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Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels

View ORCID ProfileRaúl A. González-Pech, View ORCID ProfileYibi Chen, View ORCID ProfileTimothy G. Stephens, View ORCID ProfileSarah Shah, View ORCID ProfileAmin R. Mohamed, Rémi Lagorce, View ORCID ProfileDebashish Bhattacharya, View ORCID ProfileMark A. Ragan, View ORCID ProfileCheong Xin Chan
doi: https://doi.org/10.1101/800482
Raúl A. González-Pech
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Yibi Chen
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Timothy G. Stephens
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Sarah Shah
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Amin R. Mohamed
2Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia, QLD 4072, Australia
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Rémi Lagorce
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
3École Polytechnique Universitaire de l’Université de Nice, Université Nice-Sophia-Antipolis, Nice, Provence-Alpes-Côte d’Azur 06410, France
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Debashish Bhattacharya
4Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, U.S.A.
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Mark A. Ragan
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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Cheong Xin Chan
1Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
5School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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  • For correspondence: c.chan1@uq.edu.au
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Abstract

Dinoflagellates of the family Symbiodiniaceae (Order Suessiales) are predominantly symbiotic, and many are known for their association with corals. The genetic and functional diversity among Symbiodiniaceae is well acknowledged, but the genome-wide sequence divergence among these lineages remains little known. Here, we present de novo genome assemblies of five isolates from the basal genus Symbiodinium, encompassing distinct ecological niches. Incorporating existing data from Symbiodiniaceae and other Suessiales (15 genome datasets in total), we investigated genome features that are common or unique to these Symbiodiniaceae, to genus Symbiodinium, and to the individual species S. microadriaticum and S. tridacnidorum. Our whole-genome comparisons reveal extensive sequence divergence, with no sequence regions common to all 15. Based on similarity of k-mers from whole-genome sequences, the distances among Symbiodinium isolates are similar to those between isolates of distinct genera. We observed extensive structural rearrangements among symbiodiniacean genomes; those from two distinct Symbiodinium species share the most (853) syntenic gene blocks. Functions enriched in genes core to Symbiodiniaceae are also enriched in those core to Symbiodinium. Gene functions related to symbiosis and stress response exhibit similar relative abundance in all analysed genomes. Our results suggest that structural rearrangements contribute to genome sequence divergence in Symbiodiniaceae even within a same species, but the gene functions have remained largely conserved in Suessiales. This is the first comprehensive comparison of Symbiodiniaceae based on whole-genome sequence data, including comparisons at the intra-genus and intra-species levels.

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  • https://cloudstor.aarnet.edu.au/plus/s/095Tqepmq2VBztd

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted October 10, 2019.
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Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels
Raúl A. González-Pech, Yibi Chen, Timothy G. Stephens, Sarah Shah, Amin R. Mohamed, Rémi Lagorce, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
bioRxiv 800482; doi: https://doi.org/10.1101/800482
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Genomes of Symbiodiniaceae reveal extensive sequence divergence but conserved functions at family and genus levels
Raúl A. González-Pech, Yibi Chen, Timothy G. Stephens, Sarah Shah, Amin R. Mohamed, Rémi Lagorce, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
bioRxiv 800482; doi: https://doi.org/10.1101/800482

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