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1. Near-chromosome level genome assembly of devil firefish, Pterois miles

Author

Kitsoulis, Christos V., Papadogiannis, Vasileios, Kristoffersen, Jon B., Kaitetzidou, Elisavet, Sterioti, Aspasia, Tsigenopoulos, Costas S., and Manousaki, Tereza

Subjects
Archaeology, CC1-960, Science
Abstract

Devil firefish (Pterois miles), a member of Scorpaenidae family, is one of the most successful marine non-native species, dominating around the world, that was rapidly spread into the Mediterranean Sea, through the Suez Canal, originating from the Indian Ocean. Even though lionfishes (Scorpaenidae) are identified among the most prosperous marine invaders, within this taxonomic group, the genomic resources are scant, while reference genome assemblies are totally absent. Here, we built and analyzed the first reference genome assembly of P. miles and explored its evolutionary background. The resulting genome assembly consisted of 660 contigs and scaffolds (N50 = 14,5 Mb) with a total size of about 902 Mb, while delivering 98% BUSCO completeness. We identified and described the large amount of transposable elements present in the genome and based on genomic data we constructed the first teleost phylogeny which includes a member of genus Pterois. The high-quality and contiguity de novo genome assembly built herein provides a valuable resource for future studies in species’ biology and ecology, lionfish phylogeny, the influence of transposable elements on the evolution of vertebrate genomes and fish toxins evolution.

Published
2023
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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. Genome analysis of Lagocephalus sceleratus: unraveling the genomic landscape of a successful invader

Author

Danis, Theodoros, primary, Papadogiannis, Vasilis, additional, Tsakogiannis, Alexandros, additional, Kristoffersen, Jon, additional, Golani, Daniel, additional, Tsaparis, Dimitris, additional, Sterioti, Aspasia, additional, Kasapidis, Panagiotis, additional, Kotoulas, Georgios, additional, Magoulas, Antonios, additional, Tsigenopoulos, Costas, additional, and Manousaki, Tereza, additional

Published
2024
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6. Extensive Loss and Gain of Conserved Noncoding Elements During Early Teleost Evolution.

Author

Iliopoulou, Elisavet, Papadogiannis, Vasileios, Tsigenopoulos, Costas S, and Manousaki, Tereza

Subjects
GENETIC regulation, GENETIC transcription regulation, BINDING sites, TRANSCRIPTION factors, EMBRYOLOGY, FISH genetics, COMPARATIVE genomics
Abstract

Conserved noncoding elements in vertebrates are enriched around transcription factor loci associated with development. However, loss and rapid divergence of conserved noncoding elements has been reported in teleost fish, albeit taking only few genomes into consideration. Taking advantage of the recent increase in high-quality teleost genomes, we focus on studying the evolution of teleost conserved noncoding elements, carrying out targeted genomic alignments and comparisons within the teleost phylogeny to detect conserved noncoding elements and reconstruct the ancestral teleost conserved noncoding elements repertoire. This teleost-centric approach confirms previous observations of extensive vertebrate conserved noncoding elements loss early in teleost evolution, but also reveals massive conserved noncoding elements gain in the teleost stem-group over 300 million years ago. Using synteny-based association to link conserved noncoding elements to their putatively regulated target genes, we show the most teleost gained conserved noncoding elements are found in the vicinity of orthologous loci involved in transcriptional regulation and embryonic development that are also associated with conserved noncoding elements in other vertebrates. Moreover, teleost and vertebrate conserved noncoding elements share a highly similar motif and transcription factor binding site vocabulary. We suggest that early teleost conserved noncoding element gains reflect a restructuring of the ancestral conserved noncoding element repertoire through both extreme divergence and de novo emergence. Finally, we support newly identified pan-teleost conserved noncoding elements have potential for accurate resolution of teleost phylogenetic placements in par with coding sequences, unlike ancestral only elements shared with spotted gar. This work provides new insight into conserved noncoding element evolution with great value for follow-up work on phylogenomics, comparative genomics, and the study of gene regulation evolution in teleosts. [ABSTRACT FROM AUTHOR]

Published
2024
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7. The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Author

Braasch, Ingo, Gehrke, Andrew R, Smith, Jeramiah J, Kawasaki, Kazuhiko, Manousaki, Tereza, Pasquier, Jeremy, Amores, Angel, Desvignes, Thomas, Batzel, Peter, Catchen, Julian, Berlin, Aaron M, Campbell, Michael S, Barrell, Daniel, Martin, Kyle J, Mulley, John F, Ravi, Vydianathan, Lee, Alison P, Nakamura, Tetsuya, Chalopin, Domitille, Fan, Shaohua, Wcisel, Dustin, Cañestro, Cristian, Sydes, Jason, Beaudry, Felix EG, Sun, Yi, Hertel, Jana, Beam, Michael J, Fasold, Mario, Ishiyama, Mikio, Johnson, Jeremy, Kehr, Steffi, Lara, Marcia, Letaw, John H, Litman, Gary W, Litman, Ronda T, Mikami, Masato, Ota, Tatsuya, Saha, Nil Ratan, Williams, Louise, Stadler, Peter F, Wang, Han, Taylor, John S, Fontenot, Quenton, Ferrara, Allyse, Searle, Stephen MJ, Aken, Bronwen, Yandell, Mark, Schneider, Igor, Yoder, Jeffrey A, Volff, Jean-Nicolas, Meyer, Axel, Amemiya, Chris T, Venkatesh, Byrappa, Holland, Peter WH, Guiguen, Yann, Bobe, Julien, Shubin, Neil H, Di Palma, Federica, Alföldi, Jessica, Lindblad-Toh, Kerstin, and Postlethwait, John H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Animals, Evolution, Molecular, Female, Fishes, Genome, Humans, Karyotype, Models, Genetic, Organ Specificity, Sequence Analysis, DNA, Transcriptome, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before teleost genome duplication (TGD). The slowly evolving gar genome has conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization and development (mediated, for example, by Hox, ParaHox and microRNA genes). Numerous conserved noncoding elements (CNEs; often cis regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles for such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses showed that the sums of expression domains and expression levels for duplicated teleost genes often approximate the patterns and levels of expression for gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes and the function of human regulatory sequences.

