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      Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat

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          Abstract

          Adaptation to specialized diets often requires modifications at both genomic and microbiome levels. We applied a hologenomic approach to the common vampire bat ( Desmodus rotundus), one of the only three obligate blood-feeding (sanguivorous) mammals, to study the evolution of its complex dietary adaptation. Specifically, we assembled its high-quality reference genome (scaffold N50=26.9 Mb, contig N50=36.6 Kb) and gut metagenome, and compared them against those of insectivorous, frugivorous, and carnivorous bats. Our analyses showed i) a particular common vampire bat genomic landscape regarding integrated viral elements, ii) a dietary and phylogenetic influence on gut microbiome taxonomic and functional profiles, and iii) that both genetic elements harbor key traits related to the nutritional (e.g. vitamins and lipids shortage) and non-nutritional challenges (e.g. nitrogen waste and osmotic homeostasis) of sanguivory. These findings highlight the value of a holistic study of both host and microbiota when attempting to decipher adaptations underlying radical dietary lifestyles.

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          Most cited references51

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          Is Open Access

          Tree of Life Reveals Clock-Like Speciation and Diversification

          Genomic data are rapidly resolving the tree of living species calibrated to time, the timetree of life, which will provide a framework for research in diverse fields of science. Previous analyses of taxonomically restricted timetrees have found a decline in the rate of diversification in many groups of organisms, often attributed to ecological interactions among species. Here, we have synthesized a global timetree of life from 2,274 studies representing 50,632 species and examined the pattern and rate of diversification as well as the timing of speciation. We found that species diversity has been mostly expanding overall and in many smaller groups of species, and that the rate of diversification in eukaryotes has been mostly constant. We also identified, and avoided, potential biases that may have influenced previous analyses of diversification including low levels of taxon sampling, small clade size, and the inclusion of stem branches in clade analyses. We found consistency in time-to-speciation among plants and animals, ∼2 My, as measured by intervals of crown and stem species times. Together, this clock-like change at different levels suggests that speciation and diversification are processes dominated by random events and that adaptive change is largely a separate process.
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            Repbase update: a database and an electronic journal of repetitive elements.

            J Jurka (2000)
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              The Universal Protein Resource (UniProt)

              The Universal Protein Resource (UniProt) provides a stable, comprehensive, freely accessible, central resource on protein sequences and functional annotation. The UniProt Consortium is a collaboration between the European Bioinformatics Institute (EBI), the Protein Information Resource (PIR) and the Swiss Institute of Bioinformatics (SIB). The core activities include manual curation of protein sequences assisted by computational analysis, sequence archiving, development of a user-friendly UniProt website, and the provision of additional value-added information through cross-references to other databases. UniProt is comprised of four major components, each optimized for different uses: the UniProt Knowledgebase, the UniProt Reference Clusters, the UniProt Archive and the UniProt Metagenomic and Environmental Sequences database. UniProt is updated and distributed every three weeks, and can be accessed online for searches or download at http://www.uniprot.org.
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                Author and article information

                Journal
                101698577
                46074
                Nat Ecol Evol
                Nat Ecol Evol
                Nature ecology & evolution
                2397-334X
                16 January 2018
                19 February 2018
                April 2018
                19 August 2018
                : 2
                : 4
                : 659-668
                Affiliations
                [a ]Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark
                [b ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
                [c ]China National GeneBank, BGI-Shenzhen, Shenzhen, 518083, China
                [d ]Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), Alfred-Kowalke-Straße 17, 10315 Berlin, Germany
                [e ]Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
                [f ]Institute of Biodiversity, Animal Health and Comparative Medicine & MRC-University of Glasgow Centre for Virus Research, University of Glasgow, G12 8QQ, Glasgow, United Kingdom
                [g ]Department of Biology, Stanford University, 371 Serra Mall, 94305-5020 Stanford CA, USA
                [h ]Centro Nacional de Investigación Disciplinaria en Microbiología Animal-INIFAP, Km 15.5, Blvrd. Reforma, Zedec Sta. Fé, 01219 Ciudad de México, D.F., Mexico
                [i ]San Diego Zoo Institute for Conservation Research, 15600 San Pasqual Valley Road. Escondido, 92027 CA, USA
                [j ]Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Chamilpa 62210, Cuernavaca Morelos, Mexico
                [k ]Undergraduate Program for Genomic Sciences, Center for Genomic Sciences, National Autonomous University of Mexico, Av. Universidad s/n Col. Chamilpa 62210, Cuernavaca, Morelos, Mexico
                [l ]Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
                [m ]Center for Zoo and Wild Animal Health, Copenhagen Zoo, Roskildevej 38, 2000 Frederiksberg, Denmark
                [n ]Australian Wildlife Forensic Services, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia
                [o ]Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, 6102 Perth, Australia
                [p ]Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, 2100 Copenhagen, Denmark
                [q ]Center for Biological Sequence Analysis, Department of Bio and Health Informatics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
                [r ]Norwegian University of Science and Technology, University Museum, 7491 Trondheim, Norway
                Author notes
                [* ]Correspondence should be addressed to M.L.Z.M. ( lisandracady@ 123456gmail.com ), T.S.-P. ( thomas@ 123456cbs.dtu.dk ) or M.T.P.G ( tgilbert@ 123456snm.ku.dk ).
                Article
                EMS75709
                10.1038/s41559-018-0476-8
                5868727
                29459707
                e0fe1fec-be23-475a-bee2-fcde4985e9dc

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