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Chen X, Bourque G, Goubert C. Genotyping of Transposable Element Insertions Segregating in Human Populations Using Short-Read Realignments. Methods Mol Biol 2023; 2607:63-83. [PMID: 36449158 DOI: 10.1007/978-1-0716-2883-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Transposable element (TE) insertions are a major source of structural variation in the human genome. Due to the repetitive nature and biological importance of TEs, many bioinformatic tools have been developed to identify and genotype TE insertion polymorphisms using high-throughput short-reads. In this chapter, we outline recently developed methods to characterize TE insertion polymorphisms in human populations. We also provide detailed protocols to tackle this question primarily using three software: MELT2, ERVcaller, and TypeREF.
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Affiliation(s)
- Xun Chen
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan.
| | - Guillaume Bourque
- Institute for the Advanced Study of Human Biology (ASHBi), Kyoto University, Kyoto, Japan
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Human Genetics, McGill University, Montreal, QC, Canada
| | - Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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2
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Abstract
The detection and quantification of transposable elements (TE) are notoriously challenging despite their relevance in evolutionary genomics and molecular ecology. The main hurdle is caused by the dependence of numerous tools on genome assemblies, whose level of completion directly affects the comparability of the results across species or populations. dnaPipeTE, whose use is demonstrated here, tackles this issue by directly performing TE detection, classification, and quantification from unassembled short reads. This chapter details all the required steps to perform a comparative analysis of the TE content between two related species, starting from the installation of a recently containerized version of the program to the post-processing of the outputs.
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Affiliation(s)
- Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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Groza C, Bourque G, Goubert C. A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms. Methods Mol Biol 2023; 2607:85-94. [PMID: 36449159 DOI: 10.1007/978-1-0716-2883-6_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Pangenome graphs are flexible data structures that contain the genetic variation that exists in a population of genomes and describe the sequences of the many possible ensuing haplotypes. Here, we use such a pangenome graph to represent and genotype transposable element (TE) polymorphisms. By combining the transposable element annotation (Alus, L1s, and SVAs) of the human genome reference with novel transposable element insertions observed in two high-quality assemblies (HG002 and HG00733), we show how to create a transposable element pangenome that consists of ~1.2 million reference and 2939 non-reference transposable elements. We then demonstrate this approach by aligning short-read sequencing data and genotyping transposable element deletions and insertions with reasonable specificity and sensitivity (0.85 F1-score).
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Affiliation(s)
- Cristian Groza
- Quantitative Life Sciences, McGill University, Montreal, QC, Canada.
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan
- McGill Genome Centre, Montreal, QC, Canada
- Human Genetics, McGill University, Montreal, QC, Canada
| | - Clément Goubert
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.
- McGill Genome Centre, Montreal, QC, Canada.
- Human Genetics, McGill University, Montreal, QC, Canada.
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Barnada SM, Isopi A, Tejada-Martinez D, Goubert C, Patoori S, Pagliaroli L, Tracewell M, Trizzino M. Genomic features underlie the co-option of SVA transposons as cis-regulatory elements in human pluripotent stem cells. PLoS Genet 2022; 18:e1010225. [PMID: 35704668 PMCID: PMC9239442 DOI: 10.1371/journal.pgen.1010225] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/28/2022] [Accepted: 04/28/2022] [Indexed: 01/08/2023] Open
Abstract
