Full-length transcriptome maps of reef-building coral illuminate the molecular basis of calcification, symbiosis, and circadian genes

We sequenced the full-length transcriptomes of four common and frequently dominant reef-building corals, including two Robusta clade species, <i>Pocillopora damicornis</i> and <i>Pocillopora verrucosa</i>, and two Complexa clade species, <i>Acropora muricata</i> and <i>Montipora foliosa</i><i>,</i> using the PacBio Sequel II platform. We obtained information on gene functions, structures and expression profiles. Among them, a comparative analysis of biomineralization-related genes provided insights into the molecular basis of coral skeletal density. The gene expression profiles of the symbiote Symbiodiniaceae were also isolated and annotated from the holobiont sequence data; these profiles showed more highly convergent traits related to gene structure and expression level than those of coral hosts. Interestingly, we observed that intracellular algal cells share some evolutionary convergence between intracellular symbiosis in corals and intracellular digestion in amphioxus. Finally, a phylogenetic analysis of key circadian clock genes among 27 evolutionarily representative species indicated that there are four key members in early metazoans, including <i>cry </i>genes; <i>Clock</i> or <i>Npas2</i>; <i>cyc</i> or <i>Arntl</i>; and <i>tim</i>, while <i>per</i>, as the fifth member, occurs in Bilateria.

本研究采用PacBio Sequel II测序平台，对4种常见且为优势种的造礁珊瑚开展全长转录组测序：其中包含2种粗壮演化支（Robusta clade）物种，即鹿角杯形珊瑚（<i>Pocillopora damicornis</i>）与疣杯形珊瑚（<i>Pocillopora verrucosa</i>）；以及2种复杂演化支（Complexa clade）物种，即枝状轴孔珊瑚（<i>Acropora muricata</i>）与叶状微孔珊瑚（<i>Montipora foliosa</i>）。本研究获取了这些样本的基因功能、结构与表达谱信息。其中，针对生物矿化（biomineralization）相关基因的比较分析，为解析珊瑚骨骼密度的分子基础提供了重要见解。研究人员同时从全共生体（holobiont）测序数据中分离并注释了共生伙伴虫黄藻科（Symbiodiniaceae）的基因表达谱；相较于珊瑚宿主，虫黄藻的基因结构与表达水平呈现出更为显著的趋同演化特征。有趣的是，本研究观察到胞内藻类细胞在珊瑚的胞内共生与文昌鱼的胞内消化之间存在部分演化趋同现象。最后，本研究对27种具有演化代表性的物种的关键生物钟（circadian clock）基因开展系统发育分析，结果显示早期后生动物中存在4个核心生物钟基因成员，分别为<i>cry</i>基因、<i>Clock</i>或<i>Npas2</i>、<i>cyc</i>或<i>Arntl</i>以及<i>tim</i>；而作为第5个核心成员的<i>per</i>基因仅存在于两侧对称动物（Bilateria）中。