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24 results on '"Flot, Jean-Francois"'

1. Champuru 2: Improved scoring of alignments and a user-friendly graphical interface

Author

Spöri, Yann and Flot, Jean-François

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Champuru is a web software tool that helps determine the two sequences present in mixed Sanger chromatograms obtained by sequencing simultaneously two DNA templates of unequal lengths. A previous version (Champuru 1.0) was published as a simple Perl CGI (Common Gateway Interface) application, but the server hosting it was discontinued, which prompted us to update it and develop it further. The new Champuru 2, implemented in Haxe and hosted at GitHub Pages, offers an improved graphical user interface as well as more sophisticated algorithms to compute alignment scores, making it more efficient at detecting the most likely alignment positions between forward and reverse traces. Champuru 2 now make it possible to analyze other offset pairs than the one detected as most likely by the selected algorithm. Champuru 2 is freely accessible at https://eeg-ebe.github.io/Champuru/, including both a graphical user interface (running a JavaScript version transpiled from the Haxe source code) and a compiled command-line version (obtained by transpiling the Haxe source code into C++)., Comment: 13 pages, 3 figures

Published
2024

3. Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs

Author

Limasset, Antoine, Flot, Jean-Francois, and Peterlongo, Pierre

Subjects
Computer Science - Data Structures and Algorithms, Quantitative Biology - Quantitative Methods
Abstract

Motivations Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large data sets or consider reads as mere suites of k-mers, without taking into account their full-length read information. Results We propose a new method to correct short reads using de Bruijn graphs, and implement it as a tool called Bcool. As a first st ep, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing from most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond. Availability and Implementation The implementation is open source and available at http://github.com/Malfoy/BCOOL under the Affero GPL license. Contact Antoine Limasset antoine.limasset@gmail.com & Jean-Fran\c{c}ois Flot jflot@ulb.ac.be & Pierre Peterlongo pierre.peterlongo@inria.fr, Comment: RECOMB SEQ 2018 Submission

Published
2017
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4. The era of reference genomes in conservation genomics

Author

Formenti, Giulio, Theissinger, Kathrin, Fernandes, Carlos, Bista, Iliana, Bombarely, Aureliano, Bleidorn, Christoph, Čiampor, Fedor, Ciofi, Claudio, Crottini, Angelica, Godoy, José A., Hoglund, Jacob, Malukiewicz, Joanna, Mouton, Alice, Oomen, Rebekah A., Paez, Sadye, Palsbøll, Per, Pampoulie, Christophe, Ruiz-López, María José, Svardal, Hannes, Theofanopoulou, Constantina, de Vries, Jan, Waldvogel, Ann-Marie, Zhang, Goujie, Mazzoni, Camila J., Jarvis, Erich, Bálint, Miklós, Aghayan, Sargis A., Alioto, Tyler S., Almudi, Isabel, Alvarez, Nadir, Alves, Paulo C., Amorim, Isabel R., Antunes, Agostinho, Arribas, Paula, Baldrian, Petr, Berg, Paul R., Bertorelle, Giorgio, Böhne, Astrid, Bonisoli-Alquati, Andrea, Boštjančić, Ljudevit L., Boussau, Bastien, Breton, Catherine M., Buzan, Elena, Campos, Paula F., Carreras, Carlos, Castro, L. FIlipe, Chueca, Luis J., Conti, Elena, Cook-Deegan, Robert, Croll, Daniel, Cunha, Mónica V., Delsuc, Frédéric, Dennis, Alice B., Dimitrov, Dimitar, Faria, Rui, Favre, Adrien, Fedrigo, Olivier D., Fernández, Rosa, Ficetola, Gentile Francesco, Flot, Jean-François, Gabaldón, Toni, Galea Agius, Dolores R., Gallo, Guido R., Giani, Alice M., Gilbert, M. Thomas P., Grebenc, Tine, Guschanski, Katerina, Guyot, Romain, Hausdorf, Bernhard, Hawlitschek, Oliver, Heintzman, Peter D., Heinze, Berthold, Hiller, Michael, Husemann, Martin, Iannucci, Alessio, Irisarri, Iker, Jakobsen, Kjetill S., Jentoft, Sissel, Klinga, Peter, Kloch, Agnieszka, Kratochwil, Claudius F., Kusche, Henrik, Layton, Kara K.S., Leonard, Jennifer A., Lerat, Emmanuelle, Liti, Gianni, Manousaki, Tereza, Marques-Bonet, Tomas, Matos-Maraví, Pável, Matschiner, Michael, Maumus, Florian, Mc Cartney, Ann M., Meiri, Shai, Melo-Ferreira, José, Mengual, Ximo, Monaghan, Michael T., Montagna, Matteo, Mysłajek, Robert W., Neiber, Marco T., Nicolas, Violaine, Novo, Marta, Ozretić, Petar, Palero, Ferran, Pârvulescu, Lucian, Pascual, Marta, Paulo, Octávio S., Pavlek, Martina, Pegueroles, Cinta, Pellissier, Loïc, Pesole, Graziano, Primmer, Craig R., Riesgo, Ana, Rüber, Lukas, Rubolini, Diego, Salvi, Daniele, Seehausen, Ole, Seidel, Matthias, Secomandi, Simona, Studer, Bruno, Theodoridis, Spyros, Thines, Marco, Urban, Lara, Vasemägi, Anti, Vella, Adriana, Vella, Noel, Vernes, Sonja C., Vernesi, Cristiano, Vieites, David R., Waterhouse, Robert M., Wheat, Christopher W., Wörheide, Gert, Wurm, Yannick, Zammit, Gabrielle, Höglund, Jacob, Palsbøll, Per J., Ruiz-López, María J., Zhang, Guojie, and Jarvis, Erich D.

