Publications HAL du labo/EPI 104665;1002240

2023

Journal articles

titre
A chromosome-scale assembly of the quinoa genome provides insights into the structure and dynamics of its subgenomes
auteur
Elodie Rey, Peter Maughan, Florian Maumus, Daniel Lewis, Leanne Wilson, Juliana Fuller, Sandra Schmöckel, Eric Jellen, Mark Tester, David Jarvis
article
Communications Biology, 2023, 6 (1), pp.1263. ⟨10.1038/s42003-023-05613-4⟩
resume
Abstract Quinoa ( Chenopodium quinoa Willd.) is an allotetraploid seed crop with the potential to help address global food security concerns. Genomes have been assembled for four accessions of quinoa; however, all assemblies are fragmented and do not reflect known chromosome biology. Here, we use in vitro and in vivo Hi-C data to produce a chromosome-scale assembly of the Chilean accession PI 614886 (QQ74). The final assembly spans 1.326 Gb, of which 90.5% is assembled into 18 chromosome-scale scaffolds. The genome is annotated with 54,499 protein-coding genes, 96.9% of which are located on the 18 largest scaffolds. We also report an updated genome assembly for the B-genome diploid C. suecicum and use it, together with the A-genome diploid C. pallidicaule , to identify genomic rearrangements within the quinoa genome, including a large pericentromeric inversion representing 71.7% of chromosome Cq3B. Repetitive sequences comprise 65.2%, 48.6%, and 57.9% of the quinoa, C. pallidicaule , and C. suecicum genomes, respectively. Evidence suggests that the B subgenome is more dynamic and has expanded more than the A subgenome. These genomic resources will enable more accurate assessments of genome evolution within the Amaranthaceae and will facilitate future efforts to identify variation in genes underlying important agronomic traits in quinoa.
DOI
DOI : 10.1038/s42003-023-05613-4
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titre
Between but Not Within-Species Variation in the Distribution of Fitness Effects
auteur
Jennifer James, Chedly Kastally, Katharina B Budde, Santiago C. Gonzalez-Martinez, Pascal Milesi, Tanja Pyhäjärvi, Martin Lascoux, Paraskevi Alizoti, Ricardo Alía, Olivier Ambrosio, Filippos A Aravanopoulos, Georg von Arx, Audrey Albet, Francisco Auñón, Camilla Avanzi, Evangelia Avramidou, Francesca Bagnoli, Marko Bajc, Eduardo Ballesteros, Evangelos Barbas, José M García del Barrio, Cristina C Bastias, Catherine Bastien, Giorgia Beffa, Raquel Benavides, Vanina Benoit, Frédéric Bernier, Henri Bignalet, Guillaume Bodineau, Damien Bouic, Sabine Brodbeck, William Brunetto, Jurata Buchovska, Corinne Buret, Melanie Buy, Ana M Cabanillas-Saldaña, Bárbara Carvalho, Stephen Cavers, Fernando del Caño, Sandra Cervantes, Nicolas Cheval, José M Climent, Marianne Correard, Eva Cremer, Darius Danusevičius, Benjamin Dauphin, Jean-Luc Denou, Bernard Dokhelar, Alexis Ducousso, Bruno Fady, Patricia Faivre-Rampant, Anna-Maria Farsakoglou, Patrick Fonti, Ioannis Ganopoulos, Olivier Gilg, Nicolas de Girardi, René Graf, Alan Gray, Delphine Grivet, Felix Gugerli, Christoph Hartleitner, Katrin Heer, Enja Hollenbach, Agathe Hurel, Bernard Issenhuth, Florence Jean, Véronique Jorge, Arnaud Jouineau, Jan-Philipp Kappner, Robert Kesälahti, Florian Knutzen, Sonja T Kujala, Timo A Kumpula, Katri Kärkkäinen, Mariaceleste Labriola, Celine Lalanne, Johannes Lambertz, Gregoire Le-Provost, Vincent Lejeune, Isabelle Lesur-Kupin, Joseph Levillain, Mirko Liesebach, David López-Quiroga, Ermioni Malliarou, Jérémy Marchon, Nicolas Mariotte, Antonio Mas, Silvia Matesanz, Benjamin Meier, Helge Meischner, Célia Michotey, Sandro Morganti, Tor Myking, Daniel Nievergelt, Anne Eskild Nilsen, Eduardo Notivol, Dario I Ojeda, Sanna Olsson, Lars Opgenoorth, Geir Ostreng, Birte Pakull, Annika Perry, Sara Pinosio, Andrea Piotti, Christophe Plomion, Nicolas Poinot, Mehdi Pringarbe, Luc Puzos, Annie Raffin, José A Ramírez-Valiente, Christian Rellstab, Dourthe Remi, Oliver Reutimann, Sebastian Richter, Juan J Robledo-Arnuncio, Odile Rogier, Elisabet Martínez Sancho, Outi Savolainen, Simone Scalabrin, Volker Schneck, Silvio Schueler, Ivan Scotti, Sergio San Segundo, Vladimir Semerikov, Lenka Slámová, Ilaria Spanu, Jørn Henrik Sønstebø, Jean Thevenet, Mari Mette Tollefsrud, Norbert Turion, Fernando Valladares, Giovanni G Vendramin, Marc Villar, Marjana Westergren, Johan Westin
article
Molecular Biology and Evolution, 2023, 40 (11), ⟨10.1093/molbev/msad228⟩
resume
New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.
