessive Cleft Palate in Limousine Cattle. Genet Sel Evol 2022, 54 (1), 71.
Arzelier, A.; Rivollat, M.; De Belvalet, H.; Pemonge, M.-H.; Binder, D.; Convertini, F.; Duday, H.; Gandelin, M.; Guilaine, J.; Haak, W.; Deguilloux, M.-F.; Pruvost, M. Neolithic Genomic Data from Southern France Showcase Intensified Interactions with Hunter-Gatherer Communities. iScience 2022, 25 (11), 105387.
Personnaz, J.; Piccolo, E.; Dortignac, A.; Iacovoni, J. S.; Mariette, J.; Rocher, V.; Polizzi, A.; Batut, A.; Deleruyelle, S.; Bourdens, L.; Delos, O.; Combes-Soia, L.; Paccoud, R.; Moreau, E.; Martins, F.; Clouaire, T.; Benhamed, F.; Montagner, A.; Wahli, W.; Schwabe, R. F.; Yart, A.; Castan-Laurell, I.; Bertrand-Michel, J.; Burlet-Schiltz, O.; Postic, C.; Denechaud, P.-D.; Moro, C.; Legube, G.; Lee, C.-H.; Guillou, H.; Valet, P.; Dray, C.; Pradère, J.-P. Nuclear HMGB1 Protects from Nonalcoholic Fatty Liver Disease through Negative Regulation of Liver X Receptor. Sci. Adv. 2022, 8 (12), eabg9055.
Kościelniak, P.; Glazińska, P.; Zadworny, M. OakRootRNADB—a Consolidated RNA-Seq Database for Coding and Noncoding RNA in Roots of Pedunculate Oak ( Quercus Robur ). Database 2022, 2022, baac097.
Fischer, C.-E.; Pemonge, M.-H.; Ducoussau, I.; Arzelier, A.; Rivollat, M.; Santos, F.; Barrand Emam, H.; Bertaud, A.; Beylier, A.; Ciesielski, E.; Dedet, B.; Desenne, S.; Duday, H.; Chenal, F.; Gailledrat, E.; Goepfert, S.; Gorgé, O.; Gorgues, A.; Kuhnle, G.; Lambach, F.; Lefort, A.; Mauduit, A.; Maziere, F.; Oudry, S.; Paresys, C.; Pinard, E.; Plouin, S.; Richard, I.; Roth-Zehner, M.; Roure, R.; Thevenet, C.; Thomas, Y.; Rottier, S.; Deguilloux, M.-F.; Pruvost, M. Origin and Mobility of Iron Age Gaulish Groups in Present-Day France Revealed through Archaeogenomics. iScience 2022, 25 (4), 104094.
Yu, H.; Liu, M.; Zhu, Z.; Wu, A.; Mounet, F.; Pesquet, E.; Grima-Pettenati, J.; Cassan-Wang, H. Overexpression of EgrIAA20 from Eucalyptus Grandis, a Non-Canonical Aux/IAA Gene, Specifically Decouples Lignification of the Different Cell-Types in Arabidopsis Secondary Xylem. IJMS 2022, 23 (9), 5068.
San Clemente, H.; Kolkas, H.; Canut, H.; Jamet, E. Plant Cell Wall Proteomes: The Core of Conserved Protein Families and the Case of Non-Canonical Proteins. IJMS 2022, 23 (8), 4273.
Brachi, B.; Filiault, D.; Whitehurst, H.; Darme, P.; Le Gars, P.; Le Mentec, M.; Morton, T. C.; Kerdaffrec, E.; Rabanal, F.; Anastasio, A.; Box, M. S.; Duncan, S.; Huang, F.; Leff, R.; Novikova, P.; Perisin, M.; Tsuchimatsu, T.; Woolley, R.; Dean, C.; Nordborg, M.; Holm, S.; Bergelson, J. Plant Genetic Effects on Microbial Hubs Impact Host Fitness in Repeated Field Trials. Proc. Natl. Acad. Sci. U.S.A. 2022, 119 (30), e2201285119.
Costes, V.; Chaulot-Talmon, A.; Sellem, E.; Perrier, J.-P.; Aubert-Frambourg, A.; Jouneau, L.; Pontlevoy, C.; Hozé, C.; Fritz, S.; Boussaha, M.; Le Danvic, C.; Sanchez, M.-P.; Boichard, D.; Schibler, L.; Jammes, H.; Jaffrézic, F.; Kiefer, H. Predicting Male Fertility from the Sperm Methylome: Application to 120 Bulls with Hundreds of Artificial Insemination Records. Clin Epigenet 2022, 14 (1), 54.
