Publications

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

2023

1. Eché, C., Iampietro, C., Birbes, C., Dréau, A., Kuchly, C., Di Franco, A., Klopp, C., Faraut, T., Djebali, S., Castinel, A., Zytnicki, M., Denis, E., Boussaha, M., Grohs, C., Boichard, D., Gaspin, C., Milan, D., and Donnadieu, C. (2023). A Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling. Scientific Data 10, 369. https://doi.org/10.1038/s41597-023-02249-1.

2. Ranchou-Peyruse, M., Guignard, M., Haddad, P.G., Robin, S., Boesch, F., Lanot, M., Carrier, H., Dequidt, D., Chiquet, P., Caumette, G., Cézac, P., and Ranchou-Peyruse, A. (2023). A deep continental aquifer downhole sampler for microbiological studies. Frontiers in Microbiology 13, 1012400. https://doi.org/10.3389/fmicb.2022.1012400.

3. Krasovec, M., Merret, R., Sanchez, F., Sanchez-Brosseau, S., and Piganeau, G. (2023). A High Frequency of Chromosomal Duplications in Unicellular Algae Is Compensated by Translational Regulation. Genome Biology and Evolution 15, evad086. https://doi.org/10.1093/gbe/evad086.

4. Rice, E.S., Alberdi, A., Alfieri, J., Athrey, G., Balacco, J.R., Bardou, P., Blackmon, H., Charles, M., Cheng, H.H., Fedrigo, O., Fiddaman, S.R., Formenti, G., Frantz, L.A.F., Gilbert, M.T.P., Hearn, C.J., Jarvis, E.D., Klopp, C., Marcos, S., Mason, A.S., Velez-Irizarry, D., Xu, L., and Warren, W.C. (2023). A pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants. BMC Biology 21, 267. https://doi.org/10.1186/s12915-023-01758-0.

5. Baudrin, G., Pons, J.-M., Bed’Hom, B., Gil, L., Boyer, R., Dusabyinema, Y., Jiguet, F., and Fuchs, J. (2023). A Reference Genome Assembly for the Spotted Flycatcher ( Muscicapa striata ). Genome Biology and Evolution 15, evad140. https://doi.org/10.1093/gbe/evad140.

6. Doin De Moura, G.G., Mouffok, S., Gaudu, N., Cazalé, A.-C., Milhes, M., Bulach, T., Valière, S., Roche, D., Ferdy, J.-B., Masson-Boivin, C., Capela, D., and Remigi, P. (2023). A Selective Bottleneck During Host Entry Drives the Evolution of New Legume Symbionts. Molecular Biology and Evolution 40, msad116. https://doi.org/10.1093/molbev/msad116.

7. Maigné, É., Noirot, C., Henry, J., Adu Kesewaah, Y., Badin, L., Déjean, S., Guilmineau, C., Krebs, A., Mathevet, F., Segalini, A., Thomassin, L., Colongo, D., Gaspin, C., Liaubet, L., and Vialaneix, N. (2023). Asterics: A simple tool for the ExploRation and Integration of omiCS data. BMC Bioinformatics 24, 391. https://doi.org/10.1186/s12859-023-05504-9.

8. Laroche, E., Joulian, C., Duee, C., Casiot, C., Héry, M., and Battaglia-Brunet, F. (2023). Bio-precipitation of arsenic and antimony in a sulfate-reducing bioreactor treating real acid mine drainage water. FEMS Microbiology Ecology 99, fiad075. https://doi.org/10.1093/femsec/fiad075.

9. Wen, M., Pan, Q., Larson, W., Eché, C., and Guiguen, Y. (2023). Characterization of the sex determining region of channel catfish (Ictalurus punctatus) and development of a sex-genotyping test. Gene 850, 146933. https://doi.org/10.1016/j.gene.2022.146933.

10. Doniol‐Valcroze, P., Rancilhac, L., Brito, J., Miralles, A., Geniez, P., Benoit, L., Loiseau, A., Leblois, R., Dufresnes, C., and Crochet, P. (2024). Combining RADseq and contact zone analysis to decipher cryptic diversification in reptiles: Insights from the Spiny‐footed Lizard (Reptilia, Lacertidae). Zoologica Scripta 53, 1–15. https://doi.org/10.1111/zsc.12628.

11. Poullet, N., Devarieux, O., Beramice, D., Dantec, L., Félicité, Y., Feuillet, D., Gourdine, J.-L., and Bambou, J.-C. (2023). Comparative analysis of whole blood transcriptomics between European and local Caribbean pigs in response to feed restriction in a tropical climate. BMC Genomics 24, 292. https://doi.org/10.1186/s12864-023-09381-7.

12. Libourel, C., Keller, J., Brichet, L., Cazalé, A.-C., Carrère, S., Vernié, T., Couzigou, J.-M., Callot, C., Dufau, I., Cauet, S., Marande, W., Bulach, T., Suin, A., Masson-Boivin, C., Remigi, P., Delaux, P.-M., and Capela, D. (2023). Comparative phylotranscriptomics reveals ancestral and derived root nodule symbiosis programmes. Nature Plants 9, 1067–1080. https://doi.org/10.1038/s41477-023-01441-w.