DOI
DOI : 10.1093/molbev/msad228
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https://hal.science/hal-04598142/file/James_et_al_2023_MBE.pdf BibTex
titre
SNP discovery by exome capture and resequencing in a pea genetic resource collection
auteur
Grégoire Aubert, Jonathan Kreplak, Magalie Leveugle, Hervé Duborjal, Anthony Klein, Karen Boucherot, Emilie Vieille, Marianne Chabert-Martinello, Corinne Cruaud, Virginie Bourion, Isabelle Lejeune-Hénaut, Marie-Laure Pilet-Nayel, Yanis Bouchenak-Khelladi, Nicolas Francillonne, Nadim Tayeh, Jean-Philippe Pichon, Nathalie Rivière, Judith Burstin
article
Peer Community In Genomics, 2023, 3, pp.art. e100. ⟨10.24072/pci.genomics.100237⟩
resume
Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tool
DOI
DOI : 10.24072/pci.genomics.100237
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https://hal.inrae.fr/hal-04267953/file/2023-270.pdf BibTex
titre
Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes
auteur
Baptiste Imbert, Jonathan Kreplak, Raphaël-Gauthier Flores, Grégoire Aubert, Judith Burstin, Nadim Tayeh
article
Frontiers in Artificial Intelligence, 2023, 6, pp.art. 1191122. ⟨10.3389/frai.2023.1191122⟩
resume
While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for di erent traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities o ered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.
DOI
DOI : 10.3389/frai.2023.1191122
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https://hal.inrae.fr/hal-04191716/file/2023-196.pdf BibTex
titre
Endogenous Caulimovirids: Fossils, Zombies, and Living in Plant Genomes
auteur
Héléna Vassilieff, Andrew Geering, Nathalie Choisne, Pierre-Yves Teycheney, Florian Maumus
article
Biomolecules, 2023, 13 (7), pp.1069. ⟨10.3390/biom13071069⟩
resume
The Caulimoviridae is a family of double-stranded DNA viruses that infect plants. The genomes of most vascular plants contain endogenous caulimovirids (ECVs), a class of repetitive DNA elements that is abundant in some plant genomes, resulting from the integration of viral DNA in the chromosomes of germline cells during episodes of infection that have sometimes occurred millions of years ago. In this review, we reflect on 25 years of research on ECVs that has shown that members of the Caulimoviridae have occupied an unprecedented range of ecological niches over time and shed light on their diversity and macroevolution. We highlight gaps in knowledge and prospects of future research fueled by increased access to plant genome sequence data and new tools for genome annotation for addressing the extent, impact, and role of ECVs on plant biology and the origin and evolutionary trajectories of the Caulimoviridae.
DOI
DOI : 10.3390/biom13071069
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titre
A secreted protease-like protein in Zymoseptoria tritici is responsible for avirulence on Stb9 resistance gene in wheat
auteur
Reda Amezrou, Colette Audéon, Jérôme Compain, Sandrine Gélisse, Aurélie Ducasse, Cyrille Saintenac, Nicolas Lapalu, Clémentine Louet, Simon Orford, Daniel Croll, Joëlle Amselem, Sabine Fillinger, Thierry Marcel
article
PLoS Pathogens, 2023, 19 (5), pp.e1011376. ⟨10.1371/journal.ppat.1011376⟩
resume
Zymoseptoria tritici is the fungal pathogen responsible for Septoria tritici blotch on wheat. Disease outcome in this pathosystem is partly determined by isolate-specific resistance, where wheat resistance genes recognize specific fungal factors triggering an immune response. Despite the large number of known wheat resistance genes, fungal molecular determinants involved in such cultivar-specific resistance remain largely unknown. We identified the avirulence factor AvrStb9 using association mapping and functional validation approaches. Pathotyping AvrStb9 transgenic strains on Stb9 cultivars, near isogenic lines and wheat mapping populations, showed that AvrStb9 interacts with Stb9 resistance gene, triggering an immune response. AvrStb9 encodes an unusually large avirulence gene with a predicted secretion signal and a protease domain. It belongs to a S41 protease family conserved across different filamentous fungi in the Ascomycota class and may constitute a core effector. AvrStb9 is also conserved among a global Z . tritici population and carries multiple amino acid substitutions caused by strong positive diversifying selection. These results demonstrate the contribution of an ‘atypical’ conserved effector protein to fungal avirulence and the role of sequence diversification in the escape of host recognition, adding to our understanding of host-pathogen interactions and the evolutionary processes underlying pathogen adaptation.
