Chen Yibi, Shah Sarah, Dougan Katherine E, van Oppen Madeleine J H, Bhattacharya Debashish, Chan Cheong Xin
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
School of Bioscience, The University of Melbourne, Parkville, VIC 3010, Australia.
Microorganisms. 2022 Aug 17;10(8):1662. doi: 10.3390/microorganisms10081662.
Dinoflagellates of the family Symbiodiniaceae are crucial photosymbionts in corals and other marine organisms. Of these, is one of the most dominant symbiont species in the Indo-Pacific. Here, we present an improved genome assembly of combining new long-read sequence data with previously generated short-read data. Incorporating new full-length transcripts to guide gene prediction, the 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 , 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 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.
共生藻科的甲藻是珊瑚和其他海洋生物中至关重要的光合共生体。其中，[具体物种名称]是印度-太平洋地区最主要的共生体物种之一。在此，我们结合新的长读长序列数据和先前生成的短读长数据，展示了对[具体物种名称]的改进基因组组装。纳入新的全长转录本以指导基因预测，[具体物种名称]的基因组（1.2 Gb）具有高度的完整性（基于BUSCO蛋白回收率为82.4%），并且对重复序列区域有更好的解析度；预测了45,322个基因模型，并识别出327个推定的染色体拓扑相关结构域。与其他共生藻科基因组的比较揭示了[具体物种名称]中重复序列和重复基因的普遍性，以及表明功能创新的谱系特异性基因。通过系统发育基因组学方法纳入来自96种分类学上不同的真核生物和代表性原核生物的2,841,408个蛋白质序列，我们评估了[具体物种名称]基因的进化历史。在从包含两个或更多门的同源蛋白集推断出的5246个系统发育树中，35 - 36%可能通过水平基因转移（HGT）起源，主要（19 - 23%）通过与质体内共生起源相关的祖先古质体谱系：10 - 11%是绿藻起源，包括编码光合功能的基因。我们的结果证明了长读长序列数据在解析甲藻基因组结构特征方面的效用，并突出了基因转移如何塑造了兼性共生体以及更广泛的甲藻的基因组进化。