Published
2016

9. 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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10. How genomics can help biodiversity conservation

Author

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

Published
2023
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14. Sardines at a junction: Seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

Author

Antoniou, Aglaia, primary, Manousaki, Tereza, additional, Ramírez, Francisco, additional, Cariani, Alessia, additional, Cannas, Rita, additional, Kasapidis, Panagiotis, additional, Magoulas, Antonios, additional, Albo‐Puigserver, Marta, additional, Lloret‐Lloret, Elena, additional, Bellido, Jose Maria, additional, Pennino, Maria Grazia, additional, Follesa, Maria Cristina, additional, Esteban, Antonio, additional, Saraux, Claire, additional, Sbrana, Mario, additional, Spedicato, Maria Teresa, additional, Coll, Marta, additional, and Tsigenopoulos, Costas S., additional

Published
2023
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16. Chromosome genome assembly for the meagre, Argyrosomus regius, reveals species adaptations and sciaenid sex-related locus evolution

Author

Papadogiannis, Vasileios, primary, Manousaki, Tereza, additional, Nousias, Orestis, additional, Tsakogiannis, Alexandros, additional, Kristoffersen, Jon B., additional, Mylonas, Constantinos C., additional, Batargias, Costas, additional, Chatziplis, Dimitrios, additional, and Tsigenopoulos, Costas S., additional

Published
2023
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19. Building the Molecular Biodiversity Greece Community

Author

Aravanopoulos, Filippos A, Arvanitidis, Christos, Bista, Iliana, Dailianis, Thanos, Galanis, Alex, Ioannidis, Panagiotis, Kapli, Paschalia, Klapa, Maria I., Kolovos, Petros, Kotoulas, Georgios, Magoulas, Antonios N., Manousaki, Tereza, Pafilis, Evangelos, Papageorgiou, Aristotelis C., Papakostas, Spiros, Paragkamian, Savvas, Pavlidis, Pavlos, Pavloudi, Christina, Poulakakis, Nikos, Psomopoulos, Fotis, Reczko, Martin, Sagonas, Kostas, Stamatakis, Alexandros, Theofanopoulou, Constantina, Triantafyllidis, Alexandros, Tsigenopoulos, Costas S., Vasileiadou, Katerina, and Zafeiropoulos, Haris

Subjects
strategy document, molecular biodiversity, Greece, network of networks, community building
Abstract

In the face of the biodiversity crisis, concerted efforts towards understanding the effects of climate change and habitat loss and fragmentation, both locally and globally, are urgently needed. These are often attempted by leveraging the advances of modern genomics and bioinformatics methodologies. Especially in biodiversity hotspots, the need to understand, monitor and mitigate the loss of biodiversity is pivotal. Greece is a country with especially high endemism. A large percentage of its endemic species is threatened by climate change and human activities. To this end, the national academic community in biodiversity genomics has established a corresponding network of scientists from various Greek research institutes and universities covering different disciplines of biodiversity research. The network aims to support and combine individual actions to establish a Task Force that will channel the flow of information amongst researchers, policy makers, stakeholders and the local society. Our overarching goal is to build a sustainable community and infrastructure for the efficient management of the entire molecular biodiversity data cycle (i.e., from production and storage to the analysis and modelling of data, development of computational tools, and knowledge extraction). Using national and European infrastructures, such as ELIXIR and LifeWatch, we envision to set the ground for studying biodiversity through the lens of biodiversity genomics and offer evidence-based knowledge to guide management of the habitats and the biodiversity they host, as well as the implementation of appropriate policies.

Published
2022
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20. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish

Author

Pauletto, Marianna, Manousaki, Tereza, Ferraresso, Serena, Babbucci, Massimiliano, Tsakogiannis, Alexandros, Louro, Bruno, Vitulo, Nicola, Quoc, Viet Ha, Carraro, Roberta, Bertotto, Daniela, Franch, Rafaella, Maroso, Francesco, Aslam, Muhammad L., Sonesson, Anna K., Simionati, Barbara, Malacrida, Giorgio, Cestaro, Alessandro, Caberlotto, Stefano, Sarropoulou, Elena, Mylonas, Costantinos C., Power, Deborah M., Patarnello, Tomaso, Canario, Adelino V. M., Tsigenopoulos, Costas, and Bargelloni, Luca

Published
2018
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21. Genome Wide Association (GWAS) Analysis and genomic heritability for parasite resistance and growth in European seabass

Author

Oikonomou, Stavroula, primary, Kazlari, Zoi, additional, Papapetrou, Maria, additional, Papanna, Kantham, additional, Papaharisis, Leonidas, additional, Manousaki, Tereza, additional, Loukovitis, Dimitrios, additional, Dimitroglou, Arkadios, additional, Kottaras, Lefteris, additional, Gourzioti, Evgenia, additional, Pagonis, Charalampos, additional, Kostandis, Andreas, additional, Tsigenopoulos, Costas S., additional, and Chatziplis, Dimitiros, additional

