Genòmica evolutiva i funcional
En genòmica, la qüestió clau és com varien els genomes a petita i a gran escala. El grup de recerca en Genòmica evolutiva i funcional estudia els processos moleculars de l’adaptació i les conseqüències funcionals de les mutacions adaptatives. Per poder fer un retrat complet de com funciona l’adaptació, es combinen estratègies òmiques amb anàlisis moleculars i funcionals de les mutacions adaptatives. El grup estudia tant les adaptacions induïdes per transposons com les mutacions nucleotídiques en l’organisme model Drosophila melanogaster. També estan interessats en les dinàmiques poblacionals dels transposons, ja que són els components més actius, diversos i antics dels genomes, raons per les quals conèixer-ne l’impacte i la biologia és indispensable per entendre la funció i l’evolució dels genomes.
Pàgina web: González Lab
Merenciano M, González J. 2023. The Interplay Between Developmental Stage and Environment Underlies the Adaptive Effect of a Natural Transposable Element Insertion. Molecular Biology and Evolution, 40(3). DOI:10.1093/molbev/msad044
Horváth V, Guirao-Rico S, Salces-Ortiz J, Rech GE, Green L, Aprea E, Rodeghiero M, Anfora G, González J. 2023. Gene expression differences consistent with water loss reduction underlie desiccation tolerance of natural Drosophila populations. BMC Biology, 21(1):35. DOI:10.1186/s12915-023-01530-4
Coronado-Zamora M, Salces-Ortiz J, González J. 2023. DrosOmics: A Browser to Explore -omics Variation Across High-Quality Reference Genomes From Natural Populations of Drosophila melanogaster. Molecular Biology and Evolution, 40(4). DOI:10.1093/molbev/msad075
Vargas-Chavez C, Longo Pendy NM, Nsango SE, Aguilera L, Ayala D, González J. 2022. Transposable element variants and their potential adaptive impact in urban populations of the malaria vector Anopheles coluzzii. Genome Research, 32(1):189-202. DOI:10.1101/gr.275761.121
Rech GE, Radío S, Guirao-Rico S, Aguilera L, Horvath V, Green L, Lindstadt H, Jamilloux V, Quesneville H, González J. 2022. Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. Nature Communications, 13(1):1948. DOI:10.1038/s41467-022-29518-8
Green L, Coronado-Zamora M, Radío S, Rech GE, Salces-Ortiz J, González J. 2022. The genomic basis of copper tolerance in Drosophila is shaped by a complex interplay of regulatory and environmental factors. BMC Biology, 20(1):275. DOI:10.1186/s12915-022-01479-w
Brandt M, Groom Q, Magro A, Misevic D, Narraway CL, Bruckermann T, Beniermann A, Børsen T, González J, Meeus S, Roy HE, Sá-Pinto X, Torres JR, Jenkins T. 2022. Promoting scientific literacy in evolution through citizen science. Proceedings of the Royal Society B: Biological Sciences, 289(1980):46-82. DOI:10.1098/rspb.2022.1077
Wallace MA, Coffman KA, Gilbert C, Ravindran S, Albery GF, Abbott J, Argyridou E, Bellosta P, Betancourt AJ, Colinet H, Eric K, Glaser-Schmitt A, Grath S, Jelic M, Kankare M, Kozeretska I, Loeschcke V, Montchamp-Moreau C, Ometto L, Onder BS, Orengo DJ, Parsch J, Pascual M, Patenkovic A, Puerma E, Ritchie MG, Rota-Stabelli O, Schou MF, Serga SV, Stamenkovic-Radak M, Tanaskovic M, Veselinovic MS, Vieira J, Vieira CP, Kapun M, Flatt T, González J, Staubach F, Obbard DJ. 2021. The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe. Virus Evolution, 7(1). DOI:10.1093/ve/veab031
Ullastres A, Merenciano M, González J. 2021. Regulatory regions in natural transposable element insertions drive interindividual differences in response to immune challenges in Drosophila. Genome Biology, 22(1):265. DOI:10.1186/s13059-021-02471-3