Domestication of transposable elements (TEs) into functional cis-regulatory elements is a widespread phenomenon. However, the mechanisms behind why some TEs are co-opted as functional enhancers while others are not are underappreciated. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated, nearly half of which are human-specific. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we leveraged CRISPR-interference (CRISPRi), computational and functional genomics to elucidate the genomic features that underlie SVA domestication into human stem-cell gene regulation. We found that ~750 SVAs are co-opted as functional cis-regulatory elements in human induced pluripotent stem cells. These SVAs are significantly closer to genes and harbor more transcription factor binding sites than non-co-opted SVAs. We show that a long DNA motif composed of flanking YY1/2 and OCT4 binding sites is enriched in the co-opted SVAs and that these two transcription factors bind consecutively on the TE sequence. We used CRISPRi to epigenetically repress active SVAs in stem cell-like NCCIT cells. Epigenetic perturbation of active SVAs strongly attenuated YY1/OCT4 binding and influenced neighboring gene expression. Ultimately, SVA repression resulted in ~3,000 differentially expressed genes, 131 of which were the nearest gene to an annotated SVA. In summary, we demonstrated that SVAs modulate human gene expression, and uncovered that location and sequence composition contribute to SVA domestication into gene regulatory networks. SINE-VNTR-Alus (SVAs) are the youngest group of transposons in the human genome, where ~3,700 copies are annotated. Nearly half of the SVAs annotated in the human genome are exclusive to our species. Many studies indicate that SVAs are among the most frequently co-opted TEs in human gene regulation, but the mechanisms underlying such processes have not yet been thoroughly investigated. Here, we filled this knowledge-gap by focusing on human induced pluripotent stem cells (iPSCs) and on a pluripotent-like cell line (NCCITs). Through the analysis of histone marks, gene expression profiles, and by means of genome editing (CRISPR-interference), we identified ~750 SVAs that work as enhancers and promoters in human pluripotent cells, and characterized a mechanism for SVA co-option involving the transcription factors OCT4 and YY1. With our CRISPR approach, we demonstrated that repressing the 750 active SVAs leads to alteration in the expression of ~3,000 genes.
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Affiliation(s)
- Samantha M. Barnada
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Genetics, Genomics and Cancer Biology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Andrew Isopi
- Department of Microbiology and Immunology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Biochemistry and Molecular Pharmacology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Daniela Tejada-Martinez
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Clément Goubert
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Sruti Patoori
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Luca Pagliaroli
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Mason Tracewell
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- Biochemistry and Molecular Pharmacology PhD Program, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Conart C, Saclier N, Foucher F, Goubert C, Rius-Bony A, Paramita SN, Moja S, Thouroude T, Douady C, Sun P, Nairaud B, Saint-Marcoux D, Bahut M, Jeauffre J, Hibrand Saint-Oyant L, Schuurink RC, Magnard JL, Boachon B, Dudareva N, Baudino S, Caissard JC. Duplication and specialization of NUDX1 in Rosaceae led to geraniol production in rose petals. Mol Biol Evol 2022; 39:6505224. [PMID: 35022771 PMCID: PMC8857926 DOI: 10.1093/molbev/msac002] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nudix hydrolases are conserved enzymes ubiquitously present in all kingdoms of life. Recent research revealed that several Nudix hydrolases are involved in terpenoid metabolism in plants. In modern roses, RhNUDX1 is responsible for formation of geraniol, a major compound of rose scent. Nevertheless, this compound is produced by monoterpene synthases in many geraniol-producing plants. As a consequence, this raised the question about the origin of RhNUDX1 function and the NUDX1 gene evolution in Rosaceae, in wild roses or/and during the domestication process. Here, we showed that three distinct clades of NUDX1 emerged in the Rosoidae subfamily (Nudx1-1 to Nudx1-3 clades), and two subclades evolved in the Rosa genus (Nudx1-1a and Nudx1-1b subclades). We also showed that the Nudx1-1b subclade was more ancient than the Nudx1-1a subclade, and that the NUDX1-1a gene emerged by a trans-duplication of the more ancient NUDX1-1b gene. After the transposition, NUDX1-1a was cis-duplicated, leading to a gene dosage effect on the production of geraniol in different species. Furthermore, the NUDX1-1a appearance was accompanied by the evolution of its promoter, most likely from a Copia retrotransposon origin, leading to its petal-specific expression. Thus, our data strongly suggest that the unique function of NUDX1-1a in geraniol formation was evolved naturally in the genus Rosa before domestication.