Published
2022
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5. The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

Author

Mc Cartney, Ann M, primary, Formenti, Giulio, additional, Mouton, Alice, additional, Ciofi, Claudio, additional, Waterhouse, Robert M, additional, Mazzoni, Camila J, additional, De Panis, Diego, additional, Schlude Marins, Luisa S, additional, Leitao, Henrique G, additional, Diedericks, Genevieve, additional, Kirangwa, Joseph, additional, Morselli, Marco, additional, Salces, Judit, additional, Escudero, Nuria, additional, Iannucci, Alessio, additional, Natali, Chiara, additional, Svardal, Hannes, additional, Fernandez, Rosa, additional, De Pooter, Tim, additional, Joris, Geert, additional, Strazisar, Mojca, additional, Wood, Jo, additional, Herron, Katie E, additional, Seehausen, Ole, additional, Watts, Phillip C, additional, Shaw, Felix, additional, Davey, Robert P, additional, Minotto, Alice, additional, Fernandez Gonzalez, Jose Maria, additional, Bohne, Astrid, additional, Alegria, Carla, additional, Alioto, Tyler, additional, Alves, Paulo C, additional, Amorim, Isabel R, additional, Aury, Jean-Marc, additional, Backstrom, Niclas, additional, Baldrian, Petr, additional, Ballarin, Loriano, additional, Baltrunaite, Laima, additional, Barta, Endre, additional, BedHom, Bertrand, additional, Belser, Caroline, additional, Bergsten, Johannes, additional, Bertrand, Laurie, additional, Bilandija, Helena, additional, Binzer-Panchal, Mahesh, additional, Bista, Iliana, additional, Blaxter, Mark, additional, Borges, Paulo AV, additional, Borges Dias, Guilherme, additional, Bosse, Mirte, additional, Brown, Tom, additional, Bruggmann, Remy, additional, Buena-Atienza, Elena, additional, Burgin, Josephine, additional, Buzan, Elena, additional, Casadei, Nicolas, additional, Chiara, Matteo, additional, Chozas, Sergio, additional, Ciampor, Fedor F, additional, Crottini, Angelica, additional, Cruaud, Corinne, additional, Cruz, Fernando, additional, Dalen, Love, additional, De Biase, Alessio, additional, del Campo, Javier, additional, Delic, Teo, additional, Dennis, Alice B, additional, Derks, Martijn FL, additional, Diroma, Maria Angela, additional, Djan, Mihajla, additional, Duprat, Simone, additional, Eleftheriadi, Klara, additional, Feulner, Philine GD, additional, Flot, Jean-Francois, additional, Forni, Giobbe, additional, Fosso, Bruno, additional, Fournier, Pascal, additional, Fournier-Chambrillon, Christine, additional, Gabaldon, Toni, additional, Garg, Shilpa, additional, Gissi, Carmela, additional, Giupponi, Luca, additional, Gomez-Garrido, Jessica, additional, Gonzalez, Josefa, additional, Grilo, Miguel L, additional, Gruening, Bjoern, additional, Guerin, Thomas, additional, Guiglielmoni, Nadege, additional, Gut, Marta, additional, Haesler, Marcel P, additional, Hahn, Christoph, additional, Halpern, Balint, additional, Harrison, Peter, additional, Heintz, Julia, additional, Hindrikson, Maris, additional, Hoglund, Jacob, additional, Howe, Kerstin, additional, Hughes, Graham, additional, Istace, Benjamin, additional, Cock, Mark J., additional, Jancekovic, Franc, additional, Jonsson, Zophonias O, additional, Joye-Dind, Sagane, additional, Koskimaki, Janne J., additional, Krystufek, Boris, additional, Kubacka, Justyna, additional, Kuhl, Heiner, additional, Kusza, Szilvia, additional, Labadie, Karine, additional, Lahteenaro, Meri, additional, Lantz, Henrik, additional, Lavrinienko, Anton, additional, Leclere, Lucas, additional, Lopes, Ricardo Jorge, additional, Madsen, Ole, additional, Magdelenat, Ghislaine, additional, Magoga, Giulia, additional, Manousaki, Tereza, additional, Mappes, Tapio, additional, Marques, Joao Pedro, additional, Martinez Redondo, Gemma I, additional, Maumus, Florian, additional, Megens, Hendrik-Jan, additional, Melo-Ferreira, Jose, additional, Mendes, Sofia L, additional, Montagna, Matteo, additional, Moreno, Joao, additional, Mosbech, Mai-Britt, additional, Moura, Monica, additional, Musilova, Zuzana, additional, Myers, Eugene, additional, Nash, Will J., additional, Nater, Alexander, additional, Nicholson, Pamela, additional, Niell, Manuel, additional, Nijland, Reindert, additional, Noel, Benjamin, additional, Noren, Karin, additional, Oliveira, Pedro H, additional, Olsen, Remi-Andre, additional, Ometto, Lino, additional, Ossowski, Stephan, additional, Palinauskas, Vaidas, additional, Palsson, Snaebjorn, additional, Panibe, Jerome P, additional, Pauperio, Joana, additional, Pavlek, Martina, additional, Payen, Emilie, additional, Pawlowska, Julia, additional, Pellicer, Jaume, additional, Pesole, Graziano, additional, Pimenta, Joao, additional, Pippel, Martin, additional, Pirttila, Anna Maria, additional, Poulakakis, Nikos, additional, Rajan, Jeena, additional, Rego, Ruben MC, additional, Resendes, Roberto, additional, Resl, Philipp, additional, Riesgo, Ana, additional, Rodin-Morch, Patrik, additional, Soares, Andre ER, additional, Rodriguez Fernandes, Carlos, additional, Romeiras, Maria M., additional, Roxo, Guilherme, additional, Ruber, Lukas, additional, Ruiz-Lopez, Maria Jose, additional, Saarma, Urmas, additional, Silva, Luis P, additional, Sim-Sim, Manuela, additional, Soler, Lucile, additional, Sousa, Vitor C, additional, Sousa Santos, Carla, additional, Spada, Alberto, additional, Stefanovic, Milomir, additional, Steger, Viktor, additional, Stiller, Josefin, additional, Stock, Matthias, additional, Struck, Torsten Hugo H, additional, Sudasinghe, Hiranya, additional, Tapanainen, Riikka, additional, Tellgren-Roth, Christian, additional, Trindade, Helena, additional, Tukalenko, Yevhen, additional, Urso, Ilenia, additional, Vacherie, Benoit, additional, Van Belleghem, Steven M, additional, van Oers, Kees, additional, Vargas-Chavez, Carlos, additional, Velickovic, Nevena, additional, Vella, Noel, additional, Vella, Adriana, additional, Vernesi, Cristiano, additional, Vicente, Sara, additional, Villa, Sara, additional, Vinnere Pettersson, Olga, additional, Volckaert, Filip AM, additional, Voros, Judit, additional, Wincker, Patrick, additional, and Winkler, Sylke, additional