DOI
DOI : 10.1371/journal.ppat.1011376
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https://hal.inrae.fr/hal-04102220/file/journal.ppat.1011376.pdf BibTex
titre
SyntenyViewer: a comparative genomics-driven translational research tool
auteur
Raphael Flores, Cécile Huneau, Laura Burlot, Mathilde Lainé, Erik Kimmel, Cyril Pommier, Michael Alaux, Anne-Françoise Adam-Blondon, Caroline Pont, Hadi Quesneville, Jerome Salse
article
Database - The journal of Biological Databases and Curation, 2023, 2023, ⟨10.1093/database/baad027⟩
resume
SyntenyViewer is a public web-based tool relying on a relational database available at https://urgi.versailles.inrae.fr/synteny delivering comparative genomics data and associated reservoir of conserved genes between angiosperm species for both fundamental (evolutionary studies) and applied (translational research) applications. SyntenyViewer is made available for (i) providing comparative genomics data for seven major botanical families of flowering plants, (ii) delivering a robust catalog of 103 465 conserved genes between 44 species and inferred ancestral genomes, (iii) allowing us to investigate the evolutionary fate of ancestral genes and genomic regions in modern species through duplications, inversions, deletions, fusions, fissions and translocations, (iv) use as a tool to conduct translational research of key trait-related genes from model species to crops and (v) offering to host any comparative genomics data following simplified procedures and formats Database URL: https://urgi.versailles.inrae.fr/synteny
DOI
DOI : 10.1093/database/baad027
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https://hal.inrae.fr/hal-04099923/file/baad027.pdf BibTex
titre
Sidestepping Darwin: horizontal gene transfer from plants to insects
auteur
Clément Gilbert, Florian Maumus
article
Current Opinion in Insect Science, 2023, 57, pp.101035. ⟨10.1016/j.cois.2023.101035⟩
DOI
DOI : 10.1016/j.cois.2023.101035
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https://hal.inrae.fr/hal-04072018/file/MS_COIS_07-11-2023%20-%20HAL.pdf BibTex
titre
How genomics can help biodiversity conservation
auteur
Kathrin Theissinger, Carlos Fernandes, Giulio Formenti, Iliana Bista, Paul Berg, Christoph Bleidorn, Aureliano Bombarely, Angelica Crottini, Guido Gallo, José Godoy, Sissel Jentoft, Joanna Malukiewicz, Alice Mouton, Rebekah Oomen, Sadye Paez, Per Palsbøll, Christophe Pampoulie, María Ruiz-López, Simona Secomandi, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Erich Jarvis, Miklós Bálint, Claudio Ciofi, Robert Waterhouse, Camila Mazzoni, Jacob Höglund, Sargis Aghayan, Tyler Alioto, Isabel Almudi, Nadir Alvarez, Paulo Alves, Isabel Amorim Do Rosario, Agostinho Antunes, Paula Arribas, Petr Baldrian, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit Boštjančić, Bastien Boussau, Catherine Breton, Elena Buzan, Paula Campos, Carlos Carreras, L. Filipe C. Castro, Luis Chueca, Fedor Čiampor, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica Cunha, Frédéric Delsuc, Alice Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores Agius, Alice Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill Jakobsen, Peter Klinga, Agnieszka Kloch, Claudius Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Florian Maumus, Ann Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael Monaghan, Matteo Montagna, Robert Mysłajek, Marco Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja Vernes, Cristiano Vernesi, David Vieites, Christopher Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit
article
Trends in Genetics, 2023, ⟨10.1016/j.tig.2023.01.005⟩
resume
The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
DOI
DOI : 10.1016/j.tig.2023.01.005
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https://hal.inrae.fr/hal-04082874/file/How%2520genomics%2520can%2520help%2520biodiversity%2520conservation%25202023.pdf BibTex

2022

Journal articles

titre
CAULIFINDER: a pipeline for the automated detection and annotation of caulimovirid endogenous viral elements in plant genomes
auteur
Héléna Vassilieff, Sana Haddad, Véronique Jamilloux, Nathalie Choisne, Vikas Sharma, Delphine Giraud, Mariène Wan, Saad Serfraz, Andrew D. W. Geering, Pierre-Yves Teycheney, Florian Maumus
article
Mobile DNA, 2022, 13, pp.31. ⟨10.1186/s13100-022-00288-w⟩
resume
Plant, animal and protist genomes often contain endogenous viral elements (EVEs), which correspond to partial and sometimes entire viral genomes that have been captured in the genome of their host organism through a variety of integration mechanisms. While the number of sequenced eukaryotic genomes is rapidly increasing, the annotation and characterization of EVEs remains largely overlooked. EVEs that derive from members of the family Caulimoviridae are widespread across tracheophyte plants, and sometimes they occur in very high copy numbers. However, existing programs for annotating repetitive DNA elements in plant genomes are poor at identifying and then classifying these EVEs. Other than accurately annotating plant genomes, there is intrinsic value in a tool that could identify caulimovirid EVEs as they testify to recent or ancient host-virus interactions and provide valuable insights into virus evolution. In response to this research need, we have developed CAULIFINDER, an automated and sensitive annotation software package. CAULIFINDER consists of two complementary workflows, one to reconstruct, annotate and group caulimovirid EVEs in a given plant genome and the second to classify these genetic elements into officially recognized or tentative genera in the Caulimoviridae . We have benchmarked the CAULIFINDER package using the Vitis vinifera reference genome, which contains a rich assortment of caulimovirid EVEs that have previously been characterized using manual methods. The CAULIFINDER package is distributed in the form of a Docker image.
