University of Mississippi eGrove Faculty and Student Publications Biology 1-1-2019 Giant tortoise genomes provide insights into longevity and age- related disease Víctor Quesada Instituto Universitario de Oncologia del Principado de Asturias Sandra Freitas-Rodríguez Instituto Universitario de Oncologia del Principado de Asturias Joshua Miller Yale University José G. Pérez-Silva Instituto Universitario de Oncologia del Principado de Asturias Zi Feng Jiang Institute for Genomics & Systems Biology, University of Chicago See next page for additional authors Follow this and additional works at: https://egrove.olemiss.edu/biology_facpubs Recommended Citation Quesada, V., Freitas-Rodríguez, S., Miller, J., Pérez-Silva, J. G., Jiang, Z.-F., Tapia, W., Santiago-Fernández, O., Campos-Iglesias, D., Kuderna, L. F. K., Quinzin, M., Álvarez, M. G., Carrero, D., Beheregaray, L. B., Gibbs, J. P., Chiari, Y., Glaberman, S., Ciofi, C., Araujo-Voces, M., Mayoral, P., … López-Otín, C. (2019). Giant tortoise genomes provide insights into longevity and age-related disease. Nature Ecology & Evolution, 3(1), 87–95. https://doi.org/10.1038/s41559-018-0733-x This Article is brought to you for free and open access by the Biology at eGrove. It has been accepted for inclusion in Faculty and Student Publications by an authorized administrator of eGrove. For more information, please contact [email protected]. Authors Víctor Quesada, Sandra Freitas-Rodríguez, Joshua Miller, José G. Pérez-Silva, Zi Feng Jiang, Washington Tapia, Olaya Santiago-Fernández, Diana Campos-Iglesias, Lukas F.K. Kuderna, Maud Quinzin, Miguel G. Álvarez, Dido Carrero, Luciano B. Beheregaray, James P. Gibbs, Ylenia Chiari, Scott Glaberman, Claudio Ciofi, Miguel Araujo-Voces, Pablo Mayoral, Javier R. Arango, Isaac Tamargo-Gómez, David Roiz-Valle, María Pascual-Torner, Benjamin R. Evans, Danielle L. Edwards, Ryan C. Garrick, Michael A. Russello, Nikos Poulakakis, Stephen J. Gaughran, Danny O. Rueda, Gabriel Bretones, and Tomàs Marquès-Bonet This article is available at eGrove: https://egrove.olemiss.edu/biology_facpubs/28 ARTICLES https://doi.org/10.1038/s41559-018-0733-x Giant tortoise genomes provide insights into longevity and age-related disease Víctor Quesada 1,19, Sandra Freitas-Rodríguez1,19, Joshua Miller 2,19, José G. Pérez-Silva 1,19, Zi-Feng Jiang3, Washington Tapia4,5, Olaya Santiago-Fernández1, Diana Campos-Iglesias1, Lukas F. K. Kuderna 6,7, Maud Quinzin2, Miguel G. Álvarez1, Dido Carrero1, Luciano B. Beheregaray8, James P. Gibbs9, Ylenia Chiari 10, Scott Glaberman 10, Claudio Ciofi 11, Miguel Araujo-Voces1, Pablo Mayoral1, Javier R. Arango1, Isaac Tamargo-Gómez1, David Roiz-Valle1, María Pascual-Torner1, Benjamin R. Evans 2, Danielle L. Edwards12, Ryan C. Garrick13, Michael A. Russello 14, Nikos Poulakakis15,16, Stephen J. Gaughran2, Danny O. Rueda4, Gabriel Bretones1, Tomàs Marquès-Bonet 6,7,17,18, Kevin P. White3, Adalgisa Caccone 2* and Carlos López-Otín 1* Giant tortoises are among the longest-lived vertebrate animals and, as such, provide an excellent model to study traits like longevity and age-related diseases. However, genomic and molecular evolutionary information on giant tortoises is scarce. Here, we describe a global analysis of the genomes of Lonesome George—the iconic last member of Chelonoidis abingdonii—and the Aldabra giant tortoise (Aldabrachelys gigantea). Comparison of these genomes with those of related species, using both unsupervised and supervised analyses, led us to detect lineage-specific variants affecting DNA repair genes, inflammatory mediators and genes related to cancer development. Our study also hints at specific evolutionary strategies linked to increased lifespan, and expands our understanding of the genomic determinants of ageing. These new genome sequences also provide important resources to help the efforts for restoration of giant tortoise populations. omparative genomic analyses leverage the mechanisms of nat- evolution of turtles, and provide novel candidate genes that might ural selection to find genes and biochemical pathways related underlie the extraordinary characteristics of giant tortoises, includ- Cto complex traits and processes. Multiple works have used ing their gigantism and longevity. these techniques with the genomes of long-lived mammals to shed light on the signalling and metabolic networks that might play a role Results and discussion in regulating age-related conditions1,2. Similar studies on unrelated The genome of Lonesome George was sequenced using a combina- longevous organisms might unveil novel evolutionary strategies and tion of Illumina and PacBio platforms (Supplementary Section 1.1). genetic determinants of