13. Danguy Des Déserts, A., Durand, N., Servin, B., Goudemand-Dugué, E., Alliot, J.-M., Ruiz, D., Charmet, G., Elsen, J.-M., and Bouchet, S. (2023). Comparison of genomic-enabled cross selection criteria for the improvement of inbred line breeding populations. G3: Genes, Genomes, Genetics 13, jkad195. https://doi.org/10.1093/g3journal/jkad195.

14. Courtot, É., Boisseau, M., Dhorne-Pollet, S., Serreau, D., Gesbert, A., Reigner, F., Basiaga, M., Kuzmina, T., Lluch, J., Annonay, G., Kuchly, C., Diekmann, I., Krücken, J., Von Samson-Himmelstjerna, G., Mach, N., and Sallé, G. (2023). Comparison of two molecular barcodes for the study of equine strongylid communities with amplicon sequencing. PeerJ 11, e15124. https://doi.org/10.7717/peerj.15124.

15. Lapalu, N., Simon, A., Demenou, B., Paumier, D., Guillot, M.-P., Gout, L., Suffert, F., and Valade, R. (2023). Complete Genome Sequences of Septoria linicola : A Resource for Studying a Damaging Flax Pathogen. Molecular Plant-Microbe Interactions® 36, 59–63. https://doi.org/10.1094/MPMI-09-22-0185-A.

16. Vautrin, N., Alexandre, K., Pestel-Caron, M., Bernard, E., Fabre, R., Leoz, M., Dahyot, S., and Caron, F. (2023). Contribution of Antibiotic Susceptibility Testing and CH Typing Compared to Next-Generation Sequencing for the Diagnosis of Recurrent Urinary Tract Infections Due to Genetically Identical Escherichia coli Isolates: A Prospective Cohort Study of Cystitis in Women. Microbiology Spectrum 11, e02785–22. https://doi.org/10.1128/spectrum.02785-22.

17. Kalachova, T., Jindřichová, B., Burketová, L., Monard, C., Blouin, M., Jacquiod, S., Ruelland, E., and Puga-Freitas, R. (2023). Controlled natural selection of soil microbiome through plant-soil feedback confers resistance to a foliar pathogen. Plant and Soil 485, 181–195. https://doi.org/10.1007/s11104-022-05597-w.

18. Clerissi, C., Huot, C., Portet, A., Gourbal, B., and Toulza, E. (2023). Covariation between microeukaryotes and bacteria associated with Planorbidae snails. PeerJ 11, e16639. https://doi.org/10.7717/peerj.16639.

19. Gabrielli, M., Leroy, T., Salmona, J., Nabholz, B., Milá, B., and Thébaud, C. (2024). Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole‐genome sequencing. Molecular Ecology 33, e17243. https://doi.org/10.1111/mec.17243.

20. Fay, R., Ficheux, S., Béchet, A., Besnard, A., Crochet, P., Leblois, R., Crivelli, A., Wattier, R., and Olivier, A. (2023). Direct and indirect estimates of dispersal support strong juvenile philopatry and male‐biased dispersal in a freshwater turtle species ( Emys orbicularis ). Freshwater Biology 68, 2042–2053. https://doi.org/10.1111/fwb.14171.

21. Beaumont, M., Lencina, C., Fève, K., Barilly, C., Le‐Normand, L., Combes, S., Devailly, G., and Boudry, G. (2023). Disruption of the primocolonizing microbiota alters epithelial homeostasis and imprints stem cells in the colon of neonatal piglets. The FASEB Journal 37, e23149. https://doi.org/10.1096/fj.202301182R.

22. Lo, Y., Bruxaux, J., Rodríguez de la Vega, R.C., O’Donnell, S., Snirc, A., Coton, M., Le Piver, M., Le Prieur, S., Roueyre, D., Dupont, J., Houbraken, J., Debuchy, R., Ropars, J., Giraud, T., and Branca, A. (2023). Domestication in dry‐cured meat penicillium fungi: Convergent specific phenotypes and horizontal gene transfers without strong genetic subdivision. Evolutionary Applications 16, 1637–1660. https://doi.org/10.1111/eva.13591.

23. Sartoretto, S., Ledoux, J., Gueret, E., Guillemain, D., Ravel, C., Moirand, L., and Aurelle, D. (2024). Ecological and genomic characterization of a remarkable natural heritage: A mesophotic “giant” Paramuricea clavata forest. Marine Ecology Progress Series 728, 85–101. https://doi.org/10.3354/meps14427.