Published
2022
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23. Genome Analysis of Lagocephalus sceleratus: Unraveling the Genomic Landscape of a Successful Invader

Author

Danis, Theodoros, primary, Papadogiannis, Vasileios, additional, Tsakogiannis, Alexandros, additional, Kristoffersen, Jon B., additional, Golani, Daniel, additional, Tsaparis, Dimitris, additional, Sterioti, Aspasia, additional, Kasapidis, Panagiotis, additional, Kotoulas, Georgios, additional, Magoulas, Antonios, additional, Tsigenopoulos, Costas S., additional, and Manousaki, Tereza, additional

Published
2021
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24. First linkage maps and a pilot QTL analysis for early growth performance in common dentex (Dentex dentex) and sharpsnout seabream (Diplodus puntazzo)

Author

Oikonomou, Stavroula, primary, Tsakogiannis, Alexandros, additional, Kriaridou, Christina, additional, Danis, Theodoros, additional, Manousaki, Tereza, additional, Chatziplis, Dimitris, additional, Papandroulakis, Nikos, additional, Mylonas, Constantinos C., additional, Triantafyllidis, Alexandros, additional, and Tsigenopoulos, Costas S., additional

Published
2021
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25. On the trail of detecting genetic (co)variation between resistance to parasite infections (Diplectanum aequans and Lernanthropus kroyeri) and growth in European seabass (Dicentrarchus labrax)

Author

Papapetrou, Maria, Kazlari, Zoi, Papaharisis, Leonidas, Oikonomou, Stavroula, Manousaki, Tereza, Loukovitis, Dimitrios, Kottaras, Lefteris, Dimitroglou, Arkadios, Gourzioti, Evgenia, Pagonis, Charalampos, Kostandis, Andreas, Tsigenopoulos, Costas S., and Chatziplis, Dimitrios

Subjects
Heritability, Selective breeding, Disease resistance, Parasite count, Dicentrarchus labrax, Genetic parameters
Abstract

The European seabass is one of the main commercial fish produced in Mediterranean marine aquaculture.Recently, its production has been negatively affected by losses due to frequent and recurring outbreaks ofparasitic, bacterial and viral diseases. In recent years, the gill parasites Diplectanum aequans and Lernanthropuskroyeri are increasingly becoming more dominant and contributing more significantly to the observed losses.Genetic improvement for disease resistance represents an important strategy for controlling infectious diseases infarmed fish by increasing their robustness. In order to determine the possibility of including such trait in selectivebreeding programs, we need to comprehend whether additive genetic variation for resistance against Diplectanum aequans and Lernanthropus kroyeri exists. For this purpose, two open-sea parasite cohabitation trials (for twoconsecutive years) were performed in the commercial production sites of a private company (Nireus S.A), thathad high infestation with Diplectanum aequans and Lernanthropus kroyeri. Juvenile European seabass (9425offspring from 91 full-sib and half-sib families per year), originating from the company’s breeding program wereequally divided into two groups and transferred to two commercial farming sites located in the areas of Nafpactosand Sagiada, in western Greece, for the intended cohabitation studies. The parasite numbers on all the gill archeswere counted and recorded at the end of the trials for the infestation levels. A third site (Palairos) without any parasite infestation was used as a control site. A multi-trait animal model was used to estimate the variance-covariance components and to evaluate the genetic parameters for Parasite Counts, recorded from all the gillarches of the fish, and their corresponding growth in sea cages. The estimated heritabilities for parasite count,using untransformed data, were 0.20 (D. aequans) and 0.28 (L. kroyeri) and for transformed data 0.29 and 0.26,respectively. The heritability estimates for body weight were 0.42−0.51 for D. aequans and 0.28−0.51 forL. kroyeri trials. Similarly, estimated heritabilities for the growth in sea cages were 0.43 and 0.29, respectively.Although parasite count has a low to medium unfavorable genetic correlation with body weight and growth (0.09−0.37), it seems that it is not significantly impairing selection for growth. Furthermore, the results of thisstudy are very promising in terms of the existing potential for genetic improvement of parasite resistance, andprovides a good basis for further genetic analysis using molecular markers.

Published
2021

26. Sardines at a junction: seascape genomics reveals ecological and oceanographic drivers of variation in the NW Mediterranean Sea

Author

Antoniou, Aglaia, primary, Manousaki, Tereza, additional, Ramírez, Francisco, additional, Cariani, Alessia, additional, Cannas, Rita, additional, Kasapidis, Panagiotis, additional, Magoulas, Antonios, additional, Albo-Puigserver, Marta, additional, Lloret-Lloret, Elena, additional, Bellido, Jose, additional, Pennino, Maria, additional, Follesa, Maria Cristina, additional, Esteban, Antonio, additional, Saraux, Claire, additional, Sbrana, Mario, additional, Spedicato, Maria, additional, Coll, Marta, additional, and Tsigenopoulos, Costas, additional

Published
2021
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27. 0s and 1s in marine molecular research: a regional HPC perspective