ageing in different environments. In this The assembled genome (CheloAbing 1.0) has a genomic size regard, giant tortoises constitute one of the few groups of vertebrates of 2.3 gigabases and contains 10,623 scaffolds with an N50 of with an exceptional longevity: in excess of 100 years according to 1.27 megabases (Supplementary Section 1.1 and Supplementary some estimates. Tables 1–3). We also sequenced, with the Illumina platform, the In this manuscript, we report the genomic sequencing and closely related tortoise A. gigantea at an average read depth of 28× . comparative genomic analysis of two long-lived giant tortoises: These genomic sequences were aligned to CheloAbing 1.0. Lonesome George—the last representative of Chelonoidis abingdo- TimeTree database estimations (http://www.timetree.org) indi- nii3, endemic to the island of Pinta (Galapagos Islands, Ecuador)— cate that Galapagos and Aldabra giant tortoises shared a last com- and an individual of Aldabrachelys gigantea, endemic to the Aldabra mon ancestor about 40 million years ago, while both diverged from Atoll and the only extant species of giant tortoises in the Indian the human lineage more than 300 million years ago (Supplementary Ocean4 (Fig. 1a). Unsupervised and supervised comparative analy- Section 1.4). A preliminary analysis of demographic history using ses of these genomic sequences add new genetic information on the the pairwise sequentially Markovian coalescent (PSMC)5 model 1Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología del Principado de Asturias, CIBERONC, Universidad de Oviedo, Oviedo, Spain. 2Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA. 3Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA. 4Galapagos National Park Directorate, Galapagos Islands, Ecuador. 5Galapagos Conservancy, Fairfax, VA, USA. 6Institute of Evolutionary Biology (UPF-CSIC), Barcelona, Spain. 7CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology , Barcelona, Spain. 8College of Science and Engineering, Flinders University, Adelaide, South Australia, Australia. 9College of Environmental Science and Forestry, State University of New York, Syracuse, NY, USA. 10Department of Biology, University of South Alabama, Mobile, AL, USA. 11Department of Biology, University of Florence, Florence, Italy. 12School of Natural Sciences, University of California, Merced, CA, USA. 13Department of Biology, University of Mississippi, Oxford, MS, USA. 14Department of Biology, The University of British Columbia, Kelowna, British Columbia, Canada. 15Department of Biology, School of Sciences and Engineering, University of Crete, Heraklion, Greece. 16Natural History Museum of Crete, Heraklion, Greece. 17Catalan Institution of Research and Advanced Studies, Barcelona, Spain. 18Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain. 19These authors contributed equally: Víctor Quesada, Sandra Freitas-Rodríguez, Joshua Miller, José G. Pérez-Silva. *e-mail: [email protected]; [email protected] NatURE Ecology & EvolUTION | VOL 3 | JANUARY 2019 | 87–95 | www.nature.com/natecolevol 87 ARTICLES NATURE ECOLOGY & EVOLUTION ab Pinta 5 A. gigantea Marchena Genovesa C. abingdonii Galapagos Islands 4 Santiago Fernandina Santa Cruz Pinzón 3 Santa Fé San Cristóbal Isabela 2 Floreana Española Effective population size (×10,000) 1 0 1 × 105 1 × 107 Years before present Malabar Picard Grande Terre Aldabra Atoll Fig. 1 | Geographical and temporal distribution of giant tortoises. a, Satellite view of the Galapagos Islands (top; scale bar: 50 km) and Aldabra Atoll (bottom left; scale bar: 10 km), and pictures of C. abingdonii (middle) and A. gigantea (bottom right). Both pictures are from http://eol.jsc.nasa.gov. b, Demographic history of giant tortoises, inferred using a hidden Markov model approach as implemented in the PSMC model. The default mutation rate (μ) for humans of 2.5 × 10−8 and an average generation time (g) of 25 years were used in the calculations. showed that while the effective population size of C. abingdonii expansion in a common ancestor of C. abingdonii and A. gigantea. has been steadily declining for the past million years, with a slight Almost all of these expansions were also confirmed in the genome uptick about 90,000 years ago, the population of Aldabra giant of the related, long-lived tortoise Gopherus agassizii (Supplementary tortoises experienced substantial fluctuations over this period Section 1.2 and Supplementary Table 4). Most of these genes have (Fig. 1b). Effective population size reconstructions for C. abingdonii been linked to exosome formation, suggesting that this process may lose statistical power at the million-year time frame, probably due to have been important