Published
2023
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11. Chromosomal assembly of the flat oyster (Ostrea edulis L.) genome as a new genetic resource for aquaculture

Author

Boutet, Isabelle, Monteiro, Homere J. Alves, Baudry, Lyam, Takeuchi, Takeshi, Bonnivard, Eric, Billoud, Bernard, Farhat, Sarah, Gonzales-Araya, Ricardo, Salaun, Benoit, Andersen, Ann C., Toullec, Jean-Yves, Lallier, Francois H., Flot, Jean-Francois, Guiglielmoni, Nadege, Guo, Ximing, Li, Cui, Allam, Bassem, Pales-Espinosa, Emmanuelle, Hemmer-Hansen, Jakob, Moreau, Pierrick, Marbouty, Martial, Koszul, Romain, Tanguy, Arnaud, Boutet, Isabelle, Monteiro, Homere J. Alves, Baudry, Lyam, Takeuchi, Takeshi, Bonnivard, Eric, Billoud, Bernard, Farhat, Sarah, Gonzales-Araya, Ricardo, Salaun, Benoit, Andersen, Ann C., Toullec, Jean-Yves, Lallier, Francois H., Flot, Jean-Francois, Guiglielmoni, Nadege, Guo, Ximing, Li, Cui, Allam, Bassem, Pales-Espinosa, Emmanuelle, Hemmer-Hansen, Jakob, Moreau, Pierrick, Marbouty, Martial, Koszul, Romain, and Tanguy, Arnaud