DOI
DOI : 10.1186/s13100-022-00288-w
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https://hal.inrae.fr/hal-03883611/file/s13100-022-00288-w.pdf BibTex
titre
Meeting the Challenges Facing Wheat Production: The Strategic Research Agenda of the Global Wheat Initiative
auteur
Peter Langridge, Michael Alaux, Nuno Felipe Almeida, Karim Ammar, Michael Baum, Faouzi Bekkaoui, Alison R Bentley, Brian L Beres, Bettina Berger, Hans-Joachim Braun, Gina Brown-Guedira, Christopher James Burt, Mario Jose Caccamo, Luigi Cattivelli, Gilles Charmet, Peter Civan, Sylvie Cloutier, Jean-Pierre Cohan, Pierre J Devaux, Fiona M Doohan, M. Fernanda Dreccer, Moha Ferrahi, Silvia E Germán, Stephen B Goodwin, Simon Griffiths, Carlos Guzmán, Hirokazu Handa, Malcolm John Hawkesford, Zhonghu He, Eric Huttner, Tatsuya M Ikeda, Benjamin Kilian, Ian Philip King, Julie King, John A Kirkegaard, Jacob Lage, Jacques Le Gouis, Suchismita Mondal, Ewen Mullins, Frank Ordon, Jose Ivan Ortiz-Monasterio, Hakan Özkan, İrfan Öztürk, Silvia A Pereyra, Curtis J Pozniak, Hadi Quesneville, Martín C Quincke, Greg John Rebetzke, Jochen Christoph Reif, Teresa Saavedra-Bravo, Ulrich Schurr, Shivali Sharma, Sanjay Kumar Singh, Ravi P Singh, John W Snape, Wuletaw Tadesse, Hisashi Tsujimoto, Roberto Tuberosa, Tim G Willis, Xueyong Zhang
article
Agronomy, 2022, 12 (11), pp.2767. ⟨10.3390/agronomy12112767⟩
resume
Wheat occupies a special role in global food security since, in addition to providing 20% of our carbohydrates and protein, almost 25% of the global production is traded internationally. The importance of wheat for food security was recognised by the Chief Agricultural Scientists of the G20 group of countries when they endorsed the establishment of the Wheat Initiative in 2011. The Wheat Initiative was tasked with supporting the wheat research community by facilitating collaboration, information and resource sharing and helping to build the capacity to address challenges facing production in an increasingly variable environment. Many countries invest in wheat research. Innovations in wheat breeding and agronomy have delivered enormous gains over the past few decades, with the average global yield increasing from just over 1 tonne per hectare in the early 1960s to around 3.5 tonnes in the past decade. These gains are threatened by climate change, the rapidly rising financial and environmental costs of fertilizer, and pesticides, combined with declines in water availability for irrigation in many regions. The international wheat research community has worked to identify major opportunities to help ensure that global wheat production can meet demand. The outcomes of these discussions are presented in this paper.
DOI
DOI : 10.3390/agronomy12112767
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https://hal.inrae.fr/hal-03942478/file/2022_Langridge-P_agronomy-12-02767%20%281%29.pdf BibTex
titre
Multiple Horizontal Acquisitions of Plant Genes in the Whitefly Bemisia tabaci
auteur
Clément Gilbert, Florian Maumus
article
Genome Biology and Evolution, 2022, 14 (10), ⟨10.1093/gbe/evac141⟩
resume
Abstract The extent to which horizontal gene transfer (HGT) has shaped eukaryote evolution remains an open question. Two recent studies reported four plant-like genes acquired through two HGT events by the whitefly Bemisia tabaci, a major agricultural pest (Lapadula WJ, Mascotti ML, Juri Ayub M. 2020. Whitefly genomes contain ribotoxin coding genes acquired from plants. Sci Rep. 10(1):15503; Xia J, et al. 2021. Whitefly hijacks a plant detoxification gene that neutralizes plant toxins. Cell 184(7):1693–1705 e1617.). Here, we uncovered a total of 49 plant-like genes deriving from at least 24 independent HGT events in the genome of the Middle East Asia Minor 1 (MEAM1) whitefly. Orthologs of these genes are present in three cryptic B. tabaci species, they are phylogenetically nested within plant sequences, they are expressed and have evolved under purifying selection. The predicted functions of these genes suggest that most of them are involved in plant–insect interactions. Thus, substantial plant-to-insect HGT may have facilitated the evolution of B. tabaci toward adaptation to a large host spectrum. Our study shows that eukaryote-to-eukaryote HGT may be relatively common in some lineages and it provides new candidate genes that may be targeted to improve current control strategies against whiteflies.