Machado HE, Bergland A, Taylor RW, Tilk S, Behrman E, Dyer K, Fabian DK, Flatt T, González J, Karasov TL, Kim BY, Kozeretska I, Lazzaro BP, Merritt T, Pool JE, O'Brien K, Rajpurohit S, Roy PR, Schaeffer SW, Serga S, Schmidt P, Petrov DA. 2021. Broad geographic sampling reveals the shared basis and environmental correlates of seasonal adaptation in Drosophila. eLife, 10. DOI:10.7554/eLife.67577
Kapun M, Nunez JCB, Bogaerts-Márquez M, Murga-Moreno J, Paris M, Outten J, Coronado-Zamora M, Tern C, Rota-Stabelli O, García Guerreiro MP, Casillas S, Orengo DJ, Puerma E, Kankare M, Ometto L, Loeschcke V, Onder BS, Abbott JK, Schaeffer SW, Rajpurohit S, Behrman EL, Schou MF, Merritt TJS, Lazzaro BP, Glaser-Schmitt A, Argyridou E, Staubach F, Wang Y, Tauber E, Serga SV, Fabian DK, Dyer KA, Wheat CW, Parsch J, Grath S, Veselinovic MS, Stamenkovic-Radak M, Jelic M, Buendía-Ruíz AJ, Gómez-Julián MJ, Espinosa-Jimenez ML, Gallardo-Jiménez FD, Patenkovic A, Eric K, Tanaskovic M, Ullastres A, Guio L, Merenciano M, Guirao-Rico S, Horváth V, Obbard DJ, Pasyukova E, Alatortsev VE, Vieira CP, Vieira J, Torres JR, Kozeretska I, Maistrenko OM, Montchamp-Moreau C, Mukha DV, Machado HE, Lamb K, Paulo T, Yusuf L, Barbadilla A, Petrov D, Schmidt P, Gonzalez J, Flatt T, Bergland AO. 2021. Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource. Molecular Biology and Evolution, 38(12):5782-5805. DOI: 10.1093/molbev/msab259
Guirao-Rico S, González J. 2021. Benchmarking the performance of Pool-seq SNP callers using simulated and real sequencing data. Molecular Ecology Resources, 21: 1216-1229. DOI: 10.1111/1755-0998.13343.
Bogaerts-Márquez M, Guirao-Rico S, Gautier M, González J. 2021. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Molecular Ecology, 30(4): 938-954. DOI: 10.1111/mec.15783
Salces-Ortiz J, Vargas-Chavez C, Guio L, Rech GE, González J. 2020. Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster. Philosophical Transactions of the Royal Society B: Biological Sciences, 375(1795):20190341. DOI:10.1098/rstb.2019.0341
Ruiz-Arenas C, Cáceres A, López M, Pelegrí-Sisó D, González J, González JR.2020. Identifying chromosomal subpopulations based on their recombination histories advances the study of the genetic basis of phenotypic traits. Genome Research, 30(12):1802-1814. DOI:10.1101/gr.258301.119
Kapun M, Barrón MG, Staubach F, Obbard DJ, Wiberg RAW, Vieira J, Goubert C, Rota-Stabelli O, Kankare M, Bogaerts-Márquez M, Haudry A, Waidele L, Kozeretska I, Pasyukova EG, Loeschcke V, Pascual M, Vieira CP, Serga S, Montchamp-Moreau C, Abbott J, Gibert P, Porcelli D, Posnien N, Sánchez-Gracia A, Grath S, Sucena É, Bergland AO, Guerreiro MPG, Onder BS, Argyridou E, Guio L, Schou MF, Deplancke B, Vieira C, Ritchie MG, Zwaan BJ, Tauber E, Orengo DJ, Puerma E, Aguadé M, Schmidt P, Parsch J, Betancourt AJ, Flatt T, González J. 2020. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Molecular Biology and Evolution, 37(9):2661–2678. DOI: 10.1093/molbev/msaa120
González JR, Ruiz-Arenas C, Cáceres A, Morán I, López-Sánchez M, Alonso L, Tolosana I, Guindo-Martínez M, Mercader JM, Esko T, Torrents D, González J, Pérez-Jurado LA. 2020. Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases. The American Journal of Human Genetics, 106(6):846–858. DOI: 10.1016/j.ajhg.2020.04.017
