Dinoflagellates in the family Symbiodiniaceae are taxonomically diverse, predominantly symbiotic lineages that are well-known for their association with corals. The ancestor of these taxa is believed to have been free-living. The establishment of symbiosis (i.e., symbiogenesis) is hypothesised to have occurred multiple times during Symbiodiniaceae evolution, but its impact on genome evolution of these taxa is largely unknown. Among Symbiodiniaceae, the genus Effrenium is a free-living lineage that is phylogenetically positioned between two robustly supported groups of genera within which symbiotic taxa have emerged. The apparent lack of symbiogenesis in Effrenium suggests that the ancestral features of Symbiodiniaceae may have been retained in this lineage. Here we present de novo assembled genomes (1.2–1.9 Gbp in size) and transcriptome data from three isolates of Effrenium voratum and conduct a comparative analysis that includes 16 Symbiodiniaceae taxa and the other dinoflagellates. Surprisingly, we find that genome reduction, which is often associated with a symbiotic lifestyle, predates the origin of Symbiodiniaceae. The free-living lifestyle distinguishes Effrenium from symbiotic Symbiodiniaceae vis-à-vis their longer introns, more-extensive mRNA editing, fewer (~30%) lineage-specific gene sets, and lower (~10%) level of pseudogenisation. These results demonstrate how genome reduction and the adaptation to distinct lifestyles intersect to drive diversification and genome evolution of Symbiodiniaceae.

中文翻译：

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基因组的大规模减少早于共生甲藻的分化

共生甲藻科中的甲藻在分类学上具有多样性，主要是共生谱系，因其与珊瑚的关系而闻名。这些类群的祖先被认为是自由生活的。据推测，共生关系的建立（即共生发生）在共生科进化过程中多次发生，但其对这些类群基因组进化的影响很大程度上未知。在共生科中，Effrenium 属是一个自由生活的谱系，在系统发育上位于两个得到有力支持的属群之间，在这两个属群中出现了共生类群。 Effrenium 中明显缺乏共生发生，这表明共生科的祖先特征可能保留在这个谱系中。在这里，我们展示了来自 Effrenium v​​oratum 三个分离株的从头组装的基因组（大小为 1.2-1.9 Gbp）和转录组数据，并进行了包括 16 个共生科类群和其他甲藻的比较分析。令人惊讶的是，我们发现通常与共生生活方式相关的基因组减少早于共生科的起源。自由生活的生活方式将 Effrenium 与共生共生科的区别在于其更长的内含子、更广泛的 mRNA 编辑、更少 (~30%) 的谱系特异性基因集以及更低 (~10%) 的假基因化水平。这些结果证明了基因组减少和对不同生活方式的适应如何相互交叉以推动共生科的多样化和基因组进化。