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- Microsatellites reveal high levels of genetic admixture in the natural populations of Laurus azorica, LauraceaePublication . Rego, Rúben; Vieira, Ângela F.; Silva, Luís; Elias, Rui B.; Silva, Carlos; Resendes, Roberto; Moura, MónicaLaurus (Lauraceae) species are currently restricted to isolated refugia in the southern Black Sea, Mediterranean Basin, southern Morocco, and Macaronesian archipelagos. One to three species of Laurus has been recognized: the Azorean endemic Laurus azorica, L. nobilis from the Mediterranean, and L. novocanariensis from Madeira and the Canary Islands. This study aims to determine the population structure, genetic diversity, and associated patterns of gene flow within and between Azorean populations, using eight existing SSR markers. We also included plant material from L. nobilis populations found in the Azores, for comparison. Amplification was performed in 212 samples of L. azorica and in 30 samples of L. nobilis. For L. azorica, 78 alleles were amplified (average 9.75 alleles per loci). Bayesian analysis with STRUCTURE unveiled five genetic groups for the Azorean accessions, with high level of genetic admixture. Genetic diversity was generally high, with moderate levels of genetic differentiation among L. azorica populations. Moreover, high gene flow levels, likely mediated by past human translocations and naturally, by birds, might have contributed to the high level of genetic admixture observed possibly reflecting hybridization events between L. nobilis and L. azorica. Conservation measures should be applied to some populations of São Miguel, Santa Maria, and Flores Islands, based on the number of private alleles, and further, ad hoc translocation events should be avoided. Conservation in situ and the preservation of laurel forest remains are recommended. The study of this species’ taxonomy, genetics, and population dynamics in the Macaronesian region should be continued.
- Arceuthobium Species (Viscaceae) Parasitizing an Angiosperm: The Unique Case of A. azoricum in the Azores IslandsPublication . Elias, Rui B.; Moura, Mónica; Roxo, Guilherme; Borges Silva, L; Pavão, Diogo C.; Resendes, Roberto; Pereira, Fernando; Nickrent, DanielArceuthobium azoricum Wiens & Hawksw. is a rare Azorean endemic epiphytic hemiparasite (mistletoe), which typically parasitizes branches of the gymnosperm Juniperus brevifolia (Hochst. ex Seub.) Antoine (Cupressaceae), which is also an Azorean endemic. Here, we describe a population of A. azoricum, on Pico Island, parasitizing Erica azorica Hochst. ex Seub. (Ericaceae), which is also an Azorean endemic. Our molecular analysis (using nuclear ribosomal internal transcribed spacer) showed no differences between individuals parasitizing Erica and Juniperus species. Moreover, a preliminary analysis showed no differences in morphological characteristics between accessions sampled from different hosts. Given that this is the first bona fide record of Arceuthobium sp. parasitizing an angiosperm, this population represents a unique host-shifting event, and its conservation is important because it may allow new insights into host recognition mechanisms in mistletoes. Immediate attention should be given to characterizing this Pico Island population using appropriate molecular methods and additional morphological analyses.
- A prevenção como método de conservação: O caso da Youngia japónica (crepe-do-japão) na ilha de São MiguelPublication . Roxo, Guilherme; Torres, Paulo; Afonso, Pedro; Rego, Rúben; Resendes, Roberto; Moura, MónicaUma espécie quando vive fora da sua área de distribuição nativa é denominada de espécie exótica (do grego exotikós, “de fora”). Algumas destas espécies coexistem com as espécies nativas de forma equilibrada, no entanto quando causam impactes ambientais e económicos negativos estas são designadas de espécies invasoras. No arquipélago dos Açores mais de 60% da flora vascular corresponde a espécies exóticas. Estas plantas foram introduzidas de forma consciente ou inconsciente, propagando-se e desenvolvendo-se espontaneamente, podendo impactar o nosso dia a dia quando afetam os serviços dos ecossistemas, com consequências negativas no fornecimento de água, regulação do clima, saúde pública, valor estético e cultural das paisagens, entre outras.