Bogaerts-Márquez M, Barrón MG, Fiston-Lavier AS, Vendrell-Mir P, Castanera R, Casacuberta JM, González J. 2020. T-lex3: An accurate tool to genotype and estimate population frequencies of transposable elements using the latest short-read whole genome sequencing data. Bioinformatics, 36(4):1191-1197. DOI:10.1093/bioinformatics/btz727
Almudi I, Vizueta J, Wyatt CDR, de Mendoza A, Marlétaz F, Firbas PN, Feuda R, Masiero G, Medina P, Alcaina-Caro A, Cruz F, Gómez-Garrido J, Gut M, Alioto TS, Vargas-Chavez C, Davie K, Misof B, González J, Aerts S, Lister R, Paps J, Rozas J, Sánchez-Gracia A, Irimia M, Maeso I, Casares F. 2020. Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings. Nature Communications, 11(1):1–11. DOI:10.1038/s41467-020-16284-8
Villanueva-Cañas JL, Horvath V, Aguilera L, González J. 2019. Diverse families of transposable elements affect the transcriptional regulation of stress-response genes in Drosophila melanogaster. Nucleic Acids Research, 47(13):6842-6857. DOI:10.1093/nar/gkz490
Rech GE, Bogaerts-Márquez M, Barrón MG, Merenciano M, Villanueva-Cañas JL, Horváth V, Fiston-Lavier AS, Luyten I, Venkataram S, Quesneville H, Petrov DA, González J. 2019. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLOS Genetics, 15(2). DOI:10.1371/journal.pgen.1007900
Merenciano M, Iacometti C, González J. 2019. A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster. Mobile DNA, 10(1):1-11. doi:10.1186/s13100-019-0152-9
Lerat E, Goubert C, Guirao-Rico S, Merenciano M, Dufour AB, Vieira C, González J. 2019. Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Molecular Ecology, 28(6):1506-1522. DOI:10.1111/mec.14963
Guirao-Rico S, González J. 2019. Evolutionary insights from large scale resequencing datasets in Drosophila melanogaster. Current Opinion in Insect Science, 31:70-76. DOI:10.1016/j.cois.2018.11.002
Guio L, González J. 2019. New insights on the evolution of genome content: Population dynamics of transposable elements in flies and humans. Methods in Molecular Biology, 1910:505-530. DOI:10.1007/978-1-4939-9074-0_16
Fablet M, Jacquet A, Rebollo R, Haudry A, Rey C, Salces-Ortiz J, Bajad P, Burlet N, Jantsch MF, Guerreiro MPG, Vieira C. 2019. Dynamic interactions between the genome and an endogenous retrovirus: Tirant in Drosophila simulans wild-type strains. G3: Genes, Genomes, Genetics, 9(3):855-865. DOI:10.1534/g3.118.200789
Barrón MG, Paupy C, Rahola N, Akone-Ella O, Ngangue MF, Wilson-Bahun TA, Pombi M, Kengne P, Costantini C, Simard F, González J, Ayala D. 2019. A new species in the major malaria vector complex sheds light on reticulated species evolution. Scientific Reports, 9(1):1-13. DOI:10.1038/s41598-019-49065-5.
Agostini RB, Postigo A, Rius SP, Rech GE, Campos-Bermudez VA, Vargas WA.2019. Long-lasting primed state in maize plants: Salicylic acid and steroid signaling pathways as key players in the early activation of immune responses in silks. Molecular Plant-Microbe Interactions, 32(1):90-106. DOI:10.1094/MPMI-07-18-0208-R
Mateo L, Rech GE, González J. 2018. Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations. Scientific Reports, 8(1):37-49. DOI:10.1038/s41598-018-34267-0
Li ZW, Hou XH, Chen JF, Xu YC, Wu Q, González J, Guo YL. Transposable elements contribute to the adaptation of arabidopsis thaliana. Genome Biology and Evolution. 2018;10(8):2140-2150. doi:10.1093/gbe/evy171
Guio L, Vieira C, González J. 2018. Stress affects the epigenetic marks added by natural transposable element insertions in Drosophila melanogaster. Scientific Reports, 8(1):1-10. DOI:10.1038/s41598-018-30491-w.
