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For: Lerat E, Goubert C, Guirao‐Rico S, Merenciano M, Dufour A, Vieira C, González J. Population-specific dynamics and selection patterns of transposable element insertions in European natural populations. Mol Ecol 2019;28:1506-1522. [PMID: 30506554 PMCID: PMC6849870 DOI: 10.1111/mec.14963] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/30/2018] [Accepted: 11/05/2018] [Indexed: 01/02/2023]
Number Cited by Other Article(s)
1
Groza C, Chen X, Wheeler TJ, Bourque G, Goubert C. A unified framework to analyze transposable element insertion polymorphisms using graph genomes. Nat Commun 2024;15:8915. [PMID: 39414821 PMCID: PMC11484939 DOI: 10.1038/s41467-024-53294-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 10/02/2024] [Indexed: 10/18/2024]  Open
2
Kreiner JM, Hnatovska S, Stinchcombe JR, Wright SI. Quantifying the role of genome size and repeat content in adaptive variation and the architecture of flowering time in Amaranthus tuberculatus. PLoS Genet 2023;19:e1010865. [PMID: 38150485 PMCID: PMC10775983 DOI: 10.1371/journal.pgen.1010865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/09/2024] [Accepted: 12/11/2023] [Indexed: 12/29/2023]  Open
3
Yoth M, Maupetit-Méhouas S, Akkouche A, Gueguen N, Bertin B, Jensen S, Brasset E. Reactivation of a somatic errantivirus and germline invasion in Drosophila ovaries. Nat Commun 2023;14:6096. [PMID: 37773253 PMCID: PMC10541861 DOI: 10.1038/s41467-023-41733-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 09/15/2023] [Indexed: 10/01/2023]  Open
4
Goubert C. Assembly-Free Detection and Quantification of Transposable Elements with dnaPipeTE. Methods Mol Biol 2023;2607:25-43. [PMID: 36449156 DOI: 10.1007/978-1-0716-2883-6_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
5
ONT-Based Alternative Assemblies Impact on the Annotations of Unique versus Repetitive Features in the Genome of a Romanian Strain of Drosophila melanogaster. Int J Mol Sci 2022;23:ijms232314892. [PMID: 36499217 PMCID: PMC9741293 DOI: 10.3390/ijms232314892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/29/2022]  Open
6
Abondio P, Cilli E, Luiselli D. Inferring Signatures of Positive Selection in Whole-Genome Sequencing Data: An Overview of Haplotype-Based Methods. Genes (Basel) 2022;13:genes13050926. [PMID: 35627311 PMCID: PMC9141518 DOI: 10.3390/genes13050926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/16/2022]  Open
7
Rech GE, Radío S, Guirao-Rico S, Aguilera L, Horvath V, Green L, Lindstadt H, Jamilloux V, Quesneville H, González J. Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila. Nat Commun 2022;13:1948. [PMID: 35413957 PMCID: PMC9005704 DOI: 10.1038/s41467-022-29518-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 03/15/2022] [Indexed: 12/16/2022]  Open
8
Anderson SJ, Côté SD, Richard JH, Shafer ABA. Genomic architecture of phenotypic extremes in a wild cervid. BMC Genomics 2022;23:126. [PMID: 35151275 PMCID: PMC8841092 DOI: 10.1186/s12864-022-08333-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 01/24/2022] [Indexed: 12/30/2022]  Open
9
Said I, McGurk MP, Clark AG, Barbash DA. Patterns of piRNA Regulation in Drosophila Revealed through Transposable Element Clade Inference. Mol Biol Evol 2022;39:msab336. [PMID: 34921315 PMCID: PMC8788220 DOI: 10.1093/molbev/msab336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
10
Dal Grande F, Jamilloux V, Choisne N, Calchera A, Rolshausen G, Petersen M, Schulz M, Nilsson MA, Schmitt I. Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation. BIOLOGY 2021;11:biology11010024. [PMID: 35053022 PMCID: PMC8773270 DOI: 10.3390/biology11010024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 11/16/2022]
11
Ho EKH, Bellis ES, Calkins J, Adrion JR, Latta IV LC, Schaack S. Engines of change: Transposable element mutation rates are high and variable within Daphnia magna. PLoS Genet 2021;17:e1009827. [PMID: 34723969 PMCID: PMC8594854 DOI: 10.1371/journal.pgen.1009827] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 11/16/2021] [Accepted: 09/16/2021] [Indexed: 12/22/2022]  Open
12
Kozlowski DKL, Hassanaly‐Goulamhoussen R, Da Rocha M, Koutsovoulos GD, Bailly‐Bechet M, Danchin EGJ. Movements of transposable elements contribute to the genomic plasticity and species diversification in an asexually reproducing nematode pest. Evol Appl 2021;14:1844-1866. [PMID: 34295368 PMCID: PMC8288018 DOI: 10.1111/eva.13246] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 12/14/2022]  Open
13
Bleykasten-Grosshans C, Fabrizio R, Friedrich A, Schacherer J. Species-wide transposable element repertoires retrace the evolutionary history of the Saccharomyces cerevisiae host. Mol Biol Evol 2021;38:4334-4345. [PMID: 34115140 PMCID: PMC8476168 DOI: 10.1093/molbev/msab171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
14
Mérel V, Gibert P, Buch I, Rada VR, Estoup A, Gautier M, Fablet M, Boulesteix M, Vieira C. The worldwide invasion of Drosophila suzukii is accompanied by a large increase of transposable element load and a small number of putatively adaptive insertions. Mol Biol Evol 2021;38:4252-4267. [PMID: 34021759 PMCID: PMC8476158 DOI: 10.1093/molbev/msab155] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