DOI
DOI : 10.1093/gbe/evac141
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https://hal.inrae.fr/hal-03846467/file/Gilbert_2022_HGTbemisia.pdf BibTex
titre
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
auteur
Robert Waterhouse, Anne-Françoise Adam-Blondon, Donat Agosti, Petr Baldrian, Bachir Balech, Erwan Corre, Robert Davey, Henrik Lantz, Graziano Pesole, Christian Quast, Frank Oliver Glöckner, Niels Raes, Anna Sandionigi, Monica Santamaria, Wouter Addink, Jiri Vohradsky, Amandine Nunes-Jorge, Nils Peder Willassen, Jerry Lanfear
article
F1000Research, 2022, 10, pp.1238. ⟨10.12688/f1000research.73825.2⟩
resume
Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth’s biodiversity.
DOI
DOI : 10.12688/f1000research.73825.2
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titre
Capturing Wheat Phenotypes at the Genome Level
auteur
Babar Hussain, Bala A Akpınar, Michael Alaux, Ahmed M Algharib, Deepmala Sehgal, Zulfiqar Ali, Gudbjorg I Aradottir, Jacqueline Batley, Arnaud Bellec, Alison R Bentley, Halise B Cagirici, Luigi Cattivelli, Frédéric Choulet, James Cockram, Francesca Desiderio, Pierre Devaux, Munevver Dogramaci, Gabriel Dorado, Susanne Dreisigacker, David Edwards, Khaoula El-Hassouni, Kellye Eversole, Tzion Fahima, Melania Figueroa, Sergio Gálvez, Kulvinder S Gill, Liubov Govta, Alvina Gul, Goetz Hensel, Pilar Hernandez, Leonardo Abdiel Crespo-Herrera, Amir Ibrahim, Benjamin Kilian, Viktor Korzun, Tamar Krugman, Yinghui Li, Shuyu Liu, Amer F Mahmoud, Alexey Morgounov, Tugdem Muslu, Faiza Naseer, Frank Ordon, Etienne Paux, Dragan Perovic, Gadi V P Reddy, Jochen Christoph Reif, Matthew Reynolds, Rajib Roychowdhury, Jackie Rudd, Taner Z Sen, Sivakumar Sukumaran, Bahar Sogutmaz Ozdemir, Vijay Kumar Tiwari, Naimat Ullah, Turgay Unver, Selami Yazar, Rudi Appels, Hikmet Budak
article
Frontiers in Plant Science, 2022, 13, ⟨10.3389/fpls.2022.851079⟩
resume
Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat ( Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence.
DOI
DOI : 10.3389/fpls.2022.851079
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titre
Recent Acquisition of Functional m6A RNA Demethylase Domain in Orchid Ty3/Gypsy Elements
auteur
Luis Alvarado-Marchena, Mireya Martínez-Pérez, Frederic Aparicio, Vicente Pallas, Florian Maumus
article
Frontiers in Plant Science, 2022, 13, ⟨10.3389/fpls.2022.939843⟩
resume
Long terminal repeats (LTR) retrotransposons are transposable elements (TEs) representing major components of most plant genomes. The fixation of additional conserved protein domains in their genomes is considered a rare event in the course of their evolution. Such changes can bring novel functions and increase their fitness by playing a role in the regulation of their replicative cycle or by affecting their integration landscape so that the detection of new domains can in turn reveal important aspects of host-TE interactions. We have mined angiosperm genomes for the presence of additional domains in LTR retrotransposons. We report a lineage of large (25 kbp) Gypsy-type elements in the genomes of Phalaenopsis orchids that contain an additional open reading frame containing a 2-ODD domain with close similarity to those responsible for m6A RNA demethylase activity in AlkB proteins. By performing in vitro assays, we demonstrate the RNA binding capability and the demethylase activity of the Gypsy-encoded AlkB protein, suggesting it could be functional against cognate TE mRNA or any cellular RNA in planta . In line with recent literature, we propose that the fixation of an RNA demethylase in this lineage of LTR retrotransposons may reflect an important role for epitranscriptomic control in host surveillance against TEs.
DOI
DOI : 10.3389/fpls.2022.939843
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titre
Health Education in Primary Schools: A Difficult Task
auteur
Philippe Masson, Michael Racodon, Alessandro Porrovecchio, Guillaume Duchateau
article
Central European Journal of Educational Research, 2022, 4 (1), pp.1-10. ⟨10.37441/cejer/2022/4/1/10735⟩
resume
This study was conducted in a medium-sized French city, in a neighbourhood falling into poverty, with children aged from 9 to 10 years old. Its aim is to build an adapted strategy to improve children’s healthy habits. Our study was based on a mixed methods interdisciplinary approach using interviews, questionnaires, sleep diaries and accelerometers. The unemployment rate of the target population is above 40%, and the families have four children on average. The children of the sample (N=29) practice less physical activity than recommended by the institutions in charge of health matters. The parents correctly manage the sleep cycles of their children, and stand firm when they have to go to school the next day. When the next day is a non-school day, children play more video games in the evening, both on their own and with their families. Healthy habits can be improved through cooperation with the various members of the educational community (parents, teachers and structures in charge of the children). Since it is difficult to manage health education solely during PE classes, this process must be continued both inside and outside school by the community, even more so the family.