Abstract

The European flat oyster (Ostrea edulis L.) is a native bivalve of the European coasts. Harvest of this species has declined during the last decades because of the appearance of two parasites that have led to the collapse of the stocks and the loss of the natural oyster beds. O. edulis has been the subject of numerous studies in population genetics and on the detection of the parasites Bonamia ostreae and Marteilia refringens. These studies investigated immune responses to these parasites at the molecular and cellular levels. Several genetic improvement programs have been initiated especially for parasite resistance. Within the framework of a European project (PERLE 2) that aims to produce genetic lines of O. edulis with hardiness traits (growth, survival, resistance) for the purpose of repopulating natural oyster beds in Brittany and reviving the culture of this species in the foreshore, obtaining a reference genome becomes essential as done recently in many bivalve species of aquaculture interest. Here, we present a chromosome-level genome assembly and annotation for the European flat oyster, generated by combining PacBio, Illumina, 10X linked, and Hi-C sequencing. The finished assembly is 887.2 Mb with a scaffold-N50 of 97.1 Mb scaffolded on the expected 10 pseudochromosomes. Annotation of the genome revealed the presence of 35,962 protein-coding genes. We analyzed in detail the transposable element (TE) diversity in the flat oyster genome, highlighted some specificities in tRNA and miRNA composition, and provided the first insight into the molecular response of O. edulis to M. refringens. This genome provides a reference for genomic studies on O. edulis to better understand its basic physiology and as a useful resource for genetic breeding in support of aquaculture and natural reef restoration.

Published
2022

12. Genetic diversity, clonality and connectivity in the scleractinian coral Pocillopora damicornis: a multi-scale analysis in an insular, fragmented reef system

Author

Adjeroud, Mehdi, Guerecheau, Aurelie, Vidal-Dupiol, Jeremie, Flot, Jean-Francois, Arnaud-Haond, Sophie, and Bonhomme, Francois

Subjects
Corals -- Genetic aspects, Genetic research, Biological diversity -- Research, Biological sciences
Abstract

Clonality and genetic structure of the coral Pocillopora damicornis sensu lato were assessed using five microsatellites in 12 populations from four islands of the Society Archipelago (French Polynesia) sampled in June 2008. The 427 analysed specimens fell into 132 multilocus genotypes (MLGs), suggesting that asexual reproduction plays an important role in the maintenance of these populations. A haploweb analysis of ITS2 sequences of each MLG was consistent with all of them being conspecific. Genetic differentiation was detected both between and within islands, but when a single sample per MLG was included in the analyses, the populations turned out to be nearly panmictic. These observations provide further evidence of the marked variability in reproductive strategies and genetic structure of P. damicornis throughout its geographic range; comparison with results previously obtained for the congeneric species Pocillopora meandrina underlines the importance of life history traits in shaping the genetic structure of coral populations., Introduction Coral reefs are one of the most diverse ecosystems on Earth and provide goods and services to ~500 million people (Moberg and Folke 1999; Wilkinson 2008). However, in recent [...]

Published
2014
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13. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer Adineta vaga

Author

Simion, Paul, primary, Narayan, Jitendra, additional, Houtain, Antoine, additional, Derzelle, Alessandro, additional, Baudry, Lyam, additional, Nicolas, Emilien, additional, Arora, Rohan, additional, Cariou, Marie, additional, Cruaud, Corinne, additional, Gaudray, Florence Rodriguez, additional, Gilbert, Clément, additional, Guiglielmoni, Nadège, additional, Hespeels, Boris, additional, Kozlowski, Djampa K. L., additional, Labadie, Karine, additional, Limasset, Antoine, additional, Llirós, Marc, additional, Marbouty, Martial, additional, Terwagne, Matthieu, additional, Virgo, Julie, additional, Cordaux, Richard, additional, Danchin, Etienne G. J., additional, Hallet, Bernard, additional, Koszul, Romain, additional, Lenormand, Thomas, additional, Flot, Jean-Francois, additional, and Van Doninck, Karine, additional

Published
2021
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14. Chromosome-level genome assembly reveals homologous chromosomes and recombination in asexual rotifer .

Author

UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, UNamur - DRO_Centre de recherche Informatique et Droit (CRID), Simion, Paul, Narayan, Jitendra, Houtain, Antoine, Derzelle, Alessandro, Baudry, Lyam, Nicolas, Emilien, Arora, Rohan, Cariou, Marie, Cruaud, Corinne, Gaudray, Florence Rodriguez, Gilbert, Clément, Guiglielmoni, Nadège, Hespeels, Boris, Kozlowski, Djampa K L, Labadie, Karine, Limasset, Antoine, Llirós, Marc, Marbouty, Martial, Terwagne, Matthieu, Virgo, Julie, Cordaux, Richard, Danchin, Etienne G J, Hallet, Bernard, Koszul, Romain, Lenormand, Thomas, Flot, Jean-Francois, Van Doninck, Karine, UCL - SSH/IACS - Institute of Analysis of Change in Contemporary and Historical Societies, UNamur - DRO_Centre de recherche Informatique et Droit (CRID), Simion, Paul, Narayan, Jitendra, Houtain, Antoine, Derzelle, Alessandro, Baudry, Lyam, Nicolas, Emilien, Arora, Rohan, Cariou, Marie, Cruaud, Corinne, Gaudray, Florence Rodriguez, Gilbert, Clément, Guiglielmoni, Nadège, Hespeels, Boris, Kozlowski, Djampa K L, Labadie, Karine, Limasset, Antoine, Llirós, Marc, Marbouty, Martial, Terwagne, Matthieu, Virgo, Julie, Cordaux, Richard, Danchin, Etienne G J, Hallet, Bernard, Koszul, Romain, Lenormand, Thomas, Flot, Jean-Francois, and Van Doninck, Karine

