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）属于剑尾目螯肢动物（xiphosuran chelicerates），是蛛形纲（arachnids）的姊妹群。正因如此，其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）的演化与多样化进程具有重要研究价值。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重点之一。同理，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，对于阐明螯肢动物中视蛋白的演化与多样化（目前学界对螯肢动物视蛋白的认知仍较为有限），乃至更广泛的节肢动物类群，都具备关键的科学意义。本研究对美洲鲎的高质量核基因组序列进行了测序与组装，并依托该数据注释得到了美洲鲎视蛋白的全套编码基因。我们对美洲鲎视蛋白开展了细致的系统发育分析，包括借助基因结构与同线性（synteny）信息来甄别不同视蛋白类群间的演化关联。基于所构建的系统发育树，我们识别出了塑造视蛋白演化、进而影响美洲鲎视觉系统的关键基因组事件。此外，我们还描述了所鉴定出的18种视蛋白的组织表达谱，并证实包括过氧视蛋白（peropsin）在内的多种视蛋白的转录本广泛分布于中枢神经系统中。本研究不仅大幅深化了我们对美洲鲎光敏感性的认知，为鲎类视蛋白的基因组演化提供了关键见解，同时也为解决剑尾目生理学与节肢动物演化相关的诸多科学问题提供了极具价值的基因组资源。