DOI
DOI : 10.37441/cejer/2022/4/1/10735
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ELIXIR biovalidator for semantic validation of life science metadata
auteur
Isuru Liyanage, Tony Burdett, Bert Droesbeke, Karoly Erdos, Rolando Fernandez, Alasdair Gray, Muhammad Haseeb, Simon Jupp, Flavia Penim, Cyril Pommier, Philippe Rocca-Serra, Mélanie Courtot, Frederik Coppens
article
Bioinformatics, 2022, 38 (11), pp.3141-3142. ⟨10.1093/bioinformatics/btac195⟩
resume
Abstract Summary To advance biomedical research, increasingly large amounts of complex data need to be discovered and integrated. This requires syntactic and semantic validation to ensure shared understanding of relevant entities. This article describes the ELIXIR biovalidator, which extends the syntactic validation of the widely used AJV library with ontology-based validation of JSON documents. Availability and implementation Source code: https://github.com/elixir-europe/biovalidator, Release: v1.9.1, License: Apache License 2.0, Deployed at: https://www.ebi.ac.uk/biosamples/schema/validator/validate. Supplementary information Supplementary data are available at Bioinformatics online.
DOI
DOI : 10.1093/bioinformatics/btac195
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The era of reference genomes in conservation genomics
auteur
Florian Maumus, Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Claudio Ciofi, Angelica Crottini, José Godoy, Jacob Höglund, Joanna Malukiewicz, Alice Mouton, Rebekah Oomen, Sadye Paez, Per Palsbøll, Christophe Pampoulie, María Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Guojie Zhang, Camila Mazzoni, Erich Jarvis, Miklós Bálint, Giulio Formenti, Kathrin Theissinger, Carlos Fernandes, Iliana Bista, Aureliano Bombarely, Christoph Bleidorn, Fedor Čiampor, Claudio Ciofi, Angelica Crottini, José Godoy, Jacob Hoglund, Joanna Malukiewicz, Alice Mouton, Rebekah Oomen, Sadye Paez, Per Palsbøll, Christophe Pampoulie, María José Ruiz-López, Hannes Svardal, Constantina Theofanopoulou, Jan de Vries, Ann-Marie Waldvogel, Goujie Zhang, Camila Mazzoni, Erich Jarvis, Miklós Bálint, Sargis Aghayan, Tyler Alioto, Isabel Almudi, Nadir Alvarez, Paulo Alves, Isabel Amorim, Agostinho Antunes, Paula Arribas, Petr Baldrian, Paul Berg, Giorgio Bertorelle, Astrid Böhne, Andrea Bonisoli-Alquati, Ljudevit Boštjančić, Bastien Boussau, Catherine Breton, Elena Buzan, Paula Campos, Carlos Carreras, L. Filipe Castro, Luis Chueca, Elena Conti, Robert Cook-Deegan, Daniel Croll, Mónica Cunha, Frédéric Delsuc, Alice Dennis, Dimitar Dimitrov, Rui Faria, Adrien Favre, Olivier Fedrigo, Rosa Fernández, Gentile Francesco Ficetola, Jean-François Flot, Toni Gabaldón, Dolores Galea Agius, Guido Gallo, Alice Giani, M. Thomas P. Gilbert, Tine Grebenc, Katerina Guschanski, Romain Guyot, Bernhard Hausdorf, Oliver Hawlitschek, Peter Heintzman, Berthold Heinze, Michael Hiller, Martin Husemann, Alessio Iannucci, Iker Irisarri, Kjetill Jakobsen, Sissel Jentoft, Peter Klinga, Agnieszka Kloch, Claudius Kratochwil, Henrik Kusche, Kara K.S. Layton, Jennifer Leonard, Emmanuelle Lerat, Gianni Liti, Tereza Manousaki, Tomas Marques-Bonet, Pável Matos-Maraví, Michael Matschiner, Ann Mc Cartney, Shai Meiri, José Melo-Ferreira, Ximo Mengual, Michael Monaghan, Matteo Montagna, Robert Mysłajek, Marco Neiber, Violaine Nicolas, Marta Novo, Petar Ozretić, Ferran Palero, Lucian Pârvulescu, Marta Pascual, Octávio Paulo, Martina Pavlek, Cinta Pegueroles, Loïc Pellissier, Graziano Pesole, Craig Primmer, Ana Riesgo, Lukas Rüber, Diego Rubolini, Daniele Salvi, Ole Seehausen, Matthias Seidel, Simona Secomandi, Bruno Studer, Spyros Theodoridis, Marco Thines, Lara Urban, Anti Vasemägi, Adriana Vella, Noel Vella, Sonja Vernes, Cristiano Vernesi, David Vieites, Robert Waterhouse, Christopher Wheat, Gert Wörheide, Yannick Wurm, Gabrielle Zammit
article
Trends in Ecology & Evolution, 2022, 37 (3), pp.197-202. ⟨10.1016/j.tree.2021.11.008⟩
DOI
DOI : 10.1016/j.tree.2021.11.008
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Recommendations for the formatting of Variant Call Format (VCF) files to make plant genotyping data FAIR
auteur
Sebastian Beier, Anne Fiebig, Cyril Pommier, Isuru Liyanage, Matthias Lange, Paul Kersey, Stephan Weise, Richard Finkers, Baron Koylass, Timothee Cezard, Mélanie Courtot, Bruno Contreras-Moreira, Guy Naamati, Sarah Dyer, Uwe Scholz
article
F1000Research, 2022, 11, pp.231. ⟨10.12688/f1000research.109080.1⟩
resume
In this opinion article, we discuss the formatting of files from (plant) genotyping studies, in particular the formatting of (meta-) data in Variant Call Format (VCF) files. The flexibility of the VCF format specification facilitates its use as a generic interchange format across domains but can lead to inconsistency between files in the presentation of metadata. To enable fully autonomous machine actionable data flow, generic elements need to be further specified. We strongly support the merits of the FAIR principles and see the need to facilitate them also through technical implementation specifications. VCF files are an established standard for the exchange and publication of genotyping data. Other data formats are also used to capture variant call data (for example, the HapMap format and the gVCF format), but none currently have the reach of VCF. In VCF, only the sites of variation are described, whereas in gVCF, all positions are listed, and confidence values are also provided. For the sake of simplicity, we will only discuss VCF and our recommendations for its use. However, the part of the VCF standard relating to metadata (as opposed to the actual variant calls) defines a syntactic format but no vocabulary, unique identifier or recommended content. In practice, often only sparse (if any) descriptive metadata is included. When descriptive metadata is provided, proprietary metadata fields are frequently added that have not been agreed upon within the community which may limit long-term and comprehensive interoperability. To address this, we propose recommendations for supplying and encoding metadata, focusing on use cases from the plant sciences. We expect there to be overlap, but also divergence, with the needs of other domains.