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Affiliation(s)
- Corentin Conart
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Nathanaelle Saclier
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, F-69622, France
| | - Fabrice Foucher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Clément Goubert
- Department of Human Genetics, McGill University Genome Center, 740 Dr Penfield Ave, Montreal, Quebec, H3A 0G1, Canada
| | - Aurélie Rius-Bony
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Saretta N Paramita
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Sandrine Moja
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Tatiana Thouroude
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | - Christophe Douady
- Université Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5023, ENTPE, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés, Villeurbanne, F-69622, France.,Institut Universitaire de France, Paris, F-75005, France
| | - Pulu Sun
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Baptiste Nairaud
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Denis Saint-Marcoux
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Muriel Bahut
- Univ Angers, SFR QUASAV, Angers, F-49000, France
| | - Julien Jeauffre
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, Angers, F-49000, France
| | | | - Robert C Schuurink
- Green Life Sciences Research Cluster, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, Amsterdam, 1098 XH, The Netherlands
| | - Jean-Louis Magnard
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Benoît Boachon
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN, 47907, USA.,Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Sylvie Baudino
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
| | - Jean-Claude Caissard
- Université Lyon, Université Saint-Etienne, CNRS, UMR 5079, Laboratoire de Biotechnologies Végétales appliquées aux Plantes Aromatiques et Médicinales, Saint-Etienne, F-42023, France
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6
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Parisot N, Vargas-Chávez C, Goubert C, Baa-Puyoulet P, Balmand S, Beranger L, Blanc C, Bonnamour A, Boulesteix M, Burlet N, Calevro F, Callaerts P, Chancy T, Charles H, Colella S, Da Silva Barbosa A, Dell'Aglio E, Di Genova A, Febvay G, Gabaldón T, Galvão Ferrarini M, Gerber A, Gillet B, Hubley R, Hughes S, Jacquin-Joly E, Maire J, Marcet-Houben M, Masson F, Meslin C, Montagné N, Moya A, Ribeiro de Vasconcelos AT, Richard G, Rosen J, Sagot MF, Smit AFA, Storer JM, Vincent-Monegat C, Vallier A, Vigneron A, Zaidman-Rémy A, Zamoum W, Vieira C, Rebollo R, Latorre A, Heddi A. The transposable element-rich genome of the cereal pest Sitophilus oryzae. BMC Biol 2021; 19:241. [PMID: 34749730 PMCID: PMC8576890 DOI: 10.1186/s12915-021-01158-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 09/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND The rice weevil Sitophilus oryzae is one of the most important agricultural pests, causing extensive damage to cereal in fields and to stored grains. S. oryzae has an intracellular symbiotic relationship (endosymbiosis) with the Gram-negative bacterium Sodalis pierantonius and is a valuable model to decipher host-symbiont molecular interactions. RESULTS We sequenced the Sitophilus oryzae genome using a combination of short and long reads to produce the best assembly for a Curculionidae species to date. We show that S. oryzae has undergone successive bursts of transposable element (TE) amplification, representing 72% of the genome. In addition, we show that many TE families are transcriptionally active, and changes in their expression are associated with insect endosymbiotic state. S. oryzae has undergone a high gene expansion rate, when compared to other beetles. Reconstruction of host-symbiont metabolic networks revealed that, despite its recent association with cereal weevils (30 kyear), S. pierantonius relies on the host for several amino acids and nucleotides to survive and to produce vitamins and essential amino acids required for insect development and cuticle biosynthesis. CONCLUSIONS Here we present the genome of an agricultural pest beetle, which may act as a foundation for pest control. In addition, S. oryzae may be a useful model for endosymbiosis, and studying TE evolution and regulation, along with the impact of TEs on eukaryotic genomes.