Author

Zafeiropoulos, Haris, primary, Gioti, Anastasia, additional, Ninidakis, Stelios, additional, Potirakis, Antonis, additional, Paragkamian, Savvas, additional, Angelova, Nelina, additional, Antoniou, Aglaia, additional, Danis, Theodoros, additional, Kaitetzidou, Eliza, additional, Kasapidis, Panagiotis, additional, Kristoffersen, Jon Bent, additional, Papadogiannis, Vasileios, additional, Pavloudi, Christina, additional, Ha, Quoc Viet, additional, Lagnel, Jacques, additional, Pattakos, Nikos, additional, Perantinos, Giorgos, additional, Sidirokastritis, Dimitris, additional, Vavilis, Panagiotis, additional, Kotoulas, Georgios, additional, Manousaki, Tereza, additional, Sarropoulou, Elena, additional, Tsigenopoulos, Costas S, additional, Arvanitidis, Christos, additional, Magoulas, Antonios, additional, and Pafilis, Evangelos, additional

Published
2021
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28. On the trail of detecting genetic (co)variation between resistance to parasite infections (Diplectanum aequans and Lernanthropus kroyeri) and growth in European seabass (Dicentrarchus labrax)

Author

Papapetrou, Maria, primary, Kazlari, Zoi, additional, Papanna, Kantham, additional, Papaharisis, Leonidas, additional, Oikonomou, Stavroula, additional, Manousaki, Tereza, additional, Loukovitis, Dimitrios, additional, Kottaras, Lefteris, additional, Dimitroglou, Arkadios, additional, Gourzioti, Evgenia, additional, Pagonis, Charalampos, additional, Kostandis, Andreas, additional, Tsigenopoulos, Costas S., additional, and Chatziplis, Dimitrios, additional

Published
2021
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30. The African coelacanth genome provides insights into tetrapod evolution

Author

Amemiya, Chris T., Alföldi, Jessica J, Lee, Alison P., Fan, Shaohua S, Philippe, Hervé H, MacCallum, Iain I, Braasch, Ingo I, Manousaki, Tereza T, Schneider, Igor I, Rohner, Nicolas N, Organ, Chris C, Chalopin, Domitille D, Smith, Jeramiah J., Robinson, Mark M, Dorrington, Rosemary A., Gerdol, Marco M, Aken, Bronwen B, Biscotti, Maria Assunta, Barucca, Marco M, Baurain, Denis D, Berlin, Aaron M., Blatch, Gregory L., Buonocore, Francesco F, Burmester, Thorsten T, Campbell, Michael S., Canapa, Adriana A, Cannon, John P., Christoffels, Alan A, De Moro, Gianluca G, Edkins, Adrienne L., Fan, Lin L, Fausto, Anna Maria, Feiner, Nathalie N, Forconi, Mariko M, Gamieldien, Junaid J, Gnerre, Sante S, Gnirke, Andreas A, Goldstone, Jared V., Haerty, Wilfried W, Hahn, Mark E., Hesse, Uljana U, Hoffmann, Steve S, Johnson, Jeremy J, Karchner, Sibel I., Kuraku, Shigehiro S, Lara, Marcia M, Levin, Joshua Z., Litman, Gary W., Mauceli, Evan E, Miyake, Tsutomu T, Mueller, Gail M., Nelson, David R., Nitsche, Anne A, Olmo, Ettore E, Ota, Tatsuya T, Pallavicini, Alberto A, Panji, Sumir S, Picone, Barbara B, Ponting, Chris P., Prohaska, Sonja J., Przybylski, Dariusz D, Saha, Nil Ratan, Ravi, Vydianathan V, Ribeiro, Filipe J., Sauka-Spengler, Tatjana T, Scapigliati, Giuseppe G, Searle, Stephen M. J., Sharpe, Ted T, Simakov, Oleg O, Stadler, Peter F., Stegeman, John J., Sumiyama, Kenta K, Tabbaa, Diana D, Tafer, Hakim H, Turner-Maier, Jason J, van Heusden, Peter P, White, Simon S, Williams, Louise L, Yandell, Mark M, Brinkmann, Henner H, Volff, Jean-Nicolas J, Tabin, Clifford J., Shubin, Neil N, Schartl, Manfred M, Jaffe, David B., Postlethwait, John H., Venkatesh, Byrappa B, Di Palma, Federica F, Lander, Eric S., Meyer, Axel A, and Lindblad-Toh, Kerstin K

Published
2013
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33. Building a high-quality reference genome assembly for the the eastern Mediterranean Sea invasive sprinter Lagocephalus sceleratus (Tetraodontiformes, Tetraodontidae)

Author

Danis, Theodoros, primary, Tsakogiannis, Alexandros, additional, Kristoffersen, Jon B., additional, Golani, Daniel, additional, Tsaparis, Dimitris, additional, Kasapidis, Panagiotis, additional, Kotoulas, Georgios, additional, Magoulas, Antonios, additional, Tsigenopoulos, Costas S., additional, and Manousaki, Tereza, additional

Published
2020
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34. Gearing Up for Warmer Times: Transcriptomic Response of Spongia officinalis to Elevated Temperatures Reveals Recruited Mechanisms and Potential for Resilience

Author

Koutsouveli, Vasiliki, primary, Manousaki, Tereza, additional, Riesgo, Ana, additional, Lagnel, Jacques, additional, Kollias, Spyros, additional, Tsigenopoulos, Costas S., additional, Arvanitidis, Christos, additional, Dounas, Costas, additional, Magoulas, Antonios, additional, and Dailianis, Thanos, additional

Published
2020
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36. PHYLOGENOMIC INVESTIGATION OF SPARIDS (TELEOSTEI: SPARIFORMES) USING HIGH QUALITY PROTEOMES HIGHLIGHTS THE IMPORTANCE OF TAXON SAMPLING

Author

Natsidis Paschalis, Tsakogiannis Alexandros, Pavlidis Pavlos, Tsigenopoulos Costas, and Manousaki Tereza

Abstract

Supplementary data for the Communications Biologymanuscript "Phylogenomic investigation of Sparidae (Teleostei: Spariformes) using high quality proteomes highlights the importance of taxon sampling". Contains all 31 used proteomes, allorthogroup fasta files andall four concatenated alignments used (twowith 31 species and two with14 species).