24. Díaz, F.P., Dussarrat, T., Carrasco‐Puga, G., Colombié, S., Prigent, S., Decros, G., Bernillon, S., Cassan, C., Flandin, A., Guerrero, P.C., Gibon, Y., Rolin, D., Cavieres, L.A., Pétriacq, P., Latorre, C., and Gutiérrez, R.A. (2024). Ecological and metabolic implications of the nurse effect of Maihueniopsis camachoi in the Atacama Desert. New Phytologist 241, 1074–1087. https://doi.org/10.1111/nph.19415.

25. Hu, J., Vandenkoornhuyse, P., Khalfallah, F., Causse‐Védrines, R., and Mony, C. (2023). Ecological corridors homogenize plant root endospheric mycobiota. New Phytologist 237, 1347–1362. https://doi.org/10.1111/nph.18606.

26. Wicki, M., Raoul, J., and Legarra, A. (2023). Effect of subdivision of the Lacaune dairy sheep breed on the accuracy of genomic prediction. Journal of Dairy Science 106, 5570–5581. https://doi.org/10.3168/jds.2022-23114.

27. Pedro, N., Brucato, N., Cavadas, B., Lisant, V., Camacho, R., Kinipi, C., Leavesley, M., Pereira, L., and Ricaut, F. (2023). First insight into oral microbiome diversity in Papua New Guineans reveals a specific regional signature. Molecular Ecology 32, 2551–2564. https://doi.org/10.1111/mec.16702.

28. Fruleux, A., Duclercq, J., Dubois, F., and Decocq, G. (2023). First report of ectomycorrhizae in Prunus serotina in the exotic range. Plant and Soil 484, 171–181. https://doi.org/10.1007/s11104-022-05780-z.

29. Oury, N., Noël, C., Mona, S., Aurelle, D., and Magalon, H. (2023). From genomics to integrative species delimitation? The case study of the Indo-Pacific Pocillopora corals. Molecular Phylogenetics and Evolution 184, 107803. https://doi.org/10.1016/j.ympev.2023.107803.

30. Frank, X., Lampoh, K., and Delenne, J.-Y. (2023). From stress concentrations between inclusions to probability of breakage: A two-dimensional peridynamic study of particle-embedded materials. Physical Review E 108, 034903. https://doi.org/10.1103/PhysRevE.108.034903.

31. Fuchs, S., Babin, L., Andraos, E., Bessiere, C., Willier, S., H. Schulte, J., Gaspin, C., and Meggetto, F. (2023). Generation of full-length circRNA libraries for Oxford Nanopore long-read sequencing v3. https://doi.org/10.17504/protocols.io.rm7vzy8r4lx1/v3.

32. Blois, L., Miguel, M. de, Bert, P., Girollet, N., Ollat, N., Rubio, B., Segura, V., Voss‐Fels, K.P., Schmid, J., and Marguerit, E. (2023). Genetic structure and first genome‐wide insights into the adaptation of a wild relative of grapevine, Vitis berlandieri. Evolutionary Applications 16, 1184–1200. https://doi.org/10.1111/eva.13566.

33. Bastide, H., López-Villavicencio, M., Ogereau, D., Lledo, J., Dutrillaux, A.-M., Debat, V., and Llaurens, V. (2022). Genome assembly of 3 Amazonian morpho butterfly species reveals Z-chromosome rearrangements between closely related species living in sympatry. GigaScience 12, giad033. https://doi.org/10.1093/gigascience/giad033.

34. Bovio, E., Rancurel, C., Seassau, A., Magliano, M., Gislard, M., Loisier, A., Kuchly, C., Ponchet, M., Danchin, E.G.J., and Van Ghelder, C. (2023). Genome sequence and annotation of Periconia digitata a hopeful biocontrol agent of phytopathogenic oomycetes. Scientific Data 10, 583. https://doi.org/10.1038/s41597-023-02440-4.

35. Parey, E., Louis, A., Montfort, J., Bouchez, O., Roques, C., Iampietro, C., Lluch, J., Castinel, A., Donnadieu, C., Desvignes, T., Floi Bucao, C., Jouanno, E., Wen, M., Mejri, S., Dirks, R., Jansen, H., Henkel, C., Chen, W.-J., Zahm, M., Cabau, C., Klopp, C., Thompson, A.W., Robinson-Rechavi, M., Braasch, I., Lecointre, G., Bobe, J., Postlethwait, J.H., Berthelot, C., Roest Crollius, H., and Guiguen, Y. (2023). Genome structures resolve the early diversification of teleost fishes. Science 379, 572–575. https://doi.org/10.1126/science.abq4257.

36. Postaire, B.D., Devloo‐Delva, F., Brunnschweiler, J.M., Charvet, P., Chen, X., Cliff, G., Daly, R., Drymon, J.M., Espinoza, M., Fernando, D., Glaus, K., Grant, M.I., Hernandez, S., Hyodo, S., Jabado, R.W., Jaquemet, S., Johnson, G., Naylor, G.J.P., Nevill, J.E.G., Pathirana, B.M., Pillans, R.D., Smoothey, A.F., Tachihara, K., Tillet, B.J., Valerio‐Vargas, J.A., Lesturgie, P., Magalon, H., Feutry, P., and Mona, S. (2024). Global genetic diversity and historical demography of the Bull Shark. Journal of Biogeography 51, 632–648. https://doi.org/10.1111/jbi.14774.