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Affiliation(s)
- Nicolas Parisot
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Carlos Vargas-Chávez
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Present Address: Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Clément Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Rd, Ithaca, New York, 14853, USA
- Present Address: Human Genetics, McGill University, Montreal, QC, Canada
| | | | - Séverine Balmand
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Louis Beranger
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Caroline Blanc
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aymeric Bonnamour
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Nelly Burlet
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
| | - Federica Calevro
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Patrick Callaerts
- Department of Human Genetics, Laboratory of Behavioral and Developmental Genetics, KU Leuven, University of Leuven, B-3000, Leuven, Belgium
| | - Théo Chancy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Hubert Charles
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | - Stefano Colella
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: LSTM, Laboratoire des Symbioses Tropicales et Méditerranéennes, IRD, CIRAD, INRAE, SupAgro, Univ Montpellier, Montpellier, France
| | - André Da Silva Barbosa
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Elisa Dell'Aglio
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Alex Di Genova
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
- Instituto de Ciencias de la Ingeniería, Universidad de O'Higgins, Rancagua, Chile
| | - Gérard Febvay
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Toni Gabaldón
- Life Sciences, Barcelona Supercomputing Centre (BSC-CNS), Barcelona, Spain
- Mechanisms of Disease, Institute for Research in Biomedicine (IRB), Barcelona, Spain
- Institut Catalan de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Alexandra Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | | | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS UMR 5242, Lyon, France
| | - Emmanuelle Jacquin-Joly
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Justin Maire
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: School of BioSciences, The University of Melbourne, Parkville, VIC, 3010, Australia
| | | | - Florent Masson
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Global Health Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
| | - Camille Meslin
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Nicolas Montagné
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université de Paris, Institute of Ecology and Environmental Sciences of Paris, Versailles, France
| | - Andrés Moya
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain
| | | | - Gautier Richard
- IGEPP, INRAE, Institut Agro, Université de Rennes, Domaine de la Motte, 35653, Le Rheu, France
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA, USA
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France
- ERABLE European Team, INRIA, Rhône-Alpes, France
| | | | | | | | - Agnès Vallier
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Aurélien Vigneron
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
- Present Address: Department of Evolutionary Ecology, Institute for Organismic and Molecular Evolution, Johannes Gutenberg University, 55128, Mainz, Germany
| | - Anna Zaidman-Rémy
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Waël Zamoum
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, UMR5558, Université Lyon 1, Université Lyon, Villeurbanne, France.
- ERABLE European Team, INRIA, Rhône-Alpes, France.
| | - Rita Rebollo
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
| | - Amparo Latorre
- Institute for Integrative Systems Biology (I2SySBio), Universitat de València and Spanish Research Council (CSIC), València, Spain.
- Foundation for the Promotion of Sanitary and Biomedical Research of Valencian Community (FISABIO), València, Spain.
| | - Abdelaziz Heddi
- Univ Lyon, INSA Lyon, INRAE, BF2I, UMR 203, 69621 Villeurbanne, France.
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Goubert C, Zevallos NA, Feschotte C. Correction to ‘Contribution of unfixed transposable element insertions to human regulatory variation’. Philos Trans R Soc Lond B Biol Sci 2020; 375:20200084. [DOI: 10.1098/rstb.2020.0084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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8
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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: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatiotemporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterize variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.
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Affiliation(s)
- Martin Kapun
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Evolutionary Biology and Environmental Sciences, University of Zürich, Zürich, Switzerland
- Division of Cell and Developmental Biology, Medical University of Vienna, Vienna, Austria
| | - Maite G Barrón
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Fabian Staubach
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Darren J Obbard
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - R Axel W Wiberg
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
- Department of Environmental Sciences, Zoological Institute, University of Basel, Basel, Switzerland
| | - Jorge Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Clément Goubert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Omar Rota-Stabelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’ Adige, Italy
| | - Maaria Kankare
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
| | - María Bogaerts-Márquez
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Annabelle Haudry
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Lena Waidele
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary Biology and Ecology, University of Freiburg, Freiburg, Germany
| | - Iryna Kozeretska
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