Published
2019
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38. Scanning of Genetic Variants and Genetic Mapping of Phenotypic Traits in Gilthead Sea Bream Through ddRAD Sequencing

Author

Kyriakis, Dimitrios, primary, Kanterakis, Alexandros, additional, Manousaki, Tereza, additional, Tsakogiannis, Alexandros, additional, Tsagris, Michalis, additional, Tsamardinos, Ioannis, additional, Papaharisis, Leonidas, additional, Chatziplis, Dimitris, additional, Potamias, George, additional, and Tsigenopoulos, Costas S., additional

Published
2019
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40. Discovery of genome-wide SNPs by ddRAD sequencing for two ectoparasites, Sparicotyle chrysophrii and Ceratothoa oestroides, that impact Mediterranean finfish culture

Author

Trumbić, Željka, Tsakogiannis, Alexandros, Manousaki, Tereza, Vrbatović, Anamarija, Taggart, John B., Rigos, Giorgos, Tsigenopoulos, Costas S., Mladineo, Ivona, and Mladineo, I.

Subjects
Sparicotyle chrysophrii, Ceratothoa oestroides, ddRAD, SNPs, aquaculture, wild-farmed transmission
Abstract

Interactions between wild and farmed fish, in the context of parasite transmission between populations, remain poorly understood. Wild fish may be drawn into the vicinity of farms through the presence of abundant food, provision of shelter or by signals from conspecifics and can serve as reservoirs of parasite transmission. Similarly, cultured stocks may act to amplify infectious stages in the environment, as they may be present in high numbers, be more susceptible to disease than wild fish and may accumulate higher parasite burdens due to intense rearing conditions. The monogenean Sparicotyle chrysophrii and the cymothoid isopod Ceratothoa oestroides have been identified as the most devastating ectoparasites in Mediterranean aquaculture, inflicting losses primarily in gilt head sea bream Sparus aurata and European sea bass Dicentrarchus labrax production. Their life cycles and modes of transmission have not been completely elucidated and molecular resources for their investigation are extremely scarce. In order to address this, we have used a genotyping- by-sequencing approach, double digest Restriction-site Associated DNA sequencing (ddRAD-Seq), to generate a genome-wide SNP marker dataset with the long term aim of investigating the degree of differentiation among individuals collected from farmed and wild hosts. Initial trials were conducted with S. chrysophrii and C. oestroides samples collected from Croatian and Greek farms. Two separate ddRAD libraries for S. chrysophrii and C. oestroides were constructed (96 and 138 samples in total), producing over 16 and 21 million reads with 26, 566 and 95, 697 unique RAD loci identified respectively. Considerable variability in number of reads, polymorphic loci and SNPs identified was observed between individuals for both species. SNPs genotyped in at least 50% of the individuals were identified (507 in S. chrysophrii and 1, 364 in C. oestroides) and used to compare the structure between samples currently available: wild and farmed S. chrysophrii and F1 and F2 offspring propagated in the laboratory for C. oestroides. The results provide a baseline for development of new ecological and biological studies of these species, using new genomic tools and resources, with important implications for aquaculture management and practice.

Published
2017

42. Biocluster: an NGS-dedicated HPC cluster in IMBBC, HCMR Upcoming Upgrade Usage/Partners Training

Author

Lagnel, Jacques, Manousaki, Tereza, Kotoulas, Georgios, Magoulas, Antonios, Hellenic Center for Marine Research (HCMR), and Hellenic Center for Marine Research (HCMR). GRC.

Subjects
analyse de données, Vegetal Biology, séquençage, metabarcoding, assemblage bioinformatique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, pipeline, analyse de séquences, analyse du transcriptome, analyse par cluster, Biologie végétale
Abstract

International audience; Modern biology is largely shaped by the development of next generation sequencing (NGS) technology. Researchers sequence massively model and non-model organisms from single cell transcriptomes, to whole genomes with applications that range from medicine up to ecology and conservation. However, the great challenge following the scaling up of sequencing throughput is data analysis. The amounts of data produced by NGS experiments require high computational power and cannot be analyzed in desktop computers. This fact underlines the need for HPC platforms that allow the analysis of high throughput data in reasonable timeframes. In IMBBC (HCMR), an HPC cluster named Biocluster has been built, dedicated to bioinformatics applications and NGS data analysis. Since 2010, when the cluster was first launched, we have been configuring it to accommodate more than 200 state-of-the-art pieces of software. On top of that, we have been developing parallelized pipelines for NGS data analysis with special focus on the challenges rising from sequencing non-model species. The parallelized pipelines include raw reads pre-preprocessing, gene annotation, variant discovery, population genetic analyses, metabarcoding analyses and others. Biocluster can accommodate all possible OMICS data schemes in an efficient and optimized way, allowing analyses for various experimental designs in a speed comparable to that of modern sequencing data production. The unprecedented collection of sequence analysis software and the availability of parallelized pipelines turn this platform to a unique bioinformatics tool. TMM-FPKM

