Data from: Novel predators reshape holozoan phylogeny and reveal the presence of a two-component signalling system in the ancestor of animals

Our understanding of the origin of animals has been transformed by characterizing their most closely related, unicellular sisters: the choanoflagellates, filastereans, and ichthyosporeans. Together with animals, these lineages make up the Holozoa [ 1, 2 ]. Many traits previously considered “animal specific” were subsequently found in other holozoans [ 3, 4 ], showing that they evolved before animals, although exactly when is currently uncertain because several key relationships remain unresolved [ 2, 5 ]. Here we report the morphology and transcriptome sequencing from three novel unicellular holozoans: Pigoraptor vietnamica and Pigoraptor chileana, which are related to filastereans, and Syssomonas multiformis, which forms a new lineage with Corallochytrium in phylogenomic analyses. All three species are predatory flagellates that feed on large eukaryotic prey, and all three also appear to exhibit complex life histories with several distinct stages, including multicellular clusters. Examination of genes associated with multicellularity in animals showed that the new filastereans contain a cell-adhesion gene repertoire similar to those of other species in this group. Syssomonas multiformis possessed a smaller complement overall but does encode genes absent from the earlier-branching ichthyosporeans. Analysis of the T-box transcription factor domain showed expansion of T-box transcription factors based on combination with a non-T-box domain (a receiver domain), which has not been described outside of vertebrates. This domain and other domains we identified in all unicellular holozoans are part of the two-component signaling system that has been lost in animals, suggesting the continued use of this system in the closest relatives of animals and emphasizing the importance of studying loss of function as well as gain in major evolutionary transitions.

通过对与动物亲缘关系最近的单细胞姊妹类群——领鞭毛虫（choanoflagellates）、丝足虫类（filastereans）与鱼孢霉类（ichthyosporeans）——的研究，我们对动物起源的认知已被彻底重塑。这些类群与动物共同构成全动物类群（Holozoa）[1,2]。此前被认为是"动物特有"的诸多性状，后续在其他全动物类群中均有发现[3,4]，这表明这些性状的起源早于动物，但由于若干关键亲缘关系仍未解析清楚，其具体演化时间目前尚无定论[2,5]。本研究报道了3个全新的单细胞全动物类群的形态学与转录组测序数据：分别为与丝足虫类亲缘关系相近的越南噬虫（Pigoraptor vietnamica）与智利噬虫（Pigoraptor chileana），以及在系统基因组学分析中与珊瑚囊孢菌（Corallochytrium）共同构成一新分支的多形索单胞虫（Syssomonas multiformis）。这三个物种均为以大型真核生物为食的捕食性鞭毛虫，且均展现出复杂的生活史，包含多个不同的发育阶段，其中包括多细胞集群。对动物多细胞性相关基因的分析显示，新发现的丝足虫类物种拥有一套与该类群其他物种相似的细胞黏附基因库。多形索单胞虫（Syssomonas multiformis）的整体基因总量更少，但确实编码了早期分化的鱼孢霉类所不具备的基因。对T-box转录因子结构域（T-box transcription factor domain）的分析显示，结合非T-box结构域（受体结构域）的T-box转录因子发生了扩张，这类组合在脊椎动物之外尚未见报道。我们在所有单细胞全动物类群中鉴定出的该结构域与其他结构域，均属于双组分信号系统（two-component signaling system）的组成部分，而该系统在动物中已发生丢失，这表明在动物的近缘类群中该系统仍被持续使用，同时也凸显了在重大演化过渡事件中，研究功能获得与功能丧失的重要性。