- State Institution National Antarctic Scientific Center of Ministry of Education and Science of Ukraine, Kyiv, Ukraine
| | - Elena G Pasyukova
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genome Variation, Institute of Molecular Genetics of RAS, Moscow, Russia
| | - Volker Loeschcke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
| | - Marta Pascual
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Cristina P Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto de Biologia Molecular e Celular (IBMC), University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde (I3S), University of Porto, Porto, Portugal
| | - Svitlana Serga
- The European Drosophila Population Genomics Consortium (DrosEU)
- General and Medical Genetics Department, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Catherine Montchamp-Moreau
- The European Drosophila Population Genomics Consortium (DrosEU)
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Jessica Abbott
- The European Drosophila Population Genomics Consortium (DrosEU)
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patricia Gibert
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Damiano Porcelli
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Animal and Plant Sciences, Sheffield, United Kingdom
| | - Nico Posnien
- The European Drosophila Population Genomics Consortium (DrosEU)
- Johann-Friedrich-Blumenbach-Institut für Zoologie und Anthropologie, Universität Göttingen, Göttingen, Germany
| | - Alejandro Sánchez-Gracia
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Sonja Grath
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Élio Sucena
- The European Drosophila Population Genomics Consortium (DrosEU)
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
- Departamento de Biologia Animal, Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Alan O Bergland
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Virginia, Charlottesville, VA
| | - Maria Pilar Garcia Guerreiro
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Banu Sebnem Onder
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, Faculty of Science, Hacettepe University, Ankara, Turkey
| | - Eliza Argyridou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Lain Guio
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Mads Fristrup Schou
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Bioscience—Genetics, Ecology and Evolution, Aarhus University, Aarhus C, Denmark
- Section for Evolutionary Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Bart Deplancke
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Bio-engineering, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Cristina Vieira
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratoire de Biométrie et Biologie Evolutive UMR 5558, CNRS, Université Lyon 1, Université de Lyon, Villeurbanne, France
| | - Michael G Ritchie
- The European Drosophila Population Genomics Consortium (DrosEU)
- Centre for Biological Diversity, School of Biology, University of St. Andrews, St Andrews, Scotland
| | - Bas J Zwaan
- The European Drosophila Population Genomics Consortium (DrosEU)
- Laboratory of Genetics, Department of Plant Sciences, Wageningen University, Wageningen, Netherlands
| | - Eran Tauber
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
- Institute of Evolution, University of Haifa, Haifa, Israel
| | - Dorcas J Orengo
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Eva Puerma
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Montserrat Aguadé
- The European Drosophila Population Genomics Consortium (DrosEU)
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Paul Schmidt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Biology, University of Pennsylvania, Philadelphia, PA
| | - John Parsch
- The European Drosophila Population Genomics Consortium (DrosEU)
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Andrea J Betancourt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Evolution, Ecology, and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Thomas Flatt
- The European Drosophila Population Genomics Consortium (DrosEU)
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Josefa González
- The European Drosophila Population Genomics Consortium (DrosEU)
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
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9
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Goubert C, Thomas J, Payer LM, Kidd JM, Feusier J, Watkins WS, Burns KH, Jorde LB, Feschotte C. TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data. Nucleic Acids Res 2020; 48:e36. [PMID: 32067044 PMCID: PMC7102983 DOI: 10.1093/nar/gkaa074] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 01/08/2020] [Accepted: 02/11/2020] [Indexed: 12/12/2022] Open
Abstract
Alu retrotransposons account for more than 10% of the human genome, and insertions of these elements create structural variants segregating in human populations. Such polymorphic Alus are powerful markers to understand population structure, and they represent variants that can greatly impact genome function, including gene expression. Accurate genotyping of Alus and other mobile elements has been challenging. Indeed, we found that Alu genotypes previously called for the 1000 Genomes Project are sometimes erroneous, which poses significant problems for phasing these insertions with other variants that comprise the haplotype. To ameliorate this issue, we introduce a new pipeline - TypeTE - which genotypes Alu insertions from whole-genome sequencing data. Starting from a list of polymorphic Alus, TypeTE identifies the hallmarks (poly-A tail and target site duplication) and orientation of Alu insertions using local re-assembly to reconstruct presence and absence alleles. Genotype likelihoods are then computed after re-mapping sequencing reads to the reconstructed alleles. Using a high-quality set of PCR-based genotyping of >200 loci, we show that TypeTE improves genotype accuracy from 83% to 92% in the 1000 Genomes dataset. TypeTE can be readily adapted to other retrotransposon families and brings a valuable toolbox addition for population genomics.