Abstract

Bdelloid rotifers are notorious as a speciose ancient clade comprising only asexual lineages. Thanks to their ability to repair highly fragmented DNA, most bdelloid species also withstand complete desiccation and ionizing radiation. Producing a well-assembled reference genome is a critical step to developing an understanding of the effects of long-term asexuality and DNA breakage on genome evolution. To this end, we present the first high-quality chromosome-level genome assemblies for the bdelloid Adineta vaga, composed of six pairs of homologous (diploid) chromosomes with a footprint of paleotetraploidy. The observed large-scale losses of heterozygosity are signatures of recombination between homologous chromosomes, either during mitotic DNA double-strand break repair or when resolving programmed DNA breaks during a modified meiosis. Dynamic subtelomeric regions harbor more structural diversity (e.g., chromosome rearrangements, transposable elements, and haplotypic divergence). Our results trigger the reappraisal of potential meiotic processes in bdelloid rotifers and help unravel the factors underlying their long-term asexual evolutionary success

Published
2021

16. Advancing Genomics through the Global Invertebrate Genomics Alliance (GIGA)

Author

VOOLSTRA, CHRISTIAN ROBERT, Adamski, Marcin, Agrawal, Shobhit, Antunes, Agostinho, Aranda, Manuel, Baxevanis, Andy, Blaxter, Mark, Bosch, Thomas, Bracken-Grissom, Heather, Coddington, Jonathan, Collins, Timothy, Crandall, Keith, Dahl, Mikael, Distel, Daniel, Dunn, Casey, Eitel, Michael, Flot, Jean-Francois, Giribet, Gonzalo, Ghiselli, Fabrizio, Haddock, Steven H. D., Kocot, Kevin, Liew, Yi Jin, Majeske, Audrey, Misof, Bernhard, Mungal, Christopher, O'Brien, Stephen J., Ravasi, Timothy, de Freitas Rebelo, Mauro, Riesgo, Ana, Schnitzler, Christine, Schulze, Anja, Swalla, Billie, Tagu, Denis, Toonen, Robert, da Silva, Marcela Uliano, Vargas, Sergio, Zhou, Xin, Wörheide, Gert, Lopez, Jose V., Voolstra, Christian R., Adamski, Marcin, Agrawal, Shobhit, Antunes, Agostinho, Aranda, Manuel, Baxevanis, Andy, Blaxter, Mark, Bosch, Thoma, Bracken-Grissom, Heather, Coddington, Jonathan, Collins, Timothy, Crandall, Keith, Dahl, Mikael, Distel, Daniel, Dunn, Casey, Eitel, Michael, Flot, Jean-Francoi, Giribet, Gonzalo, Ghiselli, Fabrizio, Haddock, Steven H. D., Kocot, Kevin, Liew, Yi Jin, Majeske, Audrey, Misof, Bernhard, Mungal, Christopher, O'Brien, Stephen J., Ravasi, Timothy, de Freitas Rebelo, Mauro, Riesgo, Ana, Schnitzler, Christine, Schulze, Anja, Swalla, Billie, Tagu, Deni, Toonen, Robert, da Silva, Marcela Uliano, Vargas, Sergio, Zhou, Xin, Wã¶rheide, Gert, and Lopez, Jose V.

Subjects
0106 biological sciences, 0301 basic medicine, International research, Ecology, Evolution, media_common.quotation_subject, Collaborative network, Metazoa, Genomics, Biodiversity, Information repository, Biology, 010603 evolutionary biology, 01 natural sciences, Data science, Article, Giga, 03 medical and health sciences, 030104 developmental biology, Alliance, Promotion (rank), Genetic, Ecology, Evolution, Behavior and Systematics, Diversity (politics), media_common
Abstract

The Global Invertebrate Genomics Alliance (GIGA), a collaborative network of diverse scientists, marked its second anniversary with a workshop in Munich, Germany in 2015, where international attendees focused on discussing current progress, milestones and bioinformatics resources. The community determined the recruitment and training of talented researchers as one of the most pressing future needs and identified opportunities for network funding. GIGA also promotes future research efforts to prioritise taxonomic diversity and create new synergies. Here, we announce the generation of a central and simple data repository portal with a wide coverage of available sequence data, via the compagen platform, in parallel with more focused and specialised organism databases to globally advance invertebrate genomics. This article serves the objectives of GIGA by disseminating current progress and future prospects in the science of invertebrate genomics with the aim of promotion and facilitation of interdisciplinary and international research.

