Data from: Opsin repertoire and expression patterns in horseshoe crabs: evidence from the genome of Limulus polyphemus (Arthropoda: Chelicerata)

Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus. We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.鲎（Horseshoe crabs）隶属于剑尾目螯肢动物（xiphosuran chelicerates），与蛛形纲（arachnids）互为姊妹群。正因如此，该类群对于解析真螯肢亚门（Euchelicerata）的最近共同祖先，以及节肢动物门（Arthropoda）的演化与辐射分化过程具有关键研究价值。美洲鲎（Limulus polyphemus）是目前已知的4种现存鲎类中研究最为深入的物种，其视觉系统的结构与功能长期以来都是解析节肢动物视觉系统演化的核心研究焦点。同样，针对美洲鲎视蛋白（opsins，视觉色素的蛋白组分）编码基因的研究，对于理解螯肢动物类群中视蛋白的演化与多样化至关重要——目前螯肢动物类群的视蛋白研究仍较为匮乏，该研究也可为更广范围的节肢动物视蛋白演化研究提供关键参考。本研究对美洲鲎（L. polyphemus）的高质量核基因组序列进行了测序与组装，并利用该数据注释了美洲鲎视蛋白的全套完整基因集合。我们对美洲鲎视蛋白开展了细致的系统发育分析，其中结合基因结构与同线性（synteny）信息，明确了不同视蛋白家族间的演化关系。我们依托该系统发育树，识别出塑造视蛋白演化、进而影响美洲鲎视觉系统形成的关键基因组事件。此外，我们还描述了所鉴定出的18种视蛋白的组织表达模式，并证实其中包括过氧视蛋白（peropsin）在内的多种视蛋白的转录本广泛分布于中枢神经系统（central nervous system）中。本研究不仅极大拓展了我们对美洲鲎光感受机制的认知，为鲎类视蛋白的基因组演化提供了关键见解，同时也为解答剑尾目生理学及节肢动物演化相关的诸多问题提供了极具价值的基因组学资源。