Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

Huanle Liu; Timothy G. Stephens; Raúl A. González-Pech; Victor H. Beltran; Bruno Lapeyre; Pim Bongaerts; Ira Cooke; Manuel Aranda; David G. Bourne; Sylvain Forêt; David J. Miller; Madeleine J. H. van Oppen; Christian R. Voolstra; Mark A. Ragan; Cheong Xin Chan

doi:10.1038/s42003-018-0098-3

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

Huanle Liu, Timothy G. Stephens, Raúl A. González-Pech, Victor H. Beltran, Bruno Lapeyre, Pim Bongaerts, Ira Cooke, Manuel Aranda, David G. Bourne, Sylvain Forêt, David J. Miller, Madeleine J. H. van Oppen, Christian R. Voolstra, Mark A. Ragan, Cheong Xin Chan

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Abstract

Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

Original language	English (US)
Journal	Communications Biology
Volume	1
Issue number	1
DOIs	https://doi.org/10.1038/s42003-018-0098-3
State	Published - Jul 17 2018

Bibliographical note

KAUST Repository Item: Exported on 2020-10-01
Acknowledgements: We thank Todd LaJeunesse for information on the original isolation of S. kawagutii. H.L. was supported by an Australian Research Council grant (DP150101875) awarded to M.A.R. and C.X.C. T.G.S. is supported by an Australian Government Research Training Program Scholarship. R.A.G.-P. is supported by an International Postgraduate Research Scholarship and a University of Queensland Centenary Scholarship. This project was supported by the computational resources of the Australian National Computational Infrastructure (NCI) National Facility systems through the NCI Merit Allocation Scheme (Project d85) awarded to M.A.R. and C.X.C. 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. The authors also acknowledge the work done by the Reef Future Genomics (ReFuGe) 2020 Consortium. Access to data generated by the consortium can be accessed via reefgenomics.org. In memory of S.F., our friend and colleague who is sorely missed.

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10.1038/s42003-018-0098-3

https://repository.kaust.edu.sa/bitstream/10754/630757/1/Symbodium.pdf

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Liu, H., Stephens, T. G., González-Pech, R. A., Beltran, V. H., Lapeyre, B., Bongaerts, P., Cooke, I., Aranda, M., Bourne, D. G., Forêt, S., Miller, D. J., van Oppen, M. J. H., Voolstra, C. R., Ragan, M. A., & Chan, C. X. (2018). Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 1(1). https://doi.org/10.1038/s42003-018-0098-3

@article{b3d34b8f8e6145cb8e1d0ec97136f9d3,

title = "Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis",

abstract = "Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world{\textquoteright}s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.",

author = "Huanle Liu and Stephens, {Timothy G.} and Gonz{\'a}lez-Pech, {Ra{\'u}l A.} and Beltran, {Victor H.} and Bruno Lapeyre and Pim Bongaerts and Ira Cooke and Manuel Aranda and Bourne, {David G.} and Sylvain For{\^e}t and Miller, {David J.} and {van Oppen}, {Madeleine J. H.} and Voolstra, {Christian R.} and Ragan, {Mark A.} and Chan, {Cheong Xin}",

note = "KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank Todd LaJeunesse for information on the original isolation of S. kawagutii. H.L. was supported by an Australian Research Council grant (DP150101875) awarded to M.A.R. and C.X.C. T.G.S. is supported by an Australian Government Research Training Program Scholarship. R.A.G.-P. is supported by an International Postgraduate Research Scholarship and a University of Queensland Centenary Scholarship. This project was supported by the computational resources of the Australian National Computational Infrastructure (NCI) National Facility systems through the NCI Merit Allocation Scheme (Project d85) awarded to M.A.R. and C.X.C. The data used in this project were funded by the Great Barrier Reef Foundation{\textquoteright}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. The authors also acknowledge the work done by the Reef Future Genomics (ReFuGe) 2020 Consortium. Access to data generated by the consortium can be accessed via reefgenomics.org. In memory of S.F., our friend and colleague who is sorely missed.",

year = "2018",

month = jul,

day = "17",

doi = "10.1038/s42003-018-0098-3",

language = "English (US)",

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Liu, H, Stephens, TG, González-Pech, RA, Beltran, VH, Lapeyre, B, Bongaerts, P, Cooke, I, Aranda, M, Bourne, DG, Forêt, S, Miller, DJ, van Oppen, MJH, Voolstra, CR, Ragan, MA & Chan, CX 2018, 'Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis', Communications Biology, vol. 1, no. 1. https://doi.org/10.1038/s42003-018-0098-3

TY - JOUR

T1 - Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

AU - Liu, Huanle

AU - Stephens, Timothy G.

AU - González-Pech, Raúl A.

AU - Beltran, Victor H.

AU - Lapeyre, Bruno

AU - Bongaerts, Pim

AU - Cooke, Ira

AU - Aranda, Manuel

AU - Bourne, David G.

AU - Forêt, Sylvain

AU - Miller, David J.

AU - van Oppen, Madeleine J. H.

AU - Voolstra, Christian R.

AU - Ragan, Mark A.

AU - Chan, Cheong Xin

N1 - KAUST Repository Item: Exported on 2020-10-01 Acknowledgements: We thank Todd LaJeunesse for information on the original isolation of S. kawagutii. H.L. was supported by an Australian Research Council grant (DP150101875) awarded to M.A.R. and C.X.C. T.G.S. is supported by an Australian Government Research Training Program Scholarship. R.A.G.-P. is supported by an International Postgraduate Research Scholarship and a University of Queensland Centenary Scholarship. This project was supported by the computational resources of the Australian National Computational Infrastructure (NCI) National Facility systems through the NCI Merit Allocation Scheme (Project d85) awarded to M.A.R. and C.X.C. 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. The authors also acknowledge the work done by the Reef Future Genomics (ReFuGe) 2020 Consortium. Access to data generated by the consortium can be accessed via reefgenomics.org. In memory of S.F., our friend and colleague who is sorely missed.

PY - 2018/7/17

Y1 - 2018/7/17

N2 - Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

AB - Symbiosis between dinoflagellates of the genus Symbiodinium and reef-building corals forms the trophic foundation of the world’s coral reef ecosystems. Here we present the first draft genome of Symbiodinium goreaui (Clade C, type C1: 1.03 Gbp), one of the most ubiquitous endosymbionts associated with corals, and an improved draft genome of Symbiodinium kawagutii (Clade F, strain CS-156: 1.05 Gbp) to further elucidate genomic signatures of this symbiosis. Comparative analysis of four available Symbiodinium genomes against other dinoflagellate genomes led to the identification of 2460 nuclear gene families (containing 5% of Symbiodinium genes) that show evidence of positive selection, including genes involved in photosynthesis, transmembrane ion transport, synthesis and modification of amino acids and glycoproteins, and stress response. Further, we identify extensive sets of genes for meiosis and response to light stress. These draft genomes provide a foundational resource for advancing our understanding of Symbiodinium biology and the coral-algal symbiosis.

UR - http://hdl.handle.net/10754/630757

UR - http://www.nature.com/articles/s42003-018-0098-3

UR - http://www.scopus.com/inward/record.url?scp=85077739264&partnerID=8YFLogxK

U2 - 10.1038/s42003-018-0098-3

DO - 10.1038/s42003-018-0098-3

M3 - Article

C2 - 30271976

SN - 2399-3642

VL - 1

JO - Communications Biology

JF - Communications Biology

IS - 1

ER -

Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis

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