37. Evariste, L., Mouchet, F., Pinelli, E., Flahaut, E., Gauthier, L., and Barret, M. (2023). Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles. Science of The Total Environment 857, 159515. https://doi.org/10.1016/j.scitotenv.2022.159515.

38. Salmona, J., Dresen, A., Ranaivoson, A.E., Manzi, S., Le Pors, B., Hong‐Wa, C., Razanatsoa, J., Andriaholinirina, N.V., Rasoloharijaona, S., Vavitsara, M., and Besnard, G. (2023). How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree. Molecular Ecology 32, 299–315. https://doi.org/10.1111/mec.16759.

39. Gaudino, M., Salem, E., Ducatez, M.F., and Meyer, G. (2023). Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia. Microbiology Spectrum 11, e03026–23. https://doi.org/10.1128/spectrum.03026-23.

40. Gmel, A.I., Guichard, M., Dainat, B., Williams, G.R., Eynard, S., Vignal, A., Servin, B., the Beestrong Consortium, and Neuditschko, M. (2023). Identification of runs of homozygosity in Western honey bees ( Apis mellifera ) using whole‐genome sequencing data. Ecology and Evolution 13, e9723. https://doi.org/10.1002/ece3.9723.

41. Valette, N., Legout, A., Goodell, B., Alfredsen, G., Auer, L., Gelhaye, E., and Derrien, D. (2023). Impact of Norway spruce pre-degradation stages induced by Gloeophyllum trabeum on fungal and bacterial communities. Fungal Ecology 61, 101188. https://doi.org/10.1016/j.funeco.2022.101188.

42. Darriaut, R., Tran, J., Martins, G., Ollat, N., Masneuf-Pomarède, I., and Lauvergeat, V. (2023). In grapevine decline, microbiomes are affected differently in symptomatic and asymptomatic soils. Applied Soil Ecology 183, 104767. https://doi.org/10.1016/j.apsoil.2022.104767.

43. Piles, M., Sánchez, J.P., Pascual, M., and Rodríguez‐Ramilo, S.T. (2023). Inbreeding depression on growth and prolificacy traits in two lines of rabbit. Journal of Animal Breeding and Genetics 140, 39–48. https://doi.org/10.1111/jbg.12745.

44. Orozco-Arias, S., Humberto Lopez-Murillo, L., Candamil-Cortés, M.S., Arias, M., Jaimes, P.A., Rossi Paschoal, A., Tabares-Soto, R., Isaza, G., and Guyot, R. (2023). Inpactor2: A software based on deep learning to identify and classify LTR-retrotransposons in plant genomes. Briefings in Bioinformatics 24, bbac511. https://doi.org/10.1093/bib/bbac511.

45. Barranger, A., Klopp, C., Le Bot, B., Saramito, G., Dupont, L., Llopis, S., Wiegand, C., and Binet, F. (2023). Insights into the molecular mechanisms of pesticide tolerance in the Aporrectodea caliginosa earthworm. Environmental Pollution 319, 120945. https://doi.org/10.1016/j.envpol.2022.120945.

46. Noyer, M., Bernard, M., Verneau, O., and Palacios, C. (2023). Insights on the particle-attached riverine archaeal community shifts linked to seasons and to multipollution during a Mediterranean extreme storm event. Environmental Science and Pollution Research 30, 49685–49702. https://doi.org/10.1007/s11356-023-25637-x.

47. Biget, M., Mony, C., Wang, T., Ling, N., Miteul, A., Jambon, O., Causse-Védrines, R., Michon-Coudouel, S., Hervé, M., Chable, V., Pernet, S., and Vandenkoornhuyse, P. (2024). Intra- and inter-annual changes in root endospheric microbial communities of grapevine are mainly deterministic. Plant and Soil 494, 217–233. https://doi.org/10.1007/s11104-023-06262-6.

48. Jourdain, J., Barasc, H., Faraut, T., Calgaro, A., Bonnet, N., Marcuzzo, C., Suin, A., Barbat, A., Hozé, C., Besnard, F., Taussat, S., Grohs, C., Kuchly, C., Iampietro, C., Donnadieu, C., Pinton, A., Boichard, D., and Capitan, A. (2023). Large-scale detection and characterization of interchromosomal rearrangements in normozoospermic bulls using massive genotype and phenotype data sets. Genome Research 33, 957–971. https://doi.org/10.1101/gr.277787.123.

49. Lesturgie, P., Braun, C.D., Clua, E., Mourier, J., Thorrold, S.R., Vignaud, T., Planes, S., and Mona, S. (2023). Like a rolling stone: Colonization and migration dynamics of the gray reef shark ( Carcharhinus amblyrhynchos ). Ecology and Evolution 13, e9746. https://doi.org/10.1002/ece3.9746.