Dussarrat, T.; Prigent, S.; Latorre, C.; Bernillon, S.; Flandin, A.; Díaz, F. P.; Cassan, C.; Van Delft, P.; Jacob, D.; Varala, K.; Joubes, J.; Gibon, Y.; Rolin, D.; Gutiérrez, R. A.; Pétriacq, P. Predictive Metabolomics of Multiple Atacama Plant Species Unveils a Core Set of Generic Metabolites for Extreme Climate Resilience. New Phytologist 2022, 234 (5), 1614–1628.
Gervais, L.; Morellet, N.; David, I.; Hewison, M.; Réale, D.; Goulard, M.; Chaval, Y.; Lourtet, B.; Cargnelutti, B.; Merlet, J.; Quéméré, E.; Pujol, B. Quantifying Heritability and Estimating Evolutionary Potential in the Wild When Individuals That Share Genes Also Share Environments. Journal of Animal Ecology 2022, 91 (6), 1239–1250.
Eynard, S. E.; Vignal, A.; Basso, B.; Canale‐Tabet, K.; Le Conte, Y.; Decourtye, A.; Genestout, L.; Labarthe, E.; Mondet, F.; Servin, B. Reconstructing Queen Genotypes by Pool Sequencing Colonies in Eusocial Insects: Statistical Methods and Their Application to Honeybee. Molecular Ecology Resources 2022, 22 (8), 3035–3048.
Macedo, F. L.; Astruc, J. M.; Meuwissen, T. H. E.; Legarra, A. Removing Data and Using Metafounders Alleviates Biases for All Traits in Lacaune Dairy Sheep Predictions. Journal of Dairy Science 2022, 105 (3), 2439–2452.
Gréau, L.; Blaudez, D.; Heintz, D.; Zumsteg, J.; Billet, D.; Cébron, A. Response of Poplar and Associated Fungal Endophytic Communities to a PAH Contamination Gradient. IJMS 2022, 23 (11), 5909.
Labussière, E.; Achard, C.; Dubois, S.; Combes, S.; Castex, M.; Renaudeau, D. Saccharomyces Cerevisiae Boulardii CNCM I-1079 Supplementation in Finishing Male Pigs Helps to Cope with Heat Stress through Feeding Behaviour and Gut Microbiota Modulation. Br J Nutr 2022, 127 (3), 353–368.
Demange, P.; Joly, E.; Marcoux, J.; Zanon, P. R.; Listunov, D.; Rullière, P.; Barthes, C.; Noirot, C.; Izquierdo, J.-B.; Rozié, A.; Pradines, K.; Hee, R.; de Brito, M. V.; Marcellin, M.; Serre, R.-F.; Bouchez, O.; Burlet-Schiltz, O.; Oliveira, M. C. F.; Ballereau, S.; Bernardes-Génisson, V.; Maraval, V.; Calsou, P.; Hacker, S. M.; Génisson, Y.; Chauvin, R.; Britton, S. SDR Enzymes Oxidize Specific Lipidic Alkynylcarbinols into Cytotoxic Protein-Reactive Species. eLife 2022, 11, e73913.
Charbonnel, E.; Daguin-Thiébaut, C.; Caradec, L.; Moittié, E.; Gilg, O.; Gavrilo, M. V.; Strøm, H.; Mallory, M. L.; Morrison, R. I. G.; Gilchrist, H. G.; Leblois, R.; Roux, C.; Yearsley, J. M.; Yannic, G.; Broquet, T. Searching for Genetic Evidence of Demographic Decline in an Arctic Seabird: Beware of Overlapping Generations. Heredity 2022, 128 (5), 364–376.
Budde-Rodriguez, S.; Pasche, J. S.; Mallik, I.; Gudmestad, N. C. Sensitivity of Alternaria Spp. from Potato to Pyrimethanil, Cyprodinil, and Fludioxonil. Crop Protection 2022, 152, 105855.
Duley, E.; Iribar, A.; Bisson, C.; Chave, J.; Donald, J. Soil Environmental DNA Metabarcoding Can Quantify Local Plant Diversity for Biomonitoring across Varied Environments. Restoration Ecology 2022.
Aurelle, D.; Pratlong, M.; Oury, N.; Haguenauer, A.; Gélin, P.; Magalon, H.; Adjeroud, M.; Romans, P.; Vidal-Dupiol, J.; Claereboudt, M.; Noûs, C.; Reynes, L.; Toulza, E.; Bonhomme, F.; Mitta, G.; Pontarotti, P. Species and Population Genomic Differentiation in Pocillopora Corals (Cnidaria, Hexacorallia). Genetica 2022, 150 (5), 247–262.