Published
2017

17. The house spider genome reveals an ancient whole-genome duplication during arachnid evolution

Author

Schwager, Evelyn E., Sharma, Prashant P., Clarke, Thomas, Leite, Daniel J., Wierschin, Torsten, Pechmann, Matthias, Akiyama-Oda, Yasuko, Esposito, Lauren, Bechsgaard, Jesper, Bilde, Trine, Buffry, Alexandra D., Chao, Hsu, Dinh, Huyen, Doddapaneni, HarshaVardhan, Dugan, Shannon, Eibner, Cornelius, Extavour, Cassandra G., Funch, Peter, Garb, Jessica, Gonzalez, Luis B., Gonzalez, Vanessa L., Griffiths-Jones, Sam, Han, Yi, Hayashi, Cheryl, Hilbrant, Maarten, Hughes, Daniel S. T., Janssen, Ralf, Lee, Sandra L., Maeso, Ignacio, Murali, Shwetha C., Muzny, Donna M., da Fonseca, Rodrigo Nunes, Paese, Christian L. B., Qu, Jiaxin, Ronshaugen, Matthew, Schomburg, Christoph, Schönauer, Anna, Stollewerk, Angelika, Torres-Oliva, Montserrat, Turetzek, Natascha, Vanthournout, Bram, Werren, John H., Wolff, Carsten, Worley, Kim C., Bucher, Gregor, Gibbs, Richard A., Coddington, Jonathan, Oda, Hiroki, Stanke, Mario, Ayoub, Nadia A., Prpic, Nikola-Michael, Flot, Jean-Francois, Posnien, Nico, Richards, Stephen, McGregor, Alistair P., Schwager, Evelyn E., Sharma, Prashant P., Clarke, Thomas, Leite, Daniel J., Wierschin, Torsten, Pechmann, Matthias, Akiyama-Oda, Yasuko, Esposito, Lauren, Bechsgaard, Jesper, Bilde, Trine, Buffry, Alexandra D., Chao, Hsu, Dinh, Huyen, Doddapaneni, HarshaVardhan, Dugan, Shannon, Eibner, Cornelius, Extavour, Cassandra G., Funch, Peter, Garb, Jessica, Gonzalez, Luis B., Gonzalez, Vanessa L., Griffiths-Jones, Sam, Han, Yi, Hayashi, Cheryl, Hilbrant, Maarten, Hughes, Daniel S. T., Janssen, Ralf, Lee, Sandra L., Maeso, Ignacio, Murali, Shwetha C., Muzny, Donna M., da Fonseca, Rodrigo Nunes, Paese, Christian L. B., Qu, Jiaxin, Ronshaugen, Matthew, Schomburg, Christoph, Schönauer, Anna, Stollewerk, Angelika, Torres-Oliva, Montserrat, Turetzek, Natascha, Vanthournout, Bram, Werren, John H., Wolff, Carsten, Worley, Kim C., Bucher, Gregor, Gibbs, Richard A., Coddington, Jonathan, Oda, Hiroki, Stanke, Mario, Ayoub, Nadia A., Prpic, Nikola-Michael, Flot, Jean-Francois, Posnien, Nico, Richards, Stephen, and McGregor, Alistair P.

Abstract

Background: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. Results: We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. Conclusions: Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Published
2017
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18. Substantial genetic mixing among sexual and androgenetic lineages within the clam genus Corbicula

Author

Vastrade, Martin, Etoundi, Emilie, Bournonville, Thibaut, Colinet, Mathilde, Debortoli, Nicolas, Hedtke, Shannon M., Nicolas, Emilien, Pigneur, Lise-Marie, Virgo, Julie, Flot, Jean-François, Marescaux, Jonathan, and Van Doninck, Karine

Subjects
Archaeology, CC1-960, Science
Abstract

“Occasional” sexuality occurs when a species combines clonal reproduction and genetic mixing. This strategy is predicted to combine the advantages of both asexuality and sexuality, but its actual consequences on the genetic diversity and species longevity are poorly understood. Androgenesis, a reproductive mode in which the offspring inherits its entire nuclear genome from the father, is often reported as a strictly clonal reproductive mode. Androgenesis is the predominant reproductive mode within the hermaphroditic, invasive lineages of the mollusk genus Corbicula. Their ability to reproduce clonally through androgenesis has been determinant in their invasive success, having colonized during the 20th century American and European freshwater systems, where they became notorious invaders with a widespread, global distribution. However, in androgenetic Corbicula clams, occasional genetic mixing between distinct lineages has also been observed when the sperm of one lineage fertilizes the oocyte of another one. Because of these occasional introgressions, the genetic relationships between Corbicula species remained unclear, and the biogeographic origins of the invasive androgenetic lineages have been challenging to identify. To address these issues, we analyzed the patterns of allele sharing for several nuclear and mitochondrial molecular markers among Corbicula individuals collected across both the native and invasive range. Our results show the occurrence of an allelic pool encompassing all Corbicula freshwater species worldwide, including sexual and androgenetic ones, which highlights the substantial genetic mixing within this genus. However, the differences in allele sharing patterns between invasive lineages, and the low diversity within each lineage, suggest recent, distinct biogeographic origins of invasive Corbicula androgenetic lineages. Finally, the polyploidy, high heterozygosity, and hybrid phenotypes and genotypes found in our study probably originated from hybridization events following egg parasitism between distinct Corbicula lineages. This extensive cross-lineage mixing found in Corbicula may generate nuclear diversity in an otherwise asexually reproducing species.

