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- A comprehensive compilation of Iberian Medusozoan data: Diversity, ecology, and omics insightsPublication . Rodrigues, Tomás; Almeida, Daniela; Guardiola, Francisco A.; Borges, Paulo A. V.; Antunes, AgostinhoThis study investigates the diversity and distribution of Medusozoa, a clade of the phylum Cnidaria, within the framework of the Iberian Peninsula and surrounding archipelagos. Medusozoa is notably recognized for encompassing jellyfish species with the capacity to exert detrimental ecological and socioeconomic impacts, this group of mostly marine organisms assumes a critical role in aquatic food webs and exhibits considerable biotechnological potential. A comprehensive dataset sourced from over 230 bibliographic references and public databases, comprising over 30,000 reports of Medusozoa in the Iberian region, reveals 593 species across the four medusozoan classes (549 hydrozoans, 37 scyphozoans, 5 staurozoans, and 2 cubozoans). Additionally, publicly available genomic, transcriptomic, and proteomic metadata from the phylum Cnidaria are incorporated. The analyses highlight Hydrozoa as the most frequently reported and diverse class in the Iberian region. Specifically, the order Leptothecata exhibits the highest diversity, while Siphonophorae stands out as the most documented with Physalia physalis emerging as the highest reported species. Spatial distribution patterns reveal that holoplanktonic species are more widespread and abundant than their benthic and meroplanktonic counterparts. Furthermore, medusozoans with a free-swimming life form display greater diversity and dispersal compared to sessile species. The Northeast Atlantic section of the region demonstrates greater medusozoan diversity compared to the Mediterranean. Key findings also include information into invasive and introduced species, bloom-forming organisms, and edible species. A sustained trend of discovering new species of Medusozoa over time was observed, underscoring untapped exploration potential in the Iberian region. The study reveals a clear limitation of omics data in cnidarians, particularly in the Medusozoa clade. This research provides an overall perspective on medusozoans in the Iberian region, underlining the importance of additional omics studies while highlighting growing interest in exploring the biotechnological potential of these organisms. This research serves as a valuable resource for future investigations, providing insights into underexplored species and those with greater ecological and socioeconomic importance.
- How genomics can help biodiversity conservationPublication . Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul R.; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R.; Godoy, José A.; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah A.; Paez, Sadye; Palsbøll, Per J.; Pampoulie, Christophe; Ruiz-López, María J.; Secomandi, Simona; Svardal, Hannes; Theofanopoulou, Constantina; De Vries, Jan; Waldvogel, Ann-Marie; Zhang, Guojie; Jarvis, Erich D.; Bálint, Miklós; CIOFI, CLAUDIO; Waterhouse, Robert M.; Mazzoni, Camila J.; Höglund, Jacob; Aghayan, Sargis A.; Alioto, Tyler; Alvarez, Nadir; Alves, Paulo C.; Rosário, Isabel Amorim do; Antunes, Agostinho; Arribas, Paula; Baldrian, Petr; Bertorelle, Giorgio; Böhne, Astrid; Bonisoli Alquati, Andrea; Boštjančić, Ljudevit L.; Boussau, Bastien; Breton, Catherine M.; Buzan, Elena; Campos, Paula F.; Carreras, Carlos; Castro, Luis Filipe; Chueca, Luis J.; Čiampor, Fedor; 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; Flot, Jean-François; Gabaldón, Toni; Agius, Dolores 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.; 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; 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; Studer, Bruno; Theodoridis, Spyros; Thines, Marco; Urban, Lara; Vasemägi, Anti; Vella, Adriana; Vella, Noel; Vernes, Sonja C.; Vernesi, Cristiano; Vieites, David R.; Wheat, Christopher W.; Wörheide, Gert; Wurm, Yannick; Zammit, GabrielleABSTRACT: The availability of public genomic resources can greatly assist biodiversity assessment, conservation, and restoration efforts by providing evidence for scientifically informed management decisions. Here we survey the main approaches and applications in biodiversity and conservation genomics, considering practical factors, such as cost, time, prerequisite skills, and current shortcomings of applications. Most approaches perform best in combination with reference genomes from the target species or closely related species. We review case studies to illustrate how reference genomes can facilitate biodiversity research and conservation across the tree of life. We conclude that the time is ripe to view reference genomes as fundamental resources and to integrate their use as a best practice in conservation genomics.
- Building a Portuguese Coalition for Biodiversity GenomicsPublication . Marques, João Pedro; ALVES, Paulo C; Rosário, Isabel Amorim do; Lopes, Ricardo J.; Moura, Mónica; Meyers, Gene; Sim-Sim, Manuela; Sousa-Santos, C.; Alves, M. Judite; Borges, Paulo A. V.; Brown, Thomas; Carneiro, Miguel; Carrapato, Carlos; Ceríaco, Luis; Ciofi Degli Atti, Claudio; Silva, Luís; Diedericks, Genevieve; Diroma, Maria Angela; Farelo, Liliana; Formenti, Giulio; Gil, Fátima; Grilo, Miguel; Ianucci, Alessio; Leitão, Henrique; Máguas, C.; Mc Cartney, Ann M.; Mendes, Sofia; Moreno, João; Morselli, Marco; Mouton, Alice; Natali, Chiara; Pereira, Fernando; Rego, Rúben; Resendes, Roberto; Roxo, Guilherme; Svardal, Hannes; Trindade, Helena; Vicente, Sara; Winkler, Sylke; Alvarenga, M.; Amaral, Andreia; Antunes, Agostinho; Campos, Paula; Canario, A. V. M.; Castilho, Rita; Castro, Luis Filipe; Crottini, Angelica; Cunha, Mónica; Espregueira Themudo, Gonçalo; Esteves, Pedro; Faria, Rui; Fernandes, Carlos; Ledoux, Jean-Baptiste; Louro, Bruno; Magalhães, Sara; OS, Paulo; Pearson, Gareth; Pimenta, João; Pina-Martins; Santos, Teresa; Serrao, Ester A; Melo-Ferreira, José; Sousa, VítorThe diverse physiography of the Portuguese land and marine territory, spanning from continental Europe to the Atlantic archipelagos, has made it an important repository of biodiversity throughout the Pleistocene glacial cycles, leading to a remarkable diversity of species and ecosystems. This rich biodiversity is under threat from anthropogenic drivers, such as climate change, invasive species, land use changes, overexploitation or pathogen (re)emergence. The inventory, characterization and study of biodiversity at inter- and intra-specific levels using genomics is crucial to promote its preservation and recovery by informing biodiversity conservation policies, management measures and research. The participation of researchers from Portuguese institutions in the European Reference Genome Atlas (ERGA) initiative, and its pilot effort to generate reference genomes for European biodiversity, has reinforced the establishment of Biogenome Portugal. This nascent institutional network will connect the national community of researchers in genomics. Here, we describe the Portuguese contribution to ERGA’s pilot effort, which will generate high-quality reference genomes of six species from Portugal that are endemic, iconic and/or endangered, and include plants, insects and vertebrates (fish, birds and mammals) from mainland Portugal or the Azores islands. In addition, we outline the objectives of Biogenome Portugal, which aims to (i) promote scientific collaboration, (ii) contribute to advanced training, (iii) stimulate the participation of institutions and researchers based in Portugal in international biodiversity genomics initiatives, and (iv) contribute to the transfer of knowledge to stakeholders and engaging the public to preserve biodiversity. This initiative will strengthen biodiversity genomics research in Portugal and fuel the genomic inventory of Portuguese eukaryotic species. Such efforts will be critical to the conservation of the country’s rich biodiversity and will contribute to ERGA’s goal of generating reference genomes for European species.