50. Sabra, A., Biteau, N., Dupuy, J.-W., Klopp, C., Noël, T., and Dementhon, K. (2023). Mediator Subunit Med15 Regulates Cell Morphology and Mating in Candida lusitaniae. Journal of Fungi 9, 333. https://doi.org/10.3390/jof9030333.

51. Fartash, A.H., Ben, C., Mazurier, M., Ebrahimi, A., Ghalandar, M., Gentzbittel, L., and Rickauer, M. (2023). Medicago truncatula quantitative resistance to a new strain of Verticillium alfalfae from Iran revealed by a genome-wide association study. Frontiers in Plant Science 14, 1125551. https://doi.org/10.3389/fpls.2023.1125551.

52. Boggio, G.M., Christensen, O.F., Legarra, A., Meynadier, A., and Marie-Etancelin, C. (2023). Microbiability of milk composition and genetic control of microbiota effects in sheep. Journal of Dairy Science 106, 6288–6298. https://doi.org/10.3168/jds.2022-22948.

53. Leclaire, S., Pineaux, M., Blanchard, P., White, J., and Hatch, S.A. (2023). Microbiota composition and diversity of multiple body sites vary according to reproductive performance in a seabird. Molecular Ecology 32, 2115–2133. https://doi.org/10.1111/mec.16398.

54. Homberg, N., Galvão Ferrarini, M., Gaspin, C., and Sagot, M.-F. (2023). MicroRNA Target Identification: Revisiting Accessibility and Seed Anchoring. Genes 14, 664. https://doi.org/10.3390/genes14030664.

55. Gaudino, M., Valarcher, J.-F., Hägglund, S., Näslund, K., Zohari, S., Ducatez, M.F., and Meyer, G. (2023). Molecular and genetic characterization of bovine parainfluenza type 3 European field and vaccine strains. Infection, Genetics and Evolution 113, 105483. https://doi.org/10.1016/j.meegid.2023.105483.

56. Le Provost, G., Lalanne, C., Lesur, I., Louvet, J.-M., Delzon, S., Kremer, A., Labadie, K., Aury, J.-M., Da Silva, C., Moritz, T., and Plomion, C. (2023). Oak stands along an elevation gradient have different molecular strategies for regulating bud phenology. BMC Plant Biology 23, 108. https://doi.org/10.1186/s12870-023-04069-2.

57. Aurelle, D., Haguenauer, A., Blaise, C., Reynes, L., Arnaud‐Haond, S., Boavida, J., Cabau, C., Klopp, C., Lundalv, T., Noûs, C., Sartoretto, S., Wienberg, C., Jiménez, C.E., and Orejas, C. (2024). On the specific status of eastern Mediterranean dendrophyllia corals (Cnidaria, Anthozoa): Genetic characterization and speciation scenarios. Zoologica Scripta 53, 235–247. https://doi.org/10.1111/zsc.12643.

58. Nouwen, N., Pervent, M., El M’Chirgui, F., Tellier, F., Rios, M., Horta Araújo, N., Klopp, C., Gressent, F., and Arrighi, J.-F. (2024). OROSOMUCOID PROTEIN 1 regulation of sphingolipid synthesis is required for nodulation in Aeschynomene evenia. Plant Physiology 194, 1611–1630. https://doi.org/10.1093/plphys/kiad642.

59. Allio, R., Delsuc, F., Belkhir, K., Douzery, E.J.P., Ranwez, V., and Scornavacca, C. (2024). OrthoMaM v12: A database of curated single-copy ortholog alignments and trees to study mammalian evolutionary genomics. Nucleic Acids Research 52, D529–D535. https://doi.org/10.1093/nar/gkad834.

60. Antonios, S., Legarra, A., Pong-Wong, R., Astruc, J.M., Rodríguez-Ramilo, S.T., and Vitezica, Z.G. (2023). Partitioning of the genetic trends of French dairy sheep in Mendelian samplings and long-term contributions. Journal of Dairy Science 106, 6275–6287. https://doi.org/10.3168/jds.2022-23009.

61. Boisseau, M., Mach, N., Basiaga, M., Kuzmina, T., Laugier, C., and Sallé, G. (2023). Patterns of variation in equine strongyle community structure across age groups and gut compartments. Parasites & Vectors 16, 64. https://doi.org/10.1186/s13071-022-05645-5.

62. Samain, E., Duclercq, J., Ait Barka, E., Eickermann, M., Ernenwein, C., Mazoyon, C., Sarazin, V., Dubois, F., Aussenac, T., and Selim, S. (2023). PGPR-Soil Microbial Communities’ Interactions and Their Influence on Wheat Growth Promotion and Resistance Induction against Mycosphaerella graminicola. Biology 12, 1416. https://doi.org/10.3390/biology12111416.