DOI
DOI : 10.12688/f1000research.109080.1
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Breeding for Economically and Environmentally Sustainable Wheat Varieties: An Integrated Approach from Genomics to Selection
auteur
Etienne Paux, Stéphane Lafarge, François Balfourier, Jérémy Derory, Gilles Charmet, Michael Alaux, Geoffrey Perchet, Marion Bondoux, Frédéric Baret, Romain Barillot, Catherine Ravel, Pierre Sourdille, Jacques Le Gouis
article
Biology, 2022, 11 (1), pp.1-28. ⟨10.3390/biology11010149⟩
resume
There is currently a strong societal demand for sustainability, quality, and safety in bread wheat production. To address these challenges, new and innovative knowledge, resources, tools, and methods to facilitate breeding are needed. This starts with the development of high throughput genomic tools including single nucleotide polymorphism (SNP) arrays, high density molecular marker maps, and full genome sequences. Such powerful tools are essential to perform genome-wide association studies (GWAS), to implement genomic and phenomic selection, and to characterize the worldwide diversity. This is also useful to breeders to broaden the genetic basis of elite varieties through the introduction of novel sources of genetic diversity. Improvement in varieties particularly relies on the detection of genomic regions involved in agronomical traits including tolerance to biotic (diseases and pests) and abiotic (drought, nutrient deficiency, high temperature) stresses. When enough resolution is achieved, this can result in the identification of candidate genes that could further be characterized to identify relevant alleles. Breeding must also now be approached through in silico modeling to simulate plant development, investigate genotype × environment interactions, and introduce marker–trait linkage information in the models to better implement genomic selection. Breeders must be aware of new developments and the information must be made available to the world wheat community to develop new high-yielding varieties that can meet the challenge of higher wheat production in a sustainable and fluctuating agricultural context. In this review, we compiled all knowledge and tools produced during the BREEDWHEAT project to show how they may contribute to face this challenge in the coming years.
DOI
DOI : 10.3390/biology11010149
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titre
Transposable Elements in the Genome of the Lichen-Forming Fungus Umbilicaria pustulata and Their Distribution in Different Climate Zones along Elevation
auteur
Francesco Dal Grande, Véronique Jamilloux, Nathalie Choisne, Anjuli Calchera, Gregor Rolshausen, Malte Petersen, Meike Schulz, Maria Nilsson, Imke Schmitt
article
Biology, 2022, 11 (1), pp.24. ⟨10.3390/biology11010024⟩
resume
Transposable elements (TEs) are an important source of genome plasticity across the tree of life. Drift and natural selection are important forces shaping TE distribution and accumulation. Fungi, with their multifaceted phenotypic diversity and relatively small genome size, are ideal models to study the role of TEs in genome evolution and their impact on the host’s ecological and life history traits. Here we present an account of all TEs found in a high-quality reference genome of the lichen-forming fungus Umbilicaria pustulata, a macrolichen species comprising two climatic ecotypes: Mediterranean and cold temperate. We trace the occurrence of the newly identified TEs in populations along three elevation gradients using a Pool-Seq approach to identify TE insertions of potential adaptive significance. We found that TEs cover 21.26% of the 32.9 Mbp genome, with LTR Gypsy and Copia clades being the most common TEs. We identified 28 insertions displaying consistent insertion frequency differences between the two host ecotypes across the elevation gradients. Most of the highly differentiated insertions were located near genes, indicating a putative function. This pioneering study of the content and climate niche-specific distribution of TEs in a lichen-forming fungus contributes to understanding the roles of TEs in fungal evolution.