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Affiliation(s)
- Clément Goubert
- Department of Molecular Biology and Genetics, 215 Tower Rd, Cornell University, Ithaca, NY 14853, USA
| | - Jainy Thomas
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Julie Feusier
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - W Scott Watkins
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, 215 Tower Rd, Cornell University, Ithaca, NY 14853, USA
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10
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Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, Smit AF. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci U S A 2020; 117:9451-9457. [PMID: 32300014 PMCID: PMC7196820 DOI: 10.1073/pnas.1921046117] [Citation(s) in RCA: 1042] [Impact Index Per Article: 260.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The accelerating pace of genome sequencing throughout the tree of life is driving the need for improved unsupervised annotation of genome components such as transposable elements (TEs). Because the types and sequences of TEs are highly variable across species, automated TE discovery and annotation are challenging and time-consuming tasks. A critical first step is the de novo identification and accurate compilation of sequence models representing all of the unique TE families dispersed in the genome. Here we introduce RepeatModeler2, a pipeline that greatly facilitates this process. This program brings substantial improvements over the original version of RepeatModeler, one of the most widely used tools for TE discovery. In particular, this version incorporates a module for structural discovery of complete long terminal repeat (LTR) retroelements, which are widespread in eukaryotic genomes but recalcitrant to automated identification because of their size and sequence complexity. We benchmarked RepeatModeler2 on three model species with diverse TE landscapes and high-quality, manually curated TE libraries: Drosophila melanogaster (fruit fly), Danio rerio (zebrafish), and Oryza sativa (rice). In these three species, RepeatModeler2 identified approximately 3 times more consensus sequences matching with >95% sequence identity and sequence coverage to the manually curated sequences than the original RepeatModeler. As expected, the greatest improvement is for LTR retroelements. Thus, RepeatModeler2 represents a valuable addition to the genome annotation toolkit that will enhance the identification and study of TEs in eukaryotic genome sequences. RepeatModeler2 is available as source code or a containerized package under an open license (https://github.com/Dfam-consortium/RepeatModeler, http://www.repeatmasker.org/RepeatModeler/).
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Affiliation(s)
- Jullien M Flynn
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | | | - Clément Goubert
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853
| | - Jeb Rosen
- Institute for Systems Biology, Seattle, WA 98109
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
| | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853;
| | - Arian F Smit
- Institute for Systems Biology, Seattle, WA 98109
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11
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Goubert C, Zevallos NA, Feschotte C. Contribution of unfixed transposable element insertions to human regulatory variation. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190331. [PMID: 32075552 PMCID: PMC7061991 DOI: 10.1098/rstb.2019.0331] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/09/2019] [Indexed: 12/11/2022] Open
Abstract
Thousands of unfixed transposable element (TE) insertions segregate in the human population, but little is known about their impact on genome function. Recently, a few studies associated unfixed TE insertions to mRNA levels of adjacent genes, but the biological significance of these associations, their replicability across cell types and the mechanisms by which they may regulate genes remain largely unknown. Here, we performed a TE-expression QTL analysis of 444 lymphoblastoid cell lines (LCL) and 289 induced pluripotent stem cells using a newly developed set of genotypes for 2743 polymorphic TE insertions. We identified 211 and 176 TE-eQTL acting in cis in each respective cell type. Approximately 18% were shared across cell types with strongly correlated effects. Furthermore, analysis of chromatin accessibility QTL in a subset of the LCL suggests that unfixed TEs often modulate the activity of enhancers and other distal regulatory DNA elements, which tend to lose accessibility when a TE inserts within them. We also document a case of an unfixed TE likely influencing gene expression at the post-transcriptional level. Our study points to broad and diverse cis-regulatory effects of unfixed TEs in the human population and underscores their plausible contribution to phenotypic variation. This article is part of a discussion meeting issue 'Crossroads between transposons and gene regulation'.
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Affiliation(s)
| | | | - Cédric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, 526 Campus Road, Ithaca, NY 14853, USA
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12
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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)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [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]
Abstract
Transposable elements (TEs) are ubiquitous sequences in genomes of virtually all species. While TEs have been investigated for several decades, only recently we have the opportunity to study their genome-wide population dynamics. Most of the studies so far have been restricted either to the analysis of the insertions annotated in the reference genome or to the analysis of a limited number of populations. Taking advantage of the European Drosophila population genomics consortium (DrosEU) sequencing data set, we have identified and measured the dynamics of TEs in a large sample of European Drosophila melanogaster natural populations. We showed that the mobilome landscape is population-specific and highly diverse depending on the TE family. In contrast with previous studies based on SNP variants, no geographical structure was observed for TE abundance or TE divergence in European populations. We further identified de novo individual insertions using two available programs and, as expected, most of the insertions were present at low frequencies. Nevertheless, we identified a subset of TEs present at high frequencies and located in genomic regions with a high recombination rate. These TEs are candidates for being the target of positive selection, although neutral processes should be discarded before reaching any conclusion on the type of selection acting on them. Finally, parallel patterns of association between the frequency of TE insertions and several geographical and temporal variables were found between European and North American populations, suggesting that TEs can be potentially implicated in the adaptation of populations across continents.