Published
2022
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19. Chromosome-level genome assembly and annotation of two lineages of the ant Cataglyphis hispanica: stepping stones towards genomic studies of hybridogenesis and thermal adaptation in desert ants

Author

Darras, Hugo, De Souza Araujo, Natalia, Baudry, Lyam, Guiglielmoni, Nadège, Lorite, Pedro, Marbouty, Martial, Rodriguez, Fernando, Arkhipova, Irina, Koszul, Romain, Flot, Jean-François, and Aron, Serge

Subjects
Archaeology, CC1-960, Science
Abstract

Cataglyphis are thermophilic ants that forage during the day when temperatures are highest and sometimes close to their critical thermal limit. Several Cataglyphis species have evolved unusual reproductive systems such as facultative queen parthenogenesis or social hybridogenesis, which have not yet been investigated in detail at the molecular level. We generated high-quality genome assemblies for two hybridogenetic lineages of the Iberian ant Cataglyphis hispanica using long-read Nanopore sequencing and exploited chromosome conformation capture (3C) sequencing to assemble contigs into 26 and 27 chromosomes, respectively. Further karyotype analyses confirm this difference in chromosome numbers between lineages; however, they also suggest it may not be fixed among lineages. We obtained transcriptomic data to assist gene annotation and built custom repeat libraries for each of the two assemblies. Comparative analyses with 19 other published ant genomes were also conducted. These new genomic resources pave the way for exploring the genetic mechanisms underlying the remarkable thermal adaptation and the molecular mechanisms associated with transitions between different genetic systems characteristic of the ant genus Cataglyphis.

Published
2022
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20. A deep dive into genome assemblies of non-vertebrate animals

Author

Guiglielmoni, Nadège, Rivera-Vicéns, Ramón, Koszul, Romain, and Flot, Jean-François

Subjects
Archaeology, CC1-960, Science
Abstract

Non-vertebrate species represent about 95% of known metazoan (animal) diversity. They remain to this day relatively unexplored genetically, but understanding their genome structure and function is pivotal for expanding our current knowledge of evolution, ecology and biodiversity. Following the continuous improvements and decreasing costs of sequencing technologies, many genome assembly tools have been released, leading to a significant amount of genome projects being completed in recent years. In this review, we examine the current state of genome projects of non-vertebrate animal species. We present an overview of available sequencing technologies, assembly approaches, as well as pre and post-processing steps, genome assembly evaluation methods, and their application to non-vertebrate animal genomes.

Published
2022
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21. Genomic evidence for ameiotic evolution in the bdelloid rotifer Adineta vaga

Author

Flot, Jean-Francois, Hespeels, Boris, Li, Xiang, Noel, Benjamin, Arkhipova, Irina R., Danchin, Etienne G. J., Hejno, Andreas, Henrissat, Bernard, Koszul, Romain, Aury, Jean-Marc, Barbe, Valerie, Barthelemy, Roxane-Marie, Bast, Jens, Bazykin, Georgii A., Chabrol, Olivier, Couloux, Arnaud, Da Rocha, Martine, Da Silva, Corinne, Gladyshev, Eugene A., Gouret, Philippe, Hallatschek, Oskar, Hecox-Lea, Bette, Labadie, Karine, Lejeune, Benjamin, Piskurek, Oliver, Poulain, Julie, Rodriguez, Fernando, Ryan, Joseph F., Vakhrusheva, Olga A., Wajnberg, Eric, Wirth, Benedicte, Yushenova, Irina A., Kellis, Manolis, Kondrashov, Alexey S., Mark Welch, David B., Pontarotti, Pierre, Weissenbach, Jean, Wincker, Patrick, Jaillon, Olivier, Van Doninck, Karine, Flot, Jean-Francois, Hespeels, Boris, Li, Xiang, Noel, Benjamin, Arkhipova, Irina R., Danchin, Etienne G. J., Hejno, Andreas, Henrissat, Bernard, Koszul, Romain, Aury, Jean-Marc, Barbe, Valerie, Barthelemy, Roxane-Marie, Bast, Jens, Bazykin, Georgii A., Chabrol, Olivier, Couloux, Arnaud, Da Rocha, Martine, Da Silva, Corinne, Gladyshev, Eugene A., Gouret, Philippe, Hallatschek, Oskar, Hecox-Lea, Bette, Labadie, Karine, Lejeune, Benjamin, Piskurek, Oliver, Poulain, Julie, Rodriguez, Fernando, Ryan, Joseph F., Vakhrusheva, Olga A., Wajnberg, Eric, Wirth, Benedicte, Yushenova, Irina A., Kellis, Manolis, Kondrashov, Alexey S., Mark Welch, David B., Pontarotti, Pierre, Weissenbach, Jean, Wincker, Patrick, Jaillon, Olivier, and Van Doninck, Karine

