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Article

Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes

1
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
2
School of Bioscience, The University of Melbourne, Parkville, VIC 3010, Australia
3
Australian Institute of Marine Science, Townsville, QLD 4810, Australia
4
Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
*
Author to whom correspondence should be addressed.
Academic Editors: Shauna Murray and Evgene Rosenberg
Microorganisms 2022, 10(8), 1662; https://doi.org/10.3390/microorganisms10081662
Received: 1 July 2022 / Revised: 10 August 2022 / Accepted: 15 August 2022 / Published: 17 August 2022
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, Cladocopium goreaui is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of C. goreaui combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the C. goreaui genome (1.2 Gb) exhibits a high extent of completeness (82.4% based on BUSCO protein recovery) and better resolution of repetitive sequence regions; 45,322 gene models were predicted, and 327 putative, topologically associated domains of the chromosomes were identified. Comparison with other Symbiodiniaceae genomes revealed a prevalence of repeats and duplicated genes in C. goreaui, and lineage-specific genes indicating functional innovation. Incorporating 2,841,408 protein sequences from 96 taxonomically diverse eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5246 phylogenetic trees inferred from homologous protein sets containing two or more phyla, 35–36% have putatively originated via horizontal gene transfer (HGT), predominantly (19–23%) via an ancestral Archaeplastida lineage implicated in the endosymbiotic origin of plastids: 10–11% are of green algal origin, including genes encoding photosynthetic functions. Our results demonstrate the utility of long-read sequence data in resolving structural features of a dinoflagellate genome, and highlight how genetic transfer has shaped genome evolution of a facultative symbiont, and more broadly of dinoflagellates. View Full-Text
Keywords: dinoflagellates; genome; Cladocopium goreaui; phylogenomics; horizontal gene transfer dinoflagellates; genome; Cladocopium goreaui; phylogenomics; horizontal gene transfer
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MDPI and ACS Style

Chen, Y.; Shah, S.; Dougan, K.E.; van Oppen, M.J.H.; Bhattacharya, D.; Chan, C.X. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms 2022, 10, 1662. https://doi.org/10.3390/microorganisms10081662

AMA Style

Chen Y, Shah S, Dougan KE, van Oppen MJH, Bhattacharya D, Chan CX. Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes. Microorganisms. 2022; 10(8):1662. https://doi.org/10.3390/microorganisms10081662

Chicago/Turabian Style

Chen, Yibi, Sarah Shah, Katherine E. Dougan, Madeleine J. H. van Oppen, Debashish Bhattacharya, and Cheong Xin Chan. 2022. "Improved Cladocopium goreaui Genome Assembly Reveals Features of a Facultative Coral Symbiont and the Complex Evolutionary History of Dinoflagellate Genes" Microorganisms 10, no. 8: 1662. https://doi.org/10.3390/microorganisms10081662

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