Published
2016

43. Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Author

Braasch, Ingo, Gehrke, Andrew R., Smith, Jeramiah J., Kawasaki, Kazuhiko, Manousaki, Tereza, Pasquier, Jérémy, Amores, Angel, Desvignes, Thomas, Batzel, Peter, Catchen, Julian, Berlin, Aaron M., Campbell, Michael S., Barrell, Daniel, Martin, Kyle J., Mulley, John F., Ravi, Vydianathan, Lee, Alison P., Nakamura, Tetsuya, Chalopin, Domitille, Fan, Shaohua, Wcisel, Dustin, Cañestro, Cristian, Sydes, Jason, Beaudry, Felix E.G., Sun, Yi, Hertel, Jana, Beam, Michael J., Fasold, Mario, Ishiyama, Mikio, Johnson, Jeremy, Kehr, Steffi, Lara, Marcia, Letaw, John H., Litman, Gary W., Litman, Ronda T., Mikami, Masato, Ota, Tatsuya, Saha, Nil Ratan, Williams, Louise, Stadler, Peter F., Wang, Han, Taylor, John S., Fontenot, Quenton, Ferrara, Allyse, Searle, Stephen M.J., Aken, Bronwen, Yandell, Mark, Schneider, Igor, Yoder, Jeffrey A, Volff, Jean-Nicolas, Meyer, Axel, Amemiya, Chris T, Venkatesh, Byrappa, Holland, Peter W.H., Guiguen, Yann, Bobe, Julien, Shubin, Neil H., Di Palma, Federica, Alföldi, Jessica, Lindblad-Toh, Kerstin, Postlethwait, John H., Institute of Neuroscience, National Research Council [Italy] (CNR), Department of Integrative Biology [Berkeley] (IB), University of California [Berkeley], University of California-University of California, Department of Organismal Biology and Anatomy, University of Chicago, Department of Biology, Northern Arizona University [Flagstaff], Department of Anthropology, University of California, Pennsylvania State University (Penn State), Penn State System, Hellenic Centre for Marine Research, Hellenic Center for Marine Research (HCMR), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Department of Animal Biology, University of Pennsylvania [Philadelphia], Broad Institute of MIT and Harvard (BROAD INSTITUTE), Harvard Medical School [Boston] (HMS)-Massachusetts Institute of Technology (MIT)-Massachusetts General Hospital [Boston], Eccles Institute of Human Genetics, University of Utah, Cold Spring Harbor, Cold Spring Harbor Laboratory, Wellcome Trust Genome Campus, The Wellcome Trust Sanger Institute [Cambridge], European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, Department of Zoology, Auburn University (AU), Department of Animal and Plant Sciences [Sheffield], University of Sheffield [Sheffield], School of Biological Sciences [Bangor], Bangor University, Comparative Genomics Laboratory, Agency for Science, Technology and Research (A*STAR), International Institute of Molecular and Cell Biology, Institut de Génomique Fonctionnelle de Lyon (IGFL), École normale supérieure - Lyon (ENS Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Department of Genetics, The University of Texas M.D. Anderson Cancer Center [Houston], Department of Molecular Biomedical Sciences Raleigh, North Carolina State University [Raleigh] (NC State), University of North Carolina System (UNC)-University of North Carolina System (UNC), Center for Comparative Medicine and Translational Research Raleigh, Departament de Genètica, Universitat Autònoma de Barcelona [Barcelona] (UAB), Institut de Recerca de la Biodiversitat, University of Barcelona, University of Victoria, Center for Circadian Clocks, Soochow University, School of Biology and Basic Medical Sciences, Medical College, Bioinformatics Group, Department of Computer Science, Universität Leipzig [Leipzig], Young Investigators Group Bioinformatics and Transcriptomics, Department of Proteomics, Helmholtz Centre for Environmental Research (UFZ), Department of Dental Hygiene, Nippon Dental University, Morsani College of Medicine, Department of Pediatrics, University of South Florida (USF), Department of Microbiology, Department of Evolutionary Studies of Biosystems, SOKENDAI, Graduate University for Advanced Studies, Molecular Genetics Program, Benaroya Research Institute, Department of Biological Sciences, The Open University [Milton Keynes] (OU), European Molecular Biology Laboratory, Wellcome Trust Genome Campus, European Bioinformatics Institute, Instituto de Ciências Biológicas, Federal University of Para - Universidade Federal do Para [Belem - Brésil], Department of Molecular Biomedical Sciences, University of North Carolina System (UNC)-University of North Carolina System (UNC)-College of Veterinary Medicine Raleigh, Center for Comparative Medicine and Translational Research, International Max Planck Research School for Organismal Biology (IMPRS), University of Konstanz, Genome Analysis Center, Vertebrate and Health Genomics, Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Hellenic Centre for Marine Research (HCMR), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Universitat Autònoma de Barcelona (UAB), University of Victoria [Canada] (UVIC), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), University of South Florida [Tampa] (USF), University of California [Berkeley] (UC Berkeley), University of California (UC)-University of California (UC), University of California (UC), University of Pennsylvania, École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Universität Leipzig, and Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA)

Subjects
[SDV]Life Sciences [q-bio], analyse phylogénétique, reproduction, poisson, analyse génomique, human, chromosome, analyse du transcriptome, genome, duplication des génomes, miRNA, fish, teleost, physiologie animale, séquence régulatrice, vertébré, homme, lepisosteus oculatus, interaction animal homme, lépisosté tacheté, évolution du génome, fonction des gènes, teleosteen, regulatory sequence, vertebrates, immunité, expression des gènes
Abstract

The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons (vol 48, pg 427, 2016); As we intended, other researchers have been able to use the draft spotted gar genome sequence available from the Broad Institute website since December 2011, the assembly LepOcu1 publicly available from NCBI since 13 January 2012 under accession code GCA000242695.1, and the Ensembl gene annotation (version 74, December 2013; http://www.ensembl.org/Lepisosteus_oculatus/Info/Annotation) and recent annotation by NCBI on 15 May 2014 guided by RNA sequence data from ten tissues. While this article was in review, a paper (Nature 526, 108–111, 2015) was published that arrives at conclusions similar to some of our own analyses, and we wish to acknowledge that publication, which used our unpublished data and genome annotations, emphasizing the importance of the strategy of early release of sequence data. The correction has been made to the HTML and PDF versions of the article.