63. Rancilhac, L., Miralles, A., Geniez, P., Mendez-Aranda, D., Beddek, M., Brito, J.C., Leblois, R., and Crochet, P.-A. (2023). Phylogeographic breaks and how to find them: An empirical attempt at separating vicariance from isolation by distance in a lizard with restricted dispersal. Peer Community Journal 3, e74. https://doi.org/10.24072/pcjournal.301.

64. Le Graverand, Q., Marie-Etancelin, C., Meynadier, A., Weisbecker, J.-L., Marcon, D., and Tortereau, F. (2023). Predicting feed efficiency traits in growing lambs from their ruminal microbiota. animal 17, 100824. https://doi.org/10.1016/j.animal.2023.100824.

65. Pont, F., Cerapio, J.P., Gravelle, P., Ligat, L., Valle, C., Sarot, E., Perrier, M., Lopez, F., Laurent, C., Fournié, J.J., and Tosolini, M. (2023). Single-cell spatial explorer: Easy exploration of spatial and multimodal transcriptomics. BMC Bioinformatics 24, 30. https://doi.org/10.1186/s12859-023-05150-1.

66. Duley, E., Iribar, A., Bisson, C., Chave, J., and Donald, J. (2023). Soil environmental DNA metabarcoding can quantify local plant diversity for biomonitoring across varied environments. Restoration Ecology 31, e13831. https://doi.org/10.1111/rec.13831.

67. Noujarède, J., Carrié, L., Garcia, V., Grimont, M., Eberhardt, A., Mucher, E., Genais, M., Schreuder, A., Carpentier, S., Ségui, B., Nieto, L., Levade, T., Puig, S., Torres, T., Malvehy, J., Harou, O., Lopez, J., Dalle, S., Caramel, J., Gibot, L., Riond, J., and Andrieu-Abadie, N. (2023). Sphingolipid paracrine signaling impairs keratinocyte adhesion to promote melanoma invasion. Cell Reports 42, 113586. https://doi.org/10.1016/j.celrep.2023.113586.

68. Rougemont, Q., Huber, B., Martin, S.H., Whibley, A., Estrada, C., Solano, D., Orpet, R., McMillan, W.O., Frérot, B., and Joron, M. (2023). Subtle Introgression Footprints at the End of the Speciation Continuum in a Clade of heliconius Butterflies. Molecular Biology and Evolution 40, msad166. https://doi.org/10.1093/molbev/msad166.

69. Kurylo, C., Guyomar, C., Foissac, S., and Djebali, S. (2023). TAGADA: A scalable pipeline to improve genome annotations with RNA-seq data. NAR Genomics and Bioinformatics 5, lqad089. https://doi.org/10.1093/nargab/lqad089.

70. Beaumont, M., Lencina, C., Bertide, A., Gallo, L., Barilly, C., Marrauld, C., Cauquil, L., Samson, A., and Combes, S. (2023). The Early Life Microbiota Is Not a Major Factor Underlying the Susceptibility to Postweaning Diarrhea in Piglets. Microbiology Spectrum 11, e00694–23. https://doi.org/10.1128/spectrum.00694-23.

71. Huang, K., Jahani, M., Gouzy, J., Legendre, A., Carrere, S., Lázaro-Guevara, J.M., González Segovia, E.G., Todesco, M., Mayjonade, B., Rodde, N., Cauet, S., Dufau, I., Staton, S.E., Pouilly, N., Boniface, M.-C., Tapy, C., Mangin, B., Duhnen, A., Gautier, V., Poncet, C., Donnadieu, C., Mandel, T., Hübner, S., Burke, J.M., Vautrin, S., Bellec, A., Owens, G.L., Langlade, N., Muños, S., and Rieseberg, L.H. (2023). The genomics of linkage drag in inbred lines of sunflower. Proceedings of the National Academy of Sciences 120, e2205783119. https://doi.org/10.1073/pnas.2205783119.

72. Poulet, A., Rousselot, E., Téletchéa, S., Noirot, C., Jacob, Y., Van Wolfswinkel, J., Thiriet, C., and Duc, C. (2023). The Histone Chaperone Network Is Highly Conserved in Physarum polycephalum. International Journal of Molecular Sciences 24, 1051. https://doi.org/10.3390/ijms24021051.

73. Khajavi, L., Nguyen, X.-H., Queriault, C., Chabod, M., Barateau, L., Dauvilliers, Y., Zytnicki, M., and Liblau, R. (2023). The transcriptomics profiling of blood CD4 and CD8 T-cells in narcolepsy type I. Frontiers in Immunology 14, 1249405. https://doi.org/10.3389/fimmu.2023.1249405.

74. Urvois, T., Perrier, C., Roques, A., Sauné, L., Courtin, C., Kajimura, H., Hulcr, J., Cognato, A.I., Auger‐Rozenberg, M.‐A., and Kerdelhué, C. (2023). The worldwide invasion history of a pest ambrosia beetle inferred using population genomics. Molecular Ecology 32, 4381–4400. https://doi.org/10.1111/mec.16993.

