• Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum) 

      Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès-Bonet, Tomás; Moodley, Yoshan; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)
      Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a ...
    • Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum) 

      Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; de Manuel, Marc; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe G.; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Pontén, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès-Bonet, Tomás; Moodley, Yoshan; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2021)
      Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a ...
    • Holo-Omics: Integrated Host-Microbiota Multi-omics for Basic and Applied Biological Research 

      Nyholm, Lasse; Koziol, Adam; Marcos, Sofia; Botnen, Amanda Bolt; Aizpurua, Ostaizka; Gopalakrishnan, Shyam; Limborg, Morten T.; Gilbert, Marcus Thomas Pius; Alberdi, Antton (Peer reviewed; Journal article, 2020)
      From ontogenesis to homeostasis, the phenotypes of complex organisms are shaped by the bidirectional interactions between the host organisms and their associated microbiota. Current technology can reveal many such interactions ...
    • How genomics can help biodiversity conservation 

      Theissinger, Kathrin; Fernandes, Carlos; Formenti, Giulio; Bista, Iliana; Berg, Paul Ragnar; Bleidorn, Christoph; Bombarely, Aureliano; Crottini, Angelica; Gallo, Guido R.; Godoy, José A.; Jentoft, Sissel; Malukiewicz, Joanna; Mouton, Alice; Oomen, Rebekah Alice; 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 S.; Almudí, Isabel; Alvarez, Nadir; Alves, Paulo C.; do Rosario, Isabel R. Amorim; 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, L. Filipe C.; Chueca, Luis J.; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Jakobsen, Kjetill Sigurd; Matschiner, Michael; Zammit, Gabrielle (Journal article; Peer reviewed, 2023)
      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 ...
    • Identification of transcription factor genes involved in anthocyanin biosynthesis in carrot (Daucus carota L.) using RNA-Seq 

      Kodama, Miyako; Brinch-Pedersen, Henrik; Sharma, Shrikant; Holme, Inger B.; Joernsgaard, Bjarne; Dzhanfezova, Tsaneta; Amby, Daniel Buchvaldt; Vieira, Filipe G.; Liu, Shanlin; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2018)
      Background Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic ...
    • Improved Genome Assembly and Annotation for the Rock Pigeon (Columba livia) 

      Holt, Carson; Campbell, Michael; Keays, David Anthony; Edelman, Nathaniel; Kapusta, Aurélie; Maclary, Emily; Domyan, Eric T.; Suh, Alexander; Warren, Wesley C.; Yandell, Mark; Gilbert, Marcus Thomas Pius; Shapiro, Michael D. (Journal article; Peer reviewed, 2018)
      The domestic rock pigeon (Columba livia) is among the most widely distributed and phenotypically diverse avian species. C. livia is broadly studied in ecology, genetics, physiology, behavior, and evolutionary biology, and ...
    • Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition 

      Hansen, Søren B.; Bozzi, Davide; Mak, Sarah S.T.; Clausen, Cecilie G.; Nielsen, Tue K.; Kodama, Miyako; Hansen, Lars H.; Gilbert, Marcus Thomas Pius; Limborg, Morten T. (Journal article; Peer reviewed, 2023)
      It remains a challenge to obtain the desired phenotypic traits in aquacultural production of Atlantic salmon, and part of the challenge might come from the effect that host-associated microorganisms have on the fish ...
    • Kouprey (Bos sauveli) genomes unveil polytomic origin of wild Asian Bos 

      Sinding, Mikkel-Holger S.; Ciucani, Marta M.; Ramos-Madrigal, Jazmín; Carmagnini, Alberto; Rasmussen, Jacob A.; Feng, Shaohong; Chen, Guangji; Vieira, Filipe G.; Mattiangeli, Valeria; Ganjoo, Rajinder K.; Larson, Greger; Sicheritz-Pontén, Thomas; Petersen, Bent; Frantz, Laurent A.F.; Gilbert, Marcus Thomas Pius; Bradley, Daniel G. (Peer reviewed; Journal article, 2021)
      The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely ...
    • Leech blood-meal invertebrate-derived DNA reveals differences in Bornean mammal diversity across habitats 