Published
2016

44. New tools to optmise the analysis of a large RNA-Seq dataset from non model species: development of a hybrid assembly strategy and assessment of library complexity from raw sequencing output

Author

Lagnel, Jacques, Belkhir, Khalid, Manousaki, Tereza, Desmarais, Erick, Tsagkarakou, Anastasia, Mancheron, Alban, Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Center for Marine Research (HCMR), Université Montpellier 2 - Sciences et Techniques (UM2), Hellenic Agricultural Organization Demeter (HAO Demeter), European Union (European Social Fund – ESF) and Greek national funds through the Operational Program 'Education and Lifelong Learning' of the National Strategic Reference Framework (NSRF) Research Funding Program: THALES. This work has been partially supported by the LifeWatchGreece project, funded by the GSRT (structural funds)., and Superviseur : lagnel@hcmr.gr

Subjects
base de données, Bioinformatics, séquence d'arn, Bio-informatique, forme hybride, approche omique, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], outil d'aide à la décision
Abstract

With the advance of new sequencing technologies major challenges have emerged on different levels, from library preparaRon up to data analysis. Here, we present one tool that improves the quality and feasibility of the assembly process and another that assesses the complexity of the sequenced library. Currently, transcriptome assembly strategies are either reference-based or “de novo” depending on the availability of high-quality reference sequences. For non-model species where a high-quality reference transcriptome/genome is lacking, a closely-related species reference sequence can be used as a proxy to improve the quality of the reconstructed transcriptome and decrease the computaRonal requirements. By bringing together the two complementary assembly strategies, we can take advantage of the high sensiRvity of reference- based assemblers, while leveraging the ability of de novo assemblers to detect novel transcripts. The procedure includes three steps. First, the RNA-seq reads of the target species are aligned to the reference genome/transcriptome of a closely-related species. Reads that map within the same genomic locaRon are grouped into clusters. Then, each “cluster” of aligned reads combined with the remaining unaligned reads will serve as input to a de novo assembly process running in parallel. Finally, all the resulted de novo assemblies are merged to form the final transcriptome. The de novo assembly requires important compuRng resources, parRcularly memory. The proposed strategy solves the problem of intensive memory requirements of a de novo assembly and greatly reduces the computaRonal Rme by parallelising both the first and second step of the process. Here, we test this strategy on a simulated Drosophila group dataset using various reference model species in a wide range of divergence Rmes to assess the mapping success. Our pipeline led to great improvement when closely related species were used as a reference. This was further tested on an experimental dataset decreasing the required computaRonal resources. Prior to the assembly process, sequencing experiments can be evaluated based on the success of library construcRon and sequencing. OCen, technical failures can lead to biased RNA representaRon and over-sequencing of parRcular molecules that do not represent the starRng biological sample and cause reduced complexity. The level of complexity reflects the coverage of the transcriptome. We developed a new metric that infers the diversity of unique sequences and assesses the complexity of a given library using two clustering steps of idenRcal reads. This metric can be used to compare the library construcRon success and for evaluaRon of mulRple experiments. The presented tools facilitate the analysis of RNA-Seq for non-model species improving the feasibility of the assembly and allowing for the post-sequencing evaluaRon of the library construcRon. New tools to optmise the analysis of a large RNA-Seq dataset from non model species: development of a hybrid assembly strategy and assessment of library complexity from raw sequencing output. (PDF Download Available). Available from: https://www.researchgate.net/publication/319932729_New_tools_to_optmise_the_analysis_of_a_large_RNA-Seq_dataset_from_non_model_species_development_of_a_hybrid_assembly_strategy_and_assessment_of_library_complexity_from_raw_sequencing_output [accessed Feb 28 2018].

Published
2014

45. Erratum: Corrigendum: The spotted gar genome illuminates vertebrate evolution and facilitates human-teleost comparisons

Author

Braasch, Ingo, primary, Gehrke, Andrew R, additional, Smith, Jeramiah J, additional, Kawasaki, Kazuhiko, additional, Manousaki, Tereza, additional, Pasquier, Jeremy, additional, Amores, Angel, additional, Desvignes, Thomas, additional, Batzel, Peter, additional, Catchen, Julian, additional, Berlin, Aaron M, additional, Campbell, Michael S, additional, Barrell, Daniel, additional, Martin, Kyle J, additional, Mulley, John F, additional, Ravi, Vydianathan, additional, Lee, Alison P, additional, Nakamura, Tetsuya, additional, Chalopin, Domitille, additional, Fan, Shaohua, additional, Wcisel, Dustin, additional, Cañestro, Cristian, additional, Sydes, Jason, additional, Beaudry, Felix E G, additional, Sun, Yi, additional, Hertel, Jana, additional, Beam, Michael J, additional, Fasold, Mario, additional, Ishiyama, Mikio, additional, Johnson, Jeremy, additional, Kehr, Steffi, additional, Lara, Marcia, additional, Letaw, John H, additional, Litman, Gary W, additional, Litman, Ronda T, additional, Mikami, Masato, additional, Ota, Tatsuya, additional, Saha, Nil Ratan, additional, Williams, Louise, additional, Stadler, Peter F, additional, Wang, Han, additional, Taylor, John S, additional, Fontenot, Quenton, additional, Ferrara, Allyse, additional, Searle, Stephen M J, additional, Aken, Bronwen, additional, Yandell, Mark, additional, Schneider, Igor, additional, Yoder, Jeffrey A, additional, Volff, Jean-Nicolas, additional, Meyer, Axel, additional, Amemiya, Chris T, additional, Venkatesh, Byrappa, additional, Holland, Peter W H, additional, Guiguen, Yann, additional, Bobe, Julien, additional, Shubin, Neil H, additional, Di Palma, Federica, additional, Alfo¨ldi, Jessica, additional, Lindblad-Toh, Kerstin, additional, and Postlethwait, John H, additional