Villanueva-Cañas JL, Rech GE, de Cara MAR, González J. 2017. Beyond SNPs: how to detect selection on transposable element insertions. Methods in Ecology and Evolution, 8(6):728-737. DOI:10.1111/2041-210X.12781
Villanueva-Cañas JL, Ruiz-Orera J, Agea MI, Gallo M, Andreu D, Albà MM. 2017. New genes and functional innovation in mammals. Genome Biology and Evolution, 9(7):1886-1900. DOI:10.1093/gbe/evx136
Le Manh H, Guio L, Merenciano M, Rovira Q, Barrón MG, González J. 2017. Natural and laboratory mutations in kuzbanian are associated with zinc stress phenotypes in Drosophila melanogaster. Scientific Reports, 7:1-12. DOI:10.1038/srep42663
Horváth V, Merenciano M, González J. 2017. Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response. Trends in Genetics, 33(11):832-841. DOI:10.1016/j.tig.2017.08.007
Merenciano M, Ullastres A, de Cara MAR, Barrón MG, González J. 2016. Multiple Independent Retroelement Insertions in the Promoter of a Stress Response Gene Have Variable Molecular and Functional Effects in Drosophila. PLoS Genetics, 12(8):1-24. DOI:10.1371/journal.pgen.1006249
Bergland AO, Tobler R, González J, Schmidt P, Petrov D. 2016. Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster. Molecular Ecology, 25(5):1157-1174. DOI:10.1111/mec.13455
Ullastres A, Petit N, González J. 2015. Exploring the phenotypic space and the evolutionary history of a natural mutation in drosophila melanogaster. Molecular Biology and Evolution, 32(7):1800-1814. DOI:10.1093/molbev/msv061
Guio L, González J. 2015. The dominance effect of the adaptive transposable element insertion Bari-Jheh depends on the genetic background. Genome Biology and Evolution, 7(5):1260-1266. DOI:10.1093/gbe/evv071
González J, Martínez J, Makalowski W. 2015. Lack of population differentiation patterns of previously identified putatively adaptive transposable element insertions at microgeographic scales. Biology Direct, 10(1):1-6. DOI:10.1186/s13062-015-0075-4
Fiston-Lavier AS, Barrón MG, Petrov DA, González J. 2015. T-lex2: Genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data. Nucleic Acids Research, 43(4). DOI:10.1093/nar/gku1250
Ullastres A, Farré M, Capilla L, Ruiz-Herrera A. 2014. Unraveling the effect of genomic structural changes in the rhesus macaque - implications for the adaptive role of inversions. BMC Genomics, 15(1):1-13. DOI:10.1186/1471-2164-15-530
Mateo L, Ullastres A, González J. 2014. A Transposable Element Insertion Confers Xenobiotic Resistance in Drosophila. PLoS Genetics, 10(8). DOI:10.1371/journal.pgen.1004560
Mateo L, González J. 2014. Pogo-Like transposases have been repeatedly domesticated into CENP-B-Related Proteins. Genome Biology and Evolution, 6(8):2008-2016. DOI:10.1093/gbe/evu153
Guio L, Barrõn MG, González J. 2014. The transposable element Bari-Jheh mediates oxidative stress response in Drosophila. Molecular Ecology, 23(8):2020-2030. DOI:10.1111/mec.12711
Barrón MG, Fiston-Lavier AS, Petrov DA, González J. 2014. Population genomics of transposable elements in drosophila. Annual Review of Genetics, 48:561-581. DOI:10.1146/annurev-genet-120213-092359
Ayala D, Ullastres A, González J. 2014. Adaptation through chromosomal inversions in Anopheles. Frontiers in Genetics, 5(MAY):1-10. DOI:10.3389/fgene.2014.00129
Casacuberta E, González J. 2013. The impact of transposable elements in environmental adaptation. Molecular Ecology, 22(6):1503-1517. DOI:10.1111/mec.12170
Zhu Y, Bergland AO, González J, Petrov DA. 2012. Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PLoS ONE, 7(7):1-7. DOI:10.1371/journal.pone.0041901
González J, Petrov DA. 2012. Evolution of genome content: population dynamics of transposable elements in flies and humans. Methods in Molecular Biology 855: 361-383.