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Genomic signatures in the coral holobiont reveal host adaptations driven by Holocene climate change and reef specific symbionts

journal contribution
posted on 07.01.2021, 03:53 authored by Ira CookeIra Cooke, H Ying, S Forêt, P Bongaerts, Jan StrugnellJan Strugnell, O Simakov, J Zhang, MA Field, M Rodriguez-Lanetty, SC Bell, DG Bourne, MJH van Oppen, MA Ragan, DJ Miller
Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). Genetic signatures caused by demographic and adaptive processes during past climatic shifts can inform predictions of species’ responses to anthropogenic climate change. To identify these signatures in Acropora tenuis, a reef-building coral threatened by global warming, we first assembled the genome from long reads and then used shallow whole-genome resequencing of 150 colonies from the central inshore Great Barrier Reef to inform population genomic analyses. We identify population structure in the host that reflects a Pleistocene split, whereas photosymbiont differences between reefs most likely reflect contemporary (Holocene) conditions. Signatures of selection in the host were associated with genes linked to diverse processes including osmotic regulation, skeletal development, and the establishment and maintenance of symbiosis. Our results suggest that adaptation to post-glacial climate change in A. tenuis has involved selection on many genes, while differences in symbiont specificity between reefs appear to be unrelated to host population structure.


This project was supported by a Queensland Government DSITIA Accelerate Partnerships award to the University of Queensland on behalf of the Australian Institute of Marine Science (AIMS), the Australian National University, Bioplatforms Australia, the Great Barrier Reef Foundation, the Great Barrier Reef Marine Park Authority, and James Cook University (2014). This research/project was undertaken with the assistance of resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. The data used in this project were funded by the Great Barrier Reef Foundation's Resilient Coral Reefs Successfully Adapting to Climate Change research and development program in collaboration with the Australian Government, Bioplatforms Australia through the National Collaborative Research Infrastructure Strategy (NCRIS), Rio Tinto, and a family foundation. Genome sequencing was supported by the Reef Future Genomics (ReFuGe) 2020 Consortium organized by the Great Barrier Reef Foundation.


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American Association for the Advancement of Science



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