      Drinkwater, Rosie; Jucker, Tommaso; Potter, Joshua H. T.; Swinfield, Tom; Coomes, D; Slade, Eleanor M.; Gilbert, Marcus Thomas Pius; Lewis, Owen T.; Bernard, Henry; Struebig, Matthew J.; Clare, Elizabeth; Rossiter, Stephen J. (Peer reviewed; Journal article, 2020)
      The application of metabarcoding to environmental and invertebrate‐derived DNA (eDNA and iDNA) is a new and increasingly applied method for monitoring biodiversity across a diverse range of habitats. This approach is ...
    • Mammal mitogenomics from invertebrate-derived DNA 

      Danabalan, Renita; Merkel, Kevin; Bærholm Schnell, Ida; Arandjelovic, Mimi; Boesch, Christophe; Brazzola, Gregory; Dieguez, Paula; Dupain, Jef; Kambale-Vyalengerera, Magloire; Kühl, Hjalmar S.; Hoffmann, Constanze; Lapuente, Juan; Ngoc Thinh, Van; Zimmermann, Fee; Leendertz, Fabian H.; Gilbert, Marcus Thomas Pius; Roos, Christian; Mazzoni, Camila; Gogarten, Jan F.; Calvignac-Spencer, Sébastien (Journal article; Peer reviewed, 2023)
    • Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species 

      Fietz, Katharina; Hintze, Christian O.R.; Skovrind, Mikkel; Nielsen, Tue Kjærgaard; Limborg, Morten; Krag, Marcus A.; Palsbøll, Per J.; Hansen, Lars Hestbjerg; Møller, Peter Rask; Gilbert, Marcus Thomas Pius (Journal article; Peer reviewed, 2018)
      Background Deciphering the mechanisms governing population genetic divergence and local adaptation across heterogeneous environments is a central theme in marine ecology and conservation. While population divergence and ...
    • Mitochondrial genomes of Danish vertebrate species generated for the national DNA reference database, DNAmark 

      Margaryan, Ashot; Noer, Christina Lehmkuhl; Richter, Stine R.; Restrup, Marlene Elise; Bülow-Hansen, Julie Lee; Leerhøi, Frederik; Langkjær, Emilia Marie Rolander; Gopalakrishnan, Shyam; Carøe, Christian; Gilbert, Marcus Thomas Pius; Bohmann, Kristine (Peer reviewed; Journal article, 2021)
      Biodiversity monitoring projects using environmental DNA techniques are becoming increasingly widespread. However, these techniques depend heavily on the quality and richness of the available DNA reference database against ...
    • MobiSeq: De novo SNP discovery in model and non-model species through sequencing the flanking region of transposable elements 

      Rey-Iglesia, Alba; Gopalakrishan, Shyam; Carøe, Christian; Alquezar-Planas, David E.; Ahlmann Nielsen, Anne; Röder, Timo; Bruhn Pedersen, Lene; Næsborg-Nielsen, Christina; Sinding, Mikkel Holger Strander; Fredensborg Rath, Martin; Li, Zhipeng; Petersen, Bent; Gilbert, Marcus Thomas Pius; Bunce, Michael; Mourier, Tobias; Hansen, Anders Johannes (Peer reviewed; Journal article, 2019)
      In recent years, the availability of reduced representation library (RRL) methods has catalysed an expansion of genome‐scale studies to characterize both model and non‐model organisms. Most of these methods rely on the use ...
    • Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic marine revolution 

      Tanner, Alastair R; Fuchs, Dirk; Winkelmann, Inger E; Gilbert, Marcus Thomas Pius; Pankey, M Sabrina; Ribeiro, Angela; Kocot, Kevin M.; Halanych, Kenneth M; Oakley, Todd H; Da Fonseca, Rute R.; Pisani, Davide; Vinther, Jakob (Journal article; Peer reviewed, 2017)
      Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, ...
    • Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates 