75. Wagner, S., Seguin‐Orlando, A., Leplé, J., Leroy, T., Lalanne, C., Labadie, K., Aury, J., Poirier, S., Wincker, P., Plomion, C., Kremer, A., and Orlando, L. (2024). Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood. Molecular Ecology 33, e16859. https://doi.org/10.1111/mec.16859.

76. Aumont, O., Ben Ari, T., Mariette, J., Jeanneau, L., Spiga, A., Lefort, G., Roche, P., Santerne, A., and Estevez-Torres, A. (2023). Traveling for academic research : Patterns, determinants and mitigation options. https://doi.org/10.5194/egusphere-egu23-11656.

77. Mohamed, M., Sabot, F., Varoqui, M., Mugat, B., Audouin, K., Pélisson, A., Fiston-Lavier, A.-S., and Chambeyron, S. (2023). TrEMOLO: Accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches. Genome Biology 24, 63. https://doi.org/10.1186/s13059-023-02911-2.

78. Mervant, L., Tremblay‐Franco, M., Olier, M., Jamin, E., Martin, J., Trouilh, L., Buisson, C., Naud, N., Maslo, C., Héliès‐Toussaint, C., Fouché, E., Kesse‐Guyot, E., Hercberg, S., Galan, P., Deschasaux‐Tanguy, M., Touvier, M., Pierre, F., Debrauwer, L., and Guéraud, F. (2023). Urinary Metabolome Analysis Reveals Potential Microbiota Alteration and Electrophilic Burden Induced by High Red Meat Diet: Results from the French NutriNet‐Santé Cohort and an In Vivo Intervention Study in Rats. Molecular Nutrition & Food Research 67, 2200432. https://doi.org/10.1002/mnfr.202200432.

79. Bollier, N., Micol-Ponce, R., Dakdaki, A., Maza, E., Zouine, M., Djari, A., Bouzayen, M., Chevalier, C., Delmas, F., Gonzalez, N., and Hernould, M. (2023). Various tomato cultivars display contrasting morphological and molecular responses to a chronic heat stress. Frontiers in Plant Science 14, 1278608. https://doi.org/10.3389/fpls.2023.1278608.

80. Ben-Jemaa, S., Adam, G., Boussaha, M., Bardou, P., Klopp, C., Mandonnet, N., and Naves, M. (2023). Whole genome sequencing reveals signals of adaptive admixture in Creole cattle. Scientific Reports 13, 12155. https://doi.org/10.1038/s41598-023-38774-7.

81. Boitard, S., Liaubet, L., Paris, C., Fève, K., Dehais, P., Bouquet, A., Riquet, J., and Mercat, M.-J. (2023). Whole-genome sequencing of cryopreserved resources from French Large White pigs at two distinct sampling times reveals strong signatures of convergent and divergent selection between the dam and sire lines. Genetics Selection Evolution 55, 13. https://doi.org/10.1186/s12711-023-00789-z.

82. Frohn, L., Peixoto, D., Guyomar, C., Teixeira, C., Terrier, F., Aguirre, P., Maman Haddad, S., Bobe, J., Costas, B., Richard, N., Pinel, K., and Skiba-Cassy, S. (2024). Yeast extract improves growth in rainbow trout (Oncorhynchus mykiss) fed a fishmeal-free diet and modulates the hepatic and distal intestine transcriptomic profile. Aquaculture 579, 740226. https://doi.org/10.1016/j.aquaculture.2023.740226.

83. Rodríguez De Cara, M.Á., Jay, P., Rougemont, Q., Chouteau, M., Whibley, A., Huber, B., Piron-Prunier, F., Ramos, R.R., Freitas, A.V.L., Salazar, C., Silva-Brandão, K.L., Torres, T.T., and Joron, M. (2023). Balancing selection at a wing pattern locus is associated with major shifts in genome-wide patterns of diversity and gene flow. Peer Community Journal 3, e65. https://doi.org/10.24072/pcjournal.298.

84. De Freitas Pereira, M., Cohen, D., Auer, L., Aubry, N., Bogeat‐Triboulot, M., Buré, C., Engle, N.L., Jolivet, Y., Kohler, A., Novák, O., Pavlović, I., Priault, P., Tschaplinski, T.J., Hummel, I., Vaultier, M., and Veneault‐Fourrey, C. (2023). Ectomycorrhizal symbiosis prepares its host locally and systemically for abiotic cue signaling. The Plant Journal 116, 1784–1803. https://doi.org/10.1111/tpj.16465.

85. Hévin, N.M.‐C., Kergoat, Gael.J., Clamens, A., Le Ru, B., Mansell, M.W., and Michel, B. (2023). Evolution, systematics and historical biogeography of Palparini and Palparidiini antlions (Neuroptera: Myrmeleontidae): Old origin and in situ diversification in Southern Africa. Systematic Entomology 48, 600–617. https://doi.org/10.1111/syen.12593.