Štiavnická, M.; Chaulot-Talmon, A.; Perrier, J.-P.; Hošek, P.; Kenny, D. A.; Lonergan, P.; Kiefer, H.; Fair, S. Sperm DNA Methylation Patterns at Discrete CpGs and Genes Involved in Embryonic Development Are Related to Bull Fertility. BMC Genomics 2022, 23 (1), 379.
Jacob, J.; Joulian, C.; Battaglia-Brunet, F. Start-Up and Performance of a Full Scale Passive System In-Cluding Biofilters for the Treatment of Fe, as and Mn in a Neutral Mine Drainage. Water 2022, 14 (12), 1963.
Plaisancié, P.; Buisson, C.; Fouché, E.; Martin, P.; Noirot, C.; Maslo, C.; Dupuy, J.; Guéraud, F.; Pierre, F. Study of the Colonic Epithelial-Mesenchymal Dialogue through Establishment of Two Activated or Not Mesenchymal Cell Lines: Activated and Resting Ones Differentially Modulate Colonocytes in Co-Culture. PLoS ONE 2022, 17 (8), e0273858.
Thouin, H.; Norini, M.-P.; Battaglia-Brunet, F.; Gautret, P.; Crampon, M.; Le Forestier, L. Temporal Evolution of Surface and Sub-Surface Geochemistry and Microbial Communities of Pb-Rich Mine Tailings during Phytostabilization: A One-Year Pilot-Scale Study. Journal of Environmental Management 2022, 318, 115538.
Salmona, J.; Dayon, J.; Lecompte, E.; Karamanlidis, A. A.; Aguilar, A.; Fernandez de Larrinoa, P.; Pires, R.; Mo, G.; Panou, A.; Agnesi, S.; Borrell, A.; Danyer, E.; Öztürk, B.; Tonay, A. M.; Anestis, A. K.; González, L. M.; Dendrinos, P.; Gaubert, P. The Antique Genetic Plight of the Mediterranean Monk Seal ( Monachus Monachus ). Proc. R. Soc. B. 2022, 289 (1981), 20220846.
Berné, O.; Agier, L.; Hardy, A.; Lellouch, E.; Aumont, O.; Mariette, J.; Ben-Ari, T. The Carbon Footprint of Scientific Visibility. Environ. Res. Lett. 2022, 17 (12), 124008.
Yainna, S.; Tay, W. T.; Durand, K.; Fiteni, E.; Hilliou, F.; Legeai, F.; Clamens, A.-L.; Gimenez, S.; Asokan, R.; Kalleshwaraswamy, C. M.; Deshmukh, S. S.; Meagher, R. L.; Blanco, C. A.; Silvie, P.; Brévault, T.; Dassou, A.; Kergoat, G. J.; Walsh, T.; Gordon, K.; Nègre, N.; d’Alençon, E.; Nam, K. The Evolutionary Process of Invasion in the Fall Armyworm (Spodoptera Frugiperda). Sci Rep 2022, 12 (1), 21063.
Recoules, L.; Heurteau, A.; Raynal, F.; Karasu, N.; Moutahir, F.; Bejjani, F.; Jariel-Encontre, I.; Cuvier, O.; Sexton, T.; Lavigne, A.-C.; Bystricky, K. The Histone Variant MacroH2A1.1 Regulates RNA Polymerase II-Paused Genes within Defined Chromatin Interaction Landscapes. Journal of Cell Science 2022, 135 (7), jcs259456.
Comín, J.; Madacki, J.; Rabanaque, I.; Zúñiga-Antón, M.; Ibarz, D.; Cebollada, A.; Viñuelas, J.; Torres, L.; Sahagún, J.; Klopp, C.; Gonzalo-Asensio, J.; Brosch, R.; Iglesias, M.-J.; Samper, S. The MtZ Strain: Molecular Characteristics and Outbreak Investigation of the Most Successful Mycobacterium Tuberculosis Strain in Aragon Using Whole-Genome Sequencing. Front. Cell. Infect. Microbiol. 2022, 12, 887134.
Mussard, E.; Lencina, C.; Gallo, L.; Barilly, C.; Poli, M.; Feve, K.; Albin, M.; Cauquil, L.; Knudsen, C.; Achard, C.; Devailly, G.; Soler, L.; Combes, S.; Beaumont, M. The Phenotype of the Gut Region Is More Stably Retained than Developmental Stage in Piglet Intestinal Organoids. Front. Cell Dev. Biol. 2022, 10, 983031.
Duval, H.; Heurtevin, L.; Dlalah, N.; Callot, C.; Lagnel, J. The Rm1 and Rm2 Resistance Genes to Green Peach Aphid (Myzus Persicae) Encode the Same TNL Proteins in Peach (Prunus Persica L.). Genes 2022, 13 (8), 1489.