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Affiliation(s)
- Emmanuelle Lerat
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Clément Goubert
- Molecular Biology and GeneticsCornell UniversityIthacaNew York
| | - Sara Guirao‐Rico
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Miriam Merenciano
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
| | - Anne‐Béatrice Dufour
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie EvolutiveUMR 5558Université de Lyon, Université Lyon 1, CNRSVilleurbanneFrance
| | - Josefa González
- Institute of Evolutionary Biology (CSIC‐Universitat Pompeu Fabra)BarcelonaSpain
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13
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Feusier J, Witherspoon DJ, Scott Watkins W, Goubert C, Sasani TA, Jorde LB. Discovery of rare, diagnostic AluYb8/9 elements in diverse human populations. Mob DNA 2017; 8:9. [PMID: 28770012 PMCID: PMC5531096 DOI: 10.1186/s13100-017-0093-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/17/2017] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Polymorphic human Alu elements are excellent tools for assessing population structure, and new retrotransposition events can contribute to disease. Next-generation sequencing has greatly increased the potential to discover Alu elements in human populations, and various sequencing and bioinformatics methods have been designed to tackle the problem of detecting these highly repetitive elements. However, current techniques for Alu discovery may miss rare, polymorphic Alu elements. Combining multiple discovery approaches may provide a better profile of the polymorphic Alu mobilome. AluYb8/9 elements have been a focus of our recent studies as they are young subfamilies (~2.3 million years old) that contribute ~30% of recent polymorphic Alu retrotransposition events. Here, we update our ME-Scan methods for detecting Alu elements and apply these methods to discover new insertions in a large set of individuals with diverse ancestral backgrounds. RESULTS We identified 5,288 putative Alu insertion events, including several hundred novel AluYb8/9 elements from 213 individuals from 18 diverse human populations. Hundreds of these loci were specific to continental populations, and 23 non-reference population-specific loci were validated by PCR. We provide high-quality sequence information for 68 rare AluYb8/9 elements, of which 11 have hallmarks of an active source element. Our subfamily distribution of rare AluYb8/9 elements is consistent with previous datasets, and may be representative of rare loci. We also find that while ME-Scan and low-coverage, whole-genome sequencing (WGS) detect different Alu elements in 41 1000 Genomes individuals, the two methods yield similar population structure results. CONCLUSION Current in-silico methods for Alu discovery may miss rare, polymorphic Alu elements. Therefore, using multiple techniques can provide a more accurate profile of Alu elements in individuals and populations. We improved our false-negative rate as an indicator of sample quality for future ME-Scan experiments. In conclusion, we demonstrate that ME-Scan is a good supplement for next-generation sequencing methods and is well-suited for population-level analyses.
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Affiliation(s)
- Julie Feusier
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - David J. Witherspoon
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - W. Scott Watkins
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Clément Goubert
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Thomas A. Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Lynn B. Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
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14
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Minard G, Tran FH, Van VT, Goubert C, Bellet C, Lambert G, Kim KLH, Thuy THT, Mavingui P, Valiente Moro C. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives. Front Microbiol 2015; 6:970. [PMID: 26441903 PMCID: PMC4585046 DOI: 10.3389/fmicb.2015.00970] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/01/2015] [Indexed: 01/16/2023] Open
Abstract
The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.