- The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.Publication . Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; De Panis, Diego; Marins, Luísa S; Leitão, Henrique; Diedericks, Genevieve; KIRANGWA, JOSEPH; Morselli, Marco; Salces-Ortiz, J; Escudero, Nuria; Iannucci, Alessio; Natali, Chiara; Svardal, Hannes; Fernández, Rosa; De Pooter, Tim; Joris, Geert; Strazisar, Mojca; Wood, Jo; Herron, Katie E.; Seehausen, Ole; Watts, Phillip; Shaw, Felix; Davey, Robert P; Minotto, Alice; Fernández, José M; Böhne, Astrid; Alegria, C.; Alioto, Tyler; Alves, Paulo C; Amorim, Isabel R.; AURY, Jean-Marc; Backstrom, Niclas; Baldrian, Petr; Baltrunaite, Laima; Barta, Endre; Bed'Hom, Bertrand; Belser, Caroline; Bergsten, Johannes; Bertrand, Laurie; Bilandzija, Helena; Binzer-Panchal, Mahesh; Bista, Iliana; Blaxter, Mark; Borges, Paulo A. V.; Borges Dias, Guilherme; Bosse, Mirte; Brown, Tom; Bruggmann, Rémy; Buena-Atienza, Elena; Burgin, Josephine; Buzan, Elena; Casadei, Nicolas Lougi Pascal; CHIARA, MATTEO; Chozas, Sergio; Čiampor, Fedor; Crottini, Angelica; C., Cruaud; Cruz, Fernando; Dalén, Love; DE BIASE, Alessio; Campo, Javier Del; Delić, Teo; Dennis, Alice B; Derks, Martijn FL; Diroma, Maria Angela; Djan, Mihajla; Duprat, Simone; Eleftheriadi, Klara; Feulner, Philine GD; Flot, Jean-François; Forni, Giobbe; Fosso, Bruno; Fournier, Pascal; FOURNIER-CHAMBRILON, Christine; Gabaldón, Toni; Garg, Shilpa; Gissi, Carmela; Giupponi, Luca; Gómez-Garrido, Jèssica; Gonzalez, Josefa; Grilo, Miguel; Gruening, Bjoern; Guérin, Thomas; Guiglielmoni, Nadège; Gut, Marta; Haesler, Marcel P; Hahn, Christoph; Halpern, Balint; Harrison, Peter; Heintz, Julia; Hindrikson, Maris; Höglund, Jacob; Howe, Kerstin; Hughes, Graham; Istace, Benjamin; Cock, Mark J.; Jancekovic, Franc; Jónsson, Zophonías O; Joye-Dind, Sagane; Koskimaki, Janne J.; Krystufek, Boris; Kubacka, Justyna; Kuhl, Heiner; Kusza, Szilvia; Labadie, Karine; Lahteenaro, Meri; Lantz, Henrik; Lavrinienko, Anton; Leclere, Lucas; Lopes, Ricardo Jorge; Madsen, Ole; Magdelenat, Ghislaine; MAGOGA, GIULIA; Manousaki, Tereza; Mappes, Tapio; Marques, João Pedro; Martinez Redondo, Gemma I; Maumus, Florian; Megens, Hendrik-Jan; Melo-Ferreira, José; Mendes, Sofia L; Montagna, Matteo; Moreno, João; Mosbech, Mai-Britt; Moura, Monica; Musilova, Zuzana; Myers, Eugene; Nash, Will J.; Nater, Alexander; Nicholson, Pamela; Niell, Manuel; Nijland, Reindert; Noel, Benjamin; Norén, Karin; Oliveira, Pedro H; Olsen, Remi-André; Ometto, Lino; Ossowski, Stephan; Palinauskas, Vaidas; Pálsson, Snæbjörn; Panibe, Jerome P; Paupério, Joana; Pavlek, Martina; PAYEN, Emilie; Pawłowska, Julia; Pellicer, Jaume; Pesole, Graziano; Pimenta, João; Pippel, Martin; Pirttilä, Anna Maria; Poulakakis, Nikos; Rajan, Jeena; Rego, Ruben MC; Resendes, Roberto; Resl, Philipp; Riesgo, Ana; Rödin-Mörch, Patrik; Soares, André ER; Fernandes, Carlos; Romeiras, Maria M.; Roxo, Guilherme; Rüber, Lukas; Ruiz-López, María José; Saarma, Urmas; Silva, Luís; Sim-Sim, Manuela; Soler, Lucile; Sousa, Vitor C; Sousa-Santos, C.; Spada, Alberto; Stefanovic, Milomir; Steger, Viktor; Stiller, Josefin; Stöck, Matthias; Struck, Torsten Hugo H; Sudasinghe, Hiranya; Tapanainen, Riikka; Tellgren-Roth, Christian; Trindade, Helena; Tukalenko, Yevhen; Urso, Ilenia; Vacherie, Benoit; Van Belleghem, Steven M; Van Oers, Kees; Vargas-Chavez, Carlos; Velickovic, Nevena; Vella, Noel; Vella, Adriana; Vernesi, Cristiano; Vicente, Sara; Villa, Sara; Vinnere Pettersson, Olga; Volckaert, Filip AM; Vörös, Judit; Wincker, Patrick; Winkler, Sylke; CIOFI, CLAUDIO; Waterhouse, Robert M; Mazzoni, Camila J.ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.
- Marine algal (seaweed) flora of Faial Island, AzoresPublication . Milla-Figueras, David; Neto, Ana I.; Tempera, F.; Moreu, Ignacio; Prestes, Afonso L.; Resendes, Roberto; Neto, Raul; Tittley, Ian; Afonso, PedroA comprehensive checklist of the marine flora from Faial Island, mid-north Atlantic, is still unavailable, despite the numerous works that gathered data around its coasts for over 150 years. This study brings together and harmonises all macroalgae collections and taxonomical records from multiple projects and teams over the last thirty years. The result is a list of taxonomic records and georeferenced species occurrence data that substantially increases our knowledge of the coastal Azorean marine biodiversity while providing key information for future ecological studies and to support local, marine management and conservation. A total of 2283 specimens belonging to 118 taxa of macroalgae are registered here, comprising 61 Rhodophyta, 26 Chlorophyta, 30 Ochrophyta (Phaeophyceae) and one Cyanophyta (Cyanobacteria). From these, 26 taxa are identified only at the genus level and 92 to species level (47 Rhodophyta, 21 Chlorophyta and 24 Ochrophyta). The list comprises 75 native species, 12 records of uncertain origin and five introductions (Caulerpa prolifera (Forsskål) J.V.Lamouroux, Caulerpa webbiana Montagne, Hydroclathrus tilesii (Endlicher) Santiañez & M.J.Wynne, Asparagopsis armata Harvey and Symphyocladia marchantioides (Harvey) Falkenberg). Codium elisabethiae O.C.Schmidt represents the only Macaronesian endemism known on the Island. Twenty-three species are newly recorded to the algal flora of the Island.
- 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.