Lemeunier, P.; Paux, E.; Babi, S.; Auzanneau, J.; Goudemand-Dugué, E.; Ravel, C.; Rincent, R. Training Population Optimization for Genomic Selection Improves the Predictive Ability of a Costly Measure in Bread Wheat, the Gliadin to Glutenin Ratio. Euphytica 2022, 218 (8), 111.
Kusch, S.; Larrouy, J.; Ibrahim, H. M. M.; Mounichetty, S.; Gasset, N.; Navaud, O.; Mbengue, M.; Zanchetta, C.; Lopez-Roques, C.; Donnadieu, C.; Godiard, L.; Raffaele, S. Transcriptional Response to Host Chemical Cues Underpins the Expansion of Host Range in a Fungal Plant Pathogen Lineage. ISME J 2022, 16 (1), 138–148.
Nicolas, A.; Deplanche, M.; Commere, P.-H.; Diot, A.; Genthon, C.; Marques da Silva, W.; Azevedo, V.; Germon, P.; Jamme, H.; Guédon, E.; Le Loir, Y.; Laurent, F.; Bierne, H.; Berkova, N. Transcriptome Architecture of Osteoblastic Cells Infected With Staphylococcus Aureus Reveals Strong Inflammatory Responses and Signatures of Metabolic and Epigenetic Dysregulation. Front. Cell. Infect. Microbiol. 2022, 12, 854242.
Rispe, C.; Hervet, C.; de la Cotte, N.; Daveu, R.; Labadie, K.; Noel, B.; Aury, J.-M.; Thany, S.; Taillebois, E.; Cartereau, A.; Le Mauff, A.; Charvet, C. L.; Auger, C.; Courtot, E.; Neveu, C.; Plantard, O. Transcriptome of the Synganglion in the Tick Ixodes Ricinus and Evolution of the Cys-Loop Ligand-Gated Ion Channel Family in Ticks. BMC Genomics 2022, 23 (1), 463.
Guichard, M.; Dainat, B.; Eynard, S.; Vignal, A.; Servin, B.; the Beestrong Consortium; Neuditschko, M. Two Quantitative Trait Loci Are Associated with Recapping of Varroa Destructor ‐infested Brood Cells in Apis Mellifera Mellifera. Animal Genetics 2022, 53 (1), 156–160.
Debray, K.; Le Paslier, M.-C.; Bérard, A.; Thouroude, T.; Michel, G.; Marie-Magdelaine, J.; Bruneau, A.; Foucher, F.; Malécot, V. Unveiling the Patterns of Reticulated Evolutionary Processes with Phylogenomics: Hybridization and Polyploidy in the Genus Rosa. Systematic Biology 2022, 71 (3), 547–569.
Farigoule, P.; Chartois, M.; Mesmin, X.; Lambert, M.; Rossi, J.-P.; Rasplus, J.-Y.; Cruaud, A. Vectors as Sentinels: Rising Temperatures Increase the Risk of Xylella Fastidiosa Outbreaks. Biology 2022, 11 (9), 1299.
Barassé, V.; Téné, N.; Klopp, C.; Paquet, F.; Tysklind, N.; Troispoux, V.; Lalägue, H.; Orivel, J.; Lefranc, B.; Leprince, J.; Kenne, M.; Tindo, M.; Treilhou, M.; Touchard, A.; Bonnafé, E. Venomics Survey of Six Myrmicine Ants Provides Insights into the Molecular and Structural Diversity of Their Peptide Toxins. Insect Biochemistry and Molecular Biology 2022, 151, 103876.
Toubon, G.; Butel, M.-J.; Rozé, J.-C.; Lepage, P.; Delannoy, J.; Ancel, P.-Y.; Charles, M.-A.; Aires, J.; for the EPIFLORE Study Group. Very Preterm Children Gut Microbiota Comparison at the Neonatal Period of 1 Month and 3.5 Years of Life. Front. Microbiol. 2022, 13, 919317.
Oral, M. What Reference Genome Assemblies Tell Us and How to Detect the Best Available Version: A Case Study in Trout. ase 2022, 0 (0), 0–0.
(116) Villain, P.; Catchpole, R.; Forterre, P.; Oberto, J.; da Cunha, V.; Basta, T. Expanded Dataset Reveals the Emergence and Evolution of DNA Gyrase in Archaea. Molecular Biology and Evolution 2022, 39 (8), msac155.
(117) Le Cam, S.; Julie, B.; Becquet, V.; Huet, V.; Garcia, P.; Viricel, A.; Breton, S.; Pante, E. Discordant Population Structure Inferred from Male- and Female-Type MtDNAs from Macoma Balthica , a Bivalve Species Characterized by Doubly Uniparental Inheritance of Mitochondria; preprint; Evolutionary Biology, 2022.