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Affiliation(s)
- G Minard
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
| | - F H Tran
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
| | - Van Tran Van
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
| | - C Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, INRIA, VetAgro Sup Villeurbanne, France
| | - C Bellet
- Entente Interdépartementale Rhône-Alpes pour la Démoustication Chindrieux, France
| | - G Lambert
- Entente Interdépartementale de Démoustication du Littoral Méditerranéen Montpellier, France
| | - Khanh Ly Huynh Kim
- Department of Medical Entomology and Zoonotics, Pasteur Institute in Ho Chi Minh City Vietnam
| | - Trang Huynh Thi Thuy
- Department of Medical Entomology and Zoonotics, Pasteur Institute in Ho Chi Minh City Vietnam
| | - P Mavingui
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France ; Université de La Réunion, UMR PIMIT, INSERM U1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI Saint-Denis, France
| | - C Valiente Moro
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
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15
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Goubert C, Modolo L, Vieira C, ValienteMoro C, Mavingui P, Boulesteix M. De novo assembly and annotation of the Asian tiger mosquito (Aedes albopictus) repeatome with dnaPipeTE from raw genomic reads and comparative analysis with the yellow fever mosquito (Aedes aegypti). Genome Biol Evol 2015; 7:1192-205. [PMID: 25767248 PMCID: PMC4419797 DOI: 10.1093/gbe/evv050] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Repetitive DNA, including transposable elements (TEs), is found throughout eukaryotic genomes. Annotating and assembling the “repeatome” during genome-wide analysis often poses a challenge. To address this problem, we present dnaPipeTE—a new bioinformatics pipeline that uses a sample of raw genomic reads. It produces precise estimates of repeated DNA content and TE consensus sequences, as well as the relative ages of TE families. We shows that dnaPipeTE performs well using very low coverage sequencing in different genomes, losing accuracy only with old TE families. We applied this pipeline to the genome of the Asian tiger mosquito Aedes albopictus, an invasive species of human health interest, for which the genome size is estimated to be over 1 Gbp. Using dnaPipeTE, we showed that this species harbors a large (50% of the genome) and potentially active repeatome with an overall TE class and order composition similar to that of Aedes aegypti, the yellow fever mosquito. However, intraorder dynamics show clear distinctions between the two species, with differences at the TE family level. Our pipeline’s ability to manage the repeatome annotation problem will make it helpful for new or ongoing assembly projects, and our results will benefit future genomic studies of A. albopictus.
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Affiliation(s)
- Clément Goubert
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
| | - Laurent Modolo
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
| | - Claire ValienteMoro
- Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France
| | - Patrick Mavingui
- Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France Ecologie Microbienne, UMR 5557, CNRS, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Villeurbanne, France Université de La Réunion, UMR PIMIT, CNRS 9192, INSERM 1187, IRD 249
| | - Matthieu Boulesteix
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, INRIA, VetAgro Sup, Villeurbanne, France Université de Lyon 1, Villeurbanne, France Université de Lyon, Lyon, France
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Minard G, Tran FH, Van VT, Goubert C, Bellet C, Lambert G, Kim KLH, Thuy THT, Mavingui P, Valiente Moro C. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives. Front Microbiol 2015; 6:970. [PMID: 26441903 DOI: 10.3389/fmicb.2015.00970/abstract] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/01/2015] [Indexed: 05/19/2023] Open
Abstract
The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects.
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Affiliation(s)
- G Minard
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
| | - F H Tran
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
| | - Van Tran Van
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
| | - C Goubert
- Laboratoire de Biométrie et Biologie Evolutive, UMR 5558, CNRS, INRIA, VetAgro Sup Villeurbanne, France
| | - C Bellet
- Entente Interdépartementale Rhône-Alpes pour la Démoustication Chindrieux, France
| | - G Lambert
- Entente Interdépartementale de Démoustication du Littoral Méditerranéen Montpellier, France
| | - Khanh Ly Huynh Kim
- Department of Medical Entomology and Zoonotics, Pasteur Institute in Ho Chi Minh City Vietnam
| | - Trang Huynh Thi Thuy
- Department of Medical Entomology and Zoonotics, Pasteur Institute in Ho Chi Minh City Vietnam
| | - P Mavingui
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France ; Université de La Réunion, UMR PIMIT, INSERM U1187, CNRS 9192, IRD 249, Plateforme Technologique CYROI Saint-Denis, France
| | - C Valiente Moro
- Ecologie Microbienne, UMR Centre National de la Recherche Scientifique 5557, USC INRA 1364, VetAgro Sup, FR41 BioEnvironment and Health, Université Claude Bernard Lyon 1 Villeurbanne, France
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