86. Esnault, C., Magat, T., Zine El Aabidine, A., Garcia-Oliver, E., Cucchiarini, A., Bouchouika, S., Lleres, D., Goerke, L., Luo, Y., Verga, D., Lacroix, L., Feil, R., Spicuglia, S., Mergny, J.-L., and Andrau, J.-C. (2023). G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions. Nature Genetics 55, 1359–1369. https://doi.org/10.1038/s41588-023-01437-4.

87. Olivares, J., Siegwart, M., Gautier, M., Maugin, S., Gingueneau, L., and Olivares, B. (2023). Genetic basis of codling moth (Cydia pomonella) resistance to the original isolate of C. Pomonella Granulovirus (CpGV-M). Entomologia Generalis 43, 649–658. https://doi.org/10.1127/entomologia/2023/2052.

88. Paës, C., Gidenne, T., Bébin, K., Duperray, J., Gohier, C., Guené-Grand, E., Rebours, G., Aymard, P., Debrusse, A.-M., Fortun-Lamothe, L., Beaumont, M., and Combes, S. (2023). L’introduction précoce d’aliment solide au début de la vie, une stratégie de pilotage du microbiote pour construire et préserver la santé du lapin. INRAE Productions Animales 36, 7731. https://doi.org/10.20870/productions-animales.2023.36.3.7731.

89. Park, S., Belfoul, A.M., Rastelli, M., Jang, A., Monnoye, M., Bae, H., Kamitakahara, A., Giavalisco, P., Sun, S., Barelle, P.-Y., Plows, J., Jang, C., Fodor, A., Goran, M.I., and Bouret, S.G. (2023). Maternal low-calorie sweetener consumption rewires hypothalamic melanocortin circuits via a gut microbial co-metabolite pathway. JCI Insight 8, e156397. https://doi.org/10.1172/jci.insight.156397.

90. Szadkowski, E., Lagnel, J., Touhami, N., Sayeh, A., Lopez-Roques, C., Bouchez, O., and Lefebvre, V. (2023). Phytophthora capsici genome assembly for two isolates using long-read Oxford Nanopore Technology sequencing. Microbiology Resource Announcements 12, e00196–23. https://doi.org/10.1128/MRA.00196-23.

91. Bermann, M., Aguilar, I., Lourenco, D., Misztal, I., and Legarra, A. (2023). Reliabilities of estimated breeding values in models with metafounders. Genetics Selection Evolution 55, 6. https://doi.org/10.1186/s12711-023-00778-2.

92. Oury, N., Mona, S., and Magalon, H. (2024). Same places, same stories? Genomics reveals similar structuring and demographic patterns for four pocillopora coral species in the southwestern Indian Ocean. Journal of Biogeography 51, 754–768. https://doi.org/10.1111/jbi.14788.

93. Gréau, L., Blaudez, D., Le Cordier, H., Fornasier, F., and Cébron, A. (2023). Taxonomic and functional responses of soil and root bacterial communities associated with poplar exposed to a contamination gradient of phenanthrene. FEMS Microbiology Ecology 99, fiad052. https://doi.org/10.1093/femsec/fiad052.

94. Pichler, A.C., Carrié, N., Cuisinier, M., Ghazali, S., Voisin, A., Axisa, P.-P., Tosolini, M., Mazzotti, C., Golec, D.P., Maheo, S., Do Souto, L., Ekren, R., Blanquart, E., Lemaitre, L., Feliu, V., Joubert, M.-V., Cannons, J.L., Guillerey, C., Avet-Loiseau, H., Watts, T.H., Salomon, B.L., Joffre, O., Grinberg-Bleyer, Y., Schwartzberg, P.L., Lucca, L.E., and Martinet, L. (2023). TCR-independent CD137 (4-1BB) signaling promotes CD8+-exhausted T cell proliferation and terminal differentiation. Immunity 56, 1631–1648.e10. https://doi.org/10.1016/j.immuni.2023.06.007.

95. Cruaud, A., Rasplus, J., Zhang, J., Burks, R., Delvare, G., Fusu, L., Gumovsky, A., Huber, J.T., Janšta, P., Mitroiu, M., Noyes, J.S., Van Noort, S., Baker, A., Böhmová, J., Baur, H., Blaimer, B.B., Brady, S.G., Bubeníková, K., Chartois, M., Copeland, R.S., Dale‐Skey Papilloud, N., Dal Molin, A., Dominguez, C., Gebiola, M., Guerrieri, E., Kresslein, R.L., Krogmann, L., Lemmon, E., Murray, E.A., Nidelet, S., Nieves‐Aldrey, J.L., Perry, R.K., Peters, R.S., Polaszek, A., Sauné, L., Torréns, J., Triapitsyn, S., Tselikh, E.V., Yoder, M., Lemmon, A.R., Woolley, J.B., and Heraty, J.M. (2024). The Chalcidoidea bush of life: Evolutionary history of a massive radiation of minute wasps. Cladistics 40, 34–63. https://doi.org/10.1111/cla.12561.