DOI
DOI : 10.3390/biology11010024
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Survival and growth of 711 forest tree taxa in eight French arbore-tums from three different climate regions
auteur
Catherine Ducatillion, Thierry Lamant, Richard Bellanger, Valentin Bouttier, Jean-Charles Bastien, Célia Michotey, Gautier Laurent, Bruno Fady, Brigitte Musch
article
Annals of Sylviculture Research, 2022, 47 (1), pp.30-38. ⟨10.12899/asr-2325⟩
resume
Arboretums have been used for decades for scientific, educational, horticultural and aesthetic purposes. Recently, climate change concerns have renewed the interest of the scientific community for these invaluable experimental forest systems. Here, we report a dataset from eight scientific arboretums planted in three contrasted French metropolitan bioclimates: Oceanic, Mountain and Mediterranean. In total, 92,236 trees were planted in 3,678 different plots. Originating from a worldwide range of ha-bitats, from sea-level up to 3,670 m in elevation, the collection spans 711 forest tree taxa (species, subspecies and varieties) from 177 genera. Taxa often include several geographic sources (so-called provenances), often simultaneously in different arboretums, making within species analyses possible. Cool-climate temperate Pinaceae (pines, firs, spruces, hemlocks, etc.) are well represented in the Atlantic and Mountain arboretums while Mediterranean arboretums are particularly rich with genera from the Myrtaceae (mostly eucalypts) and the Pinaceae (mostly pines). Data include survival, growth (height and diameter) and health status. Planted between 1969 and 1976, 338 taxa had survived at time of assessment and occurred as at least one individual in one plot. Data can be used to assess species suitability for ecological restoration and afforestation, and to help improve functional niche modelin
DOI
DOI : 10.12899/asr-2325
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Population-scale long-read sequencing uncovers transposable elements associated with gene expression variation and adaptive signatures in Drosophila
auteur
Gabriel Rech, Santiago Radío, Sara Guirao-Rico, Laura Aguilera, Vivien Horvath, Llewellyn Green, Hannah Lindstadt, Véronique Jamilloux, Hadi Quesneville, Josefa González
article
Nature Communications, 2022, 13 (1), pp.1-16. ⟨10.1038/s41467-022-29518-8⟩
resume
Abstract High quality reference genomes are crucial to understanding genome function, structure and evolution. The availability of reference genomes has allowed us to start inferring the role of genetic variation in biology, disease, and biodiversity conservation. However, analyses across organisms demonstrate that a single reference genome is not enough to capture the global genetic diversity present in populations. In this work, we generate 32 high-quality reference genomes for the well-known model species D. melanogaster and focus on the identification and analysis of transposable element variation as they are the most common type of structural variant. We show that integrating the genetic variation across natural populations from five climatic regions increases the number of detected insertions by 58%. Moreover, 26% to 57% of the insertions identified using long-reads were missed by short-reads methods. We also identify hundreds of transposable elements associated with gene expression variation and new TE variants likely to contribute to adaptive evolution in this species. Our results highlight the importance of incorporating the genetic variation present in natural populations to genomic studies, which is essential if we are to understand how genomes function and evolve.
DOI
DOI : 10.1038/s41467-022-29518-8
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titre
Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks
auteur
Agnès Baud, Mariène Wan, Danielle Nouaud, Nicolas Francillonne, Dominique Anxolabéhère, Hadi Quesneville
article
Peer Community Journal, 2022, 2, pp.e14. ⟨10.24072/pcjournal.68⟩
DOI
DOI : 10.24072/pcjournal.68
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Genome-Wide Screening of Transposable Elements in the Whitefly, Bemisia tabaci (Hemiptera: Aleyrodidae), Revealed Insertions with Potential Insecticide Resistance Implications
auteur
Marwa Zidi, Khouloud Klai, Johann Confais, Benoît Chénais, Aurore Caruso, Françoise Denis, Maha Khemakhem, Nathalie Casse
article
Insects, 2022, 13, pp.1-13. ⟨10.3390/insects13050396⟩
resume
Transposable elements (TEs) are genetically mobile units that move from one site to another within a genome. These units can mediate regulatory changes that can result in massive changes in genes expression. In fact, a precise identification of TEs can allow the detection of the mechanisms involving these elements in gene regulation and genome evolution. In the present study, a genome- wide analysis of the Hemipteran pest Bemisia tabaci was conducted using bioinformatics tools to identify, annotate and estimate the age of TEs, in addition to their insertion sites, within or near of the defensome genes involved in insecticide resistance. Overall, 1,292,393 TE copies were identified in the B. tabaci genome grouped into 4872 lineages. A total of 699 lineages were found to belong to Class I of TEs, 1348 belong to Class II, and 2825 were uncategorized and form the largest part of TEs (28.81%). The TE age estimation revealed that the oldest TEs invasion happened 14 million years ago (MYA) and the most recent occurred 0.2 MYA with the insertion of Class II TE elements. The analysis of TE insertion sites in defensome genes revealed 94 insertions. Six of these TE insertions were found within or near previously identified differentially expressed insecticide resistance genes. These insertions may have a potential role in the observed insecticide resistance in these pests.
DOI
DOI : 10.3390/insects13050396
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