Abstract

© The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nature 500 (2013): 453–457, doi:10.1038/nature12326., Loss of sexual reproduction is considered an evolutionary dead end for metazoans, but bdelloid rotifers challenge this view as they appear to have persisted asexually for millions of years1. Neither male sex organs nor meiosis have ever been observed in these microscopic animals: oocytes are formed through mitotic divisions, with no reduction of chromosome number and no indication of chromosome pairing2. However, current evidence does not exclude that they may engage in sex on rare, cryptic occasions. Here we report the genome of a bdelloid rotifer, Adineta vaga (Davis, 1873)3, and show that its structure is incompatible with conventional meiosis. At gene scale, the genome of A. vaga is tetraploid and comprises both anciently duplicated segments and less divergent allelic regions. However, in contrast to sexual species, the allelic regions are rearranged and sometimes even found on the same chromosome. Such structure does not allow meiotic pairing; instead, we find abundant evidence of gene conversion, which may limit the accumulation of deleterious mutations in the absence of meiosis. Gene families involved in resistance to oxidation, carbohydrate metabolism and defence against transposons are significantly expanded, which may explain why transposable elements cover only 3% of the assembled sequence. Furthermore, 8% of the genes are likely to be of non-metazoan origin and were probably acquired horizontally. This apparent convergence between bdelloids and prokaryotes sheds new light on the evolutionary significance of sex., This work was supported by Genoscope-CES (where most of the sequencing was performed), by US National Science Foundation grants MCB-0821956 and MCB-1121334 to I.A., by German Research Foundation grant HA 5163/2-1 to O.H., by grant 11.G34.31.0008 fromthe Ministry of Education and Science of the Russian Federation to A.S.K., by grant NSF CAREER number 0644282 to M.K., by US National Science Foundation grant MCB-0923676 to D.B.M.W., by FRFC grant 2.4.655.09.F from the Belgian Fonds National de la Recherche Scientifique (FNRS) and a start-up grant from the University of Namur to K.V.D.; J.F.F. and K.V.D. thank also J.-P. Descy (University of Namur) for funding support.

Published
2013

23. The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

Author

Giribet, Gonzalo, Bracken-Grissom, Heather, Collins, Allen G., Collins, Timothy, Crandall, Keith, Distel, Daniel, Dunn, Casey, Haddock, Steven, Knowlton, Nancy, Martindale, Mark, Medina, Mónica, Messing, Charles, O'Brien, Stephen J., Paulay, Gustav, Putnam, Nicolas, Ravasi, Timothy, Rouse, Greg W., Ryan, Joseph F., Schulze, Anja, Wörheide, Gert, Adamska, Maja, Bailly, Xavier, Browne, William E., Diaz, M. Christina, Evans, Nathaniel, Flot, Jean-François, Gofarty, Nicole, Johnston, Matthew, Kamel, Bishoy, Kawahara, Akito Y., Laberge, Tammy, Lavrov, Dennis, Michonneau, François, Moroz, Leonid L., Oakley, Todd, Osborne, Karen, Pomponi, Shirley A., Rhodes, Adelaide, Rodriguez-Lanetty, Mauricio, Santos, Scott R., Thacker, Robert W., Van de Peer, Yves, Satoh, Nori, Voolstra, Christian R., Welch, David Mark, Winston, Judith, and Zhou, Xin

Subjects
biodiversity, comparative genomics, consortium, evolution, GIGA, invertebrates, metazoa
Abstract

Over 95% of all metazoan (animal) species comprise the “invertebrates,” but very few genomes from these organisms have been sequenced. We have, therefore, formed a “Global Invertebrate Genomics Alliance” (GIGA). Our intent is to build a collaborative network of diverse scientists to tackle major challenges (e.g., species selection, sample collection and storage, sequence assembly, annotation, analytical tools) associated with genome/transcriptome sequencing across a large taxonomic spectrum. We aim to promote standards that will facilitate comparative approaches to invertebrate genomics and collaborations across the international scientific community. Candidate study taxa include species from Porifera, Ctenophora, Cnidaria, Placozoa, Mollusca, Arthropoda, Echinodermata, Annelida, Bryozoa, and Platyhelminthes, among others. GIGA will target 7000 noninsect/nonnematode species, with an emphasis on marine taxa because of the unrivaled phyletic diversity in the oceans. Priorities for selecting invertebrates for sequencing will include, but are not restricted to, their phylogenetic placement; relevance to organismal, ecological, and conservation research; and their importance to fisheries and human health. We highlight benefits of sequencing both whole genomes (DNA) and transcriptomes and also suggest policies for genomic-level data access and sharing based on transparency and inclusiveness. The GIGA Web site (http://giga.nova.edu) has been launched to facilitate this collaborative venture., Organismic and Evolutionary Biology

Published
2013
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