Published
2016
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46. Exploring a Nonmodel Teleost Genome Through RAD Sequencing—Linkage Mapping in Common Pandora, Pagellus erythrinus and Comparative Genomic Analysis

Author

Manousaki, Tereza, primary, Tsakogiannis, Alexandros, additional, Taggart, John B, additional, Palaiokostas, Christos, additional, Tsaparis, Dimitris, additional, Lagnel, Jacques, additional, Chatziplis, Dimitrios, additional, Magoulas, Antonios, additional, Papandroulakis, Nikos, additional, Mylonas, Constantinos C, additional, and Tsigenopoulos, Costas S, additional

Published
2016
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47. Lateralized Feeding Behavior is Associated with Asymmetrical Neuroanatomy and Lateralized Gene Expressions in the Brain in Scale-Eating Cichlid Fish.

Author

Schneider, Ralf F., Franchini, Paolo, Meyer, Axel, Hyuk Je Lee, Manousaki, Tereza, Ji Hyoun Kang, and Lein, Etienne

Subjects
BEHAVIOR genetics, GENOMICS, SYMMETRY (Biology), FISHES, TELENCEPHALON
Abstract

Lateralized behavior ("handedness") is unusual, but consistently found across diverse animal lineages, including humans. It is thought to reflect brain anatomical and/or functional asymmetries, but its neuro-molecular mechanisms remain largely unknown. Lake Tanganyika scale-eating cichlid fish, Perissodus microlepis show pronounced asymmetry in their jaw morphology as well as handedness in feedingbehavior--bitingscales preferentially only fromone or theother side of their victims. Thismakes themanideal model inwhich to investigatepotential laterality in neuroanatomyand transcription in the brain in relation to behavioral handedness. After determining behavioral handedness in P. microlepis (preferred attack side), we estimated the volume of the hemispheres of brainregions andcapturedtheir gene expressionprofiles. Our analyses revealedthat the degree of behavioralhandedness ismirrored at the level of neuroanatomical asymmetry, particularly in the tectumopticum. Transcriptome analyses showed that different brain regions (tectumopticum, telencephalon, hypothalamus, and cerebellum) display distinct expression patterns, potentially reflecting their developmental interrelationships. For numerous genes in each brain region, their extent of expression differences between hemispheres was found to be correlated with the degree of behavioral lateralization. Interestingly, the tectum opticum and telencephalon showed divergent biases on the direction of up- or down-regulation of the laterality candidate genes (e.g., grm2) in the hemispheres, highlighting the connection of handednesswith gene expression profiles and the different roles of these brain regions. Hence, handedness in predation behavior may be caused by asymmetric size of brain hemispheres and also by lateralized gene expressions in the brain. [ABSTRACT FROM AUTHOR]

Published
2017
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50. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

Author

Smith, Jeramiah J, primary, Kuraku, Shigehiro, additional, Holt, Carson, additional, Sauka-Spengler, Tatjana, additional, Jiang, Ning, additional, Campbell, Michael S, additional, Yandell, Mark D, additional, Manousaki, Tereza, additional, Meyer, Axel, additional, Bloom, Ona E, additional, Morgan, Jennifer R, additional, Buxbaum, Joseph D, additional, Sachidanandam, Ravi, additional, Sims, Carrie, additional, Garruss, Alexander S, additional, Cook, Malcolm, additional, Krumlauf, Robb, additional, Wiedemann, Leanne M, additional, Sower, Stacia A, additional, Decatur, Wayne A, additional, Hall, Jeffrey A, additional, Amemiya, Chris T, additional, Saha, Nil R, additional, Buckley, Katherine M, additional, Rast, Jonathan P, additional, Das, Sabyasachi, additional, Hirano, Masayuki, additional, McCurley, Nathanael, additional, Guo, Peng, additional, Rohner, Nicolas, additional, Tabin, Clifford J, additional, Piccinelli, Paul, additional, Elgar, Greg, additional, Ruffier, Magali, additional, Aken, Bronwen L, additional, Searle, Stephen M J, additional, Muffato, Matthieu, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Jones, Matthew, additional, Brown, C Titus, additional, Chung-Davidson, Yu-Wen, additional, Nanlohy, Kaben G, additional, Libants, Scot V, additional, Yeh, Chu-Yin, additional, McCauley, David W, additional, Langeland, James A, additional, Pancer, Zeev, additional, Fritzsch, Bernd, additional, de Jong, Pieter J, additional, Zhu, Baoli, additional, Fulton, Lucinda L, additional, Theising, Brenda, additional, Flicek, Paul, additional, Bronner, Marianne E, additional, Warren, Wesley C, additional, Clifton, Sandra W, additional, Wilson, Richard K, additional, and Li, Weiming, additional

Published
2013
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