TY - JOUR T1 - Improved <em>Cladocopium goreaui</em> genome assembly reveals features of a facultative coral symbiont and the complex evolutionary history of dinoflagellate genes JF - bioRxiv DO - 10.1101/2022.07.19.500725 SP - 2022.07.19.500725 AU - Yibi Chen AU - Sarah Shah AU - Katherine E. Dougan AU - Madeleine J. H. van Oppen AU - Debashish Bhattacharya AU - Cheong Xin Chan Y1 - 2022/01/01 UR - http://biorxiv.org/content/early/2022/07/20/2022.07.19.500725.abstract N2 - Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these algae, 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 earlier 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 broadly sampled eukaryotes and representative prokaryotes in a phylogenomic approach, we assessed the evolutionary history of C. goreaui genes. Of the 5,246 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.Competing Interest StatementThe authors have declared no competing interest. ER -