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Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium

View ORCID ProfileRaúl A. González-Pech, View ORCID ProfileTimothy G. Stephens, Yibi Chen, View ORCID ProfileAmin R. Mohamed, View ORCID ProfileYuanyuan Cheng, View ORCID ProfileDavid W. Burt, View ORCID ProfileDebashish Bhattacharya, View ORCID ProfileMark A. Ragan, View ORCID ProfileCheong Xin Chan
doi: https://doi.org/10.1101/783902
Raúl A. González-Pech
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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Yibi Chen
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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Yuanyuan Cheng
3UQ Genomics Initiative, The University of Queensland, Brisbane, QLD 4072, Australia
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David W. Burt
3UQ Genomics Initiative, The University of Queensland, Brisbane, QLD 4072, Australia
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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

Symbiodiniaceae are predominantly symbiotic dinoflagellates critical to corals and other reef organisms. Symbiodinium is a basal symbiodiniacean lineage and includes symbiotic and free-living taxa. However, the molecular mechanisms underpinning these distinct lifestyles remain little known. Here, we present high-quality de novo genome assemblies for the symbiotic Symbiodinium tridacnidorum CCMP2592 (genome size 1.3 Gbp) and the free-living Symbiodinium natans CCMP2548 (genome size 0.74 Gbp). These genomes display extensive sequence divergence, sharing only ~1.5% conserved regions (≥90% identity). We predicted 45,474 and 35,270 genes for S. tridacnidorum and S. natans, respectively; of the 58,541 homologous gene families, 28.5% are common to both genomes. We recovered a greater extent of gene duplication and higher abundance of repeats, transposable elements and pseudogenes in the genome of S. tridacnidorum than in that of S. natans. These findings demonstrate that genome structural rearrangements are pertinent to distinct lifestyles in Symbiodinium, and may contribute to the vast genetic diversity within the genus, and more broadly in Symbiodiniaceae. Moreover, the results from our whole-genome comparisons against a free-living outgroup support the notion that the symbiotic lifestyle is a derived trait in, and that the free-living lifestyle is ancestral to, Symbiodinium.

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

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Posted September 26, 2019.
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Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium
Raúl A. González-Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
bioRxiv 783902; doi: https://doi.org/10.1101/783902
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Structural rearrangements drive extensive genome divergence between symbiotic and free-living Symbiodinium
Raúl A. González-Pech, Timothy G. Stephens, Yibi Chen, Amin R. Mohamed, Yuanyuan Cheng, David W. Burt, Debashish Bhattacharya, Mark A. Ragan, Cheong Xin Chan
bioRxiv 783902; doi: https://doi.org/10.1101/783902

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