15
Fabian DK, Dönertaş HM, Fuentealba M, Partridge L, Thornton JM. Transposable Element Landscape in Drosophila Populations Selected for Longevity. Genome Biol Evol 2021;13:6141024. [PMID: 33595657 PMCID: PMC8355499 DOI: 10.1093/gbe/evab031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 12/11/2022]  Open
16
Bogaerts‐Márquez M, Guirao‐Rico S, Gautier M, González J. Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster. Mol Ecol 2021;30:938-954. [PMID: 33350518 PMCID: PMC7986194 DOI: 10.1111/mec.15783] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
17
Gilbert C, Peccoud J, Cordaux R. Transposable Elements and the Evolution of Insects. ANNUAL REVIEW OF ENTOMOLOGY 2021;66:355-372. [PMID: 32931312 DOI: 10.1146/annurev-ento-070720-074650] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
18
Weilguny L, Vlachos C, Selvaraju D, Kofler R. Reconstructing the Invasion Route of the P-Element in Drosophila melanogaster Using Extant Population Samples. Genome Biol Evol 2020;12:2139-2152. [PMID: 33210145 PMCID: PMC7750958 DOI: 10.1093/gbe/evaa190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/06/2020] [Indexed: 12/19/2022]  Open
19
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. Genomic Analysis of European Drosophila melanogaster Populations Reveals Longitudinal Structure, Continent-Wide Selection, and Previously Unknown DNA Viruses. Mol Biol Evol 2020;37:2661-2678. [PMID: 32413142 PMCID: PMC7475034 DOI: 10.1093/molbev/msaa120] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
20
Rodrigues YK, Beldade P. Thermal Plasticity in Insects’ Response to Climate Change and to Multifactorial Environments. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00271] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
21
Ferchaud AL, Leitwein M, Laporte M, Boivin-Delisle D, Bougas B, Hernandez C, Normandeau É, Thibault I, Bernatchez L. Adaptive and maladaptive genetic diversity in small populations: Insights from the Brook Charr (Salvelinus fontinalis) case study. Mol Ecol 2020;29:3429-3445. [PMID: 33463857 DOI: 10.1111/mec.15566] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/13/2020] [Accepted: 07/16/2020] [Indexed: 12/12/2022]
22
Mohamed M, Dang NTM, Ogyama Y, Burlet N, Mugat B, Boulesteix M, Mérel V, Veber P, Salces-Ortiz J, Severac D, Pélisson A, Vieira C, Sabot F, Fablet M, Chambeyron S. A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells 2020;9:E1776. [PMID: 32722451 PMCID: PMC7465170 DOI: 10.3390/cells9081776] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/17/2022]  Open
23
Mérel V, Boulesteix M, Fablet M, Vieira C. Transposable elements in Drosophila. Mob DNA 2020;11:23. [PMID: 32636946 PMCID: PMC7334843 DOI: 10.1186/s13100-020-00213-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 04/14/2020] [Indexed: 12/25/2022]  Open
24
Salces-Ortiz J, Vargas-Chavez C, Guio L, Rech GE, González J. Transposable elements contribute to the genomic response to insecticides in Drosophila melanogaster. Philos Trans R Soc Lond B Biol Sci 2020;375:20190341. [PMID: 32075557 PMCID: PMC7061994 DOI: 10.1098/rstb.2019.0341] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
25
Vendrell-Mir P, Barteri F, Merenciano M, González J, Casacuberta JM, Castanera R. A benchmark of transposon insertion detection tools using real data. Mob DNA 2019;10:53. [PMID: 31892957 PMCID: PMC6937713 DOI: 10.1186/s13100-019-0197-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 12/17/2019] [Indexed: 02/01/2023]  Open
26
Relaxed purifying selection in autopolyploids drives transposable element over-accumulation which provides variants for local adaptation. Nat Commun 2019;10:5818. [PMID: 31862875 PMCID: PMC6925279 DOI: 10.1038/s41467-019-13730-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 11/21/2019] [Indexed: 11/28/2022]  Open
27
Wellenreuther M, Mérot C, Berdan E, Bernatchez L. Going beyond SNPs: The role of structural genomic variants in adaptive evolution and species diversification. Mol Ecol 2019;28:1203-1209. [PMID: 30834648 DOI: 10.1111/mec.15066] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 02/28/2019] [Indexed: 12/17/2022]
28
Merenciano M, Iacometti C, González J. A unique cluster of roo insertions in the promoter region of a stress response gene in Drosophila melanogaster. Mob DNA 2019;10:10. [PMID: 30911338 PMCID: PMC6415491 DOI: 10.1186/s13100-019-0152-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/28/2019] [Indexed: 01/19/2023]  Open
29
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. Stress response, behavior, and development are shaped by transposable element-induced mutations in Drosophila. PLoS Genet 2019;15:e1007900. [PMID: 30753202 PMCID: PMC6372155 DOI: 10.1371/journal.pgen.1007900] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 12/16/2018] [Indexed: 11/30/2022]  Open
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