      Andrade, Pedro; Gazda, Małgorzata A.; Araújo, Pedro M.; Afonso, Sandra; Rasmussen, Jacob A.; Marques, Cristiana I.; Lopes, Ricardo J.; Gilbert, Marcus Thomas Pius; Carneiro, Miguel (Peer reviewed; Journal article, 2021)
      Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of ...
    • A multi-omics approach unravels metagenomic and metabolic alterations of a probiotic and synbiotic additive in rainbow trout (Oncorhynchus mykiss) 

      Rasmussen, Jacob Agerbo; Villumsen, Kasper Rømer; Ernst, Madeleine; Hansen, Martin; Forberg, Torunn; Gopalakrishnan, Shyam; Gilbert, Marcus Thomas Pius; Bojesen, Anders Miki; Kristiansen, Karstein; Limborg, Morten Tønsberg (Peer reviewed; Journal article, 2022)
      Background Animal protein production is increasingly looking towards microbiome-associated services such as the design of new and better probiotic solutions to further improve gut health and production sustainability. ...
    • Natural selection shaped the rise and fall of passenger pigeon genomic diversity 

      Murray, Gemma G.R.; Soares, André E.R.; Novak, Ben J.; Schaefer, Nathan K.; Cahill, James A.; Baker, Allan J.; Demboski, John R.; Doll, Andrew; Da Fonseca, Rute R.; Fulton, Tara L.; Gilbert, Marcus Thomas Pius; Heintzman, Peter D.; Letts, Brandon; McIntosh, George; O'Connell, Brendan L.; Peck, Mark; Pipes, Marie-Lorraine; Rice, Edward S.; Santos, Kathryn M.; Sohrweide, A. Gregory; Vohr, Samuel H.; Corbett-Detig, Russell B.; Green, Richard E.; Shapiro, Beth (Journal article; Peer reviewed, 2017)
      The extinct passenger pigeon was once the most abundant bird in North America, and possibly the world. Although theory predicts that large populations will be more genetically diverse, passenger pigeon genetic diversity ...
    • Near-Random Distribution of Chromosome-Derived Circular DNA in the Condensed Genome of Pigeons and the Larger, More Repeat-Rich Human Genome 

      Møller, Henrik Devitt; Ramos-Madrigal, Jazmín; Prada-Luengo, Iñigo; Gilbert, Marcus Thomas Pius; Regenberg, Birgitte (Peer reviewed; Journal article, 2020)
      Extrachromosomal circular DNA (eccDNA) elements of chromosomal origin are known to be common in a number of eukaryotic species. However, it remains to be addressed whether genomic features such as genome size, the load of ...
    • Non-invasive surveys of mammalian viruses using environmental DNA 

      Alfano, Niccolò; Dayaram, Anisha; Axtner, Jan; Tsangaras, Kyriakos; Kampmann, Marie-Louise; Mohamed, Azlan; Wong, Seth T.; Gilbert, Marcus Thomas Pius; Wilting, Andreas; Greenwood, Alex D. (Peer reviewed; Journal article, 2021)
      Environmental DNA (eDNA) and invertebrate-derived DNA (iDNA) are used to survey biodiversity non-invasively to mitigate difficulties in obtaining wildlife samples, particularly in remote areas or for rare species. Recently, ...
    • Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics 

      Tous, Núria; Marcos, Sofia; Goodarzi Boroojeni, Farshad; Pérez de Rozas, Ana; Zentek, Jürgen; Estonba, Andone; Sandvang, Dorthe; Gilbert, Marcus Thomas Pius; Esteve-Garcia, Enric; Finn, Robert; Alberdi, Antton; Tarradas, Joan (Peer reviewed; Journal article, 2022)
      Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens ...