Table S2: Similarity/identity matrix of RLuc-like predicted proteins from A puzzling homology: a brittle star using a putative cnidarian-type luciferase for bioluminescence

Bioluminescence relies on the oxidation of a luciferin substrate catalysed by a luciferase enzyme. Luciferins and luciferases are generic terms used to describe a large variety of substrates and enzymes. Whereas luciferins can be shared by phylogenetically distant organisms which feed on organisms producing them, luciferases have been thought to be lineage-specific enzymes. Numerous light emission systems would then have co-emerged independently along the tree of life resulting in a plethora of non-homologous luciferases. Here, we identify for the first time a candidate luciferase of a luminous echinoderm, the ophiuroid <i>Amphiura filiformis</i>. Phylogenomic analyses identified the brittle star predicted luciferase as homologous to the luciferase of the sea pansy <i>Renilla</i> (Cnidaria), contradicting with the traditional viewpoint according to which luciferases would generally be of convergent origins. The similarity between the <i>Renilla</i> and <i>Amphiura</i> luciferases allowed us to detect the latter using anti-<i>Renilla</i> luciferase antibodies. Luciferase expression was specifically localized in the spines which were demonstrated to be the bioluminescent organs <i>in vivo</i>. However, enzymes homologous to the <i>Renilla</i> luciferase but unable to trigger light emission were also identified in non-luminous echinoderms and metazoans. Our findings strongly indicate that those enzymes, belonging to the haloalkane dehalogenase family, might then have been convergently co-opted into luciferases in cnidarians and echinoderms. In these two benthic suspension-feeding species, similar ecological pressures would constitute strong selective forces for the functional shift of these enzymes and the emergence of bioluminescence.

生物发光（bioluminescence）依赖于由荧光素酶（luciferase）催化的荧光素（luciferin）底物氧化反应。荧光素与荧光素酶是用于描述多样底物与酶的通用术语。尽管系统发育亲缘关系较远的生物，若以产生该荧光素的生物为食，可共享荧光素，但此前学界普遍认为荧光素酶属于谱系特异性酶。据此推测，生命演化树中曾独立协同演化出诸多发光系统，由此催生了大量非同源荧光素酶。
本研究首次鉴定出一种发光棘皮动物——蛇尾纲<i>Amphiura filiformis</i>（丝鳃蛇尾）的候选荧光素酶。系统基因组分析（phylogenomic analysis）显示，该蛇尾预测的荧光素酶与海笔<i>Renilla</i>（Renilla，刺胞动物门（Cnidaria））的荧光素酶同源，这与“荧光素酶通常起源于趋同演化”的传统观点相悖。基于<i>Renilla</i>与<i>Amphiura filiformis</i>荧光素酶的序列相似性，我们可通过抗<i>Renilla</i>荧光素酶抗体检测到该酶。荧光素酶的表达特异性定位于棘突——经体内（in vivo）实验证实，棘突即为该物种的发光器官。
然而，研究人员在非发光棘皮动物与后生动物（metazoans）中，也发现了与<i>Renilla</i>荧光素酶同源但无法触发发光反应的酶。本研究结果有力表明，这类隶属于卤代烷脱卤酶家族（haloalkane dehalogenase family）的酶，可能在刺胞动物与棘皮动物中被趋同共招募为荧光素酶。在这两种底栖滤食性物种中，相似的生态压力构成了强大的选择压力，推动这些酶发生功能转变并最终催生生物发光现象。