NSF-BSF: Identifying genetic mechanisms underpinning eye loss in troglomorphic arachnids

洞穴生境是研究生物适应性和形态趋同性的重要环境。在穴居生物中反复进化的一个引人注目的特征是失去眼睛。捕食性节肢动物如蛛形纲动物（例如，蜘蛛和收割者）在洞穴生态系统中发挥着重要作用，该小组包括许多适应洞穴的盲种的例子。然而，人们对蜘蛛目动物的眼睛是如何发育的知之甚少，更不用说这些眼睛是如何在洞穴特化的蜘蛛目动物中消失的了。这个两国项目汇集了一个美国-以色列团队，以促进对蜘蛛眼睛进化发育生物学的理解。为了研究眼睛是如何在洞穴适应蛛形纲动物中丢失的，胚胎发育将在三个蛛形纲动物目（蜘蛛，鞭蜘蛛和收割者）中的每一个中比较一对姐妹物种，这些物种将通过密集的实地考察活动收集;在每一对中，表面物种具有眼睛，其姐妹物种是盲人。为了确定眼变性的基因组基础，将为这六个物种建立高质量的参考基因组，并使用并行化短读段测序对基因表达进行分析。为了验证从基因组数据集推断出的洞穴适应性的关键基因puerectin的预测，将在两种模式蛛形纲动物物种中进行基因沉默筛选，目的是在自然界观察到的模式与实验室中的功能数据集之间建立直接联系。 通过与更好地研究的脊椎动物和泛甲壳动物（例如，昆虫;等足类甲壳动物）模型，在螯肢动物的眼睛发育仍然很少研究。关于蛛形纲动物眼睛的发育遗传学，没有数据集可超越原位杂交测定;甚至蛛形纲动物眼睛的形态发生仍然从现代成像工具包的角度，相对于脊椎动物和泛甲壳类动物的同行。然而，从比较生物学的角度来看，蜘蛛目动物的眼睛是有意义的，原因有二。首先，与泛甲壳纲动物的主要一对复眼（多面）相反，蛛形纲动物有多对眼睛，大致分为两种类型的单眼，它们在结构和功能上彼此不同。蛛形纲动物的另一个复杂性是，包括蝎子和蜘蛛等谱系在内的一个目的子集经历了共享的基因组复制，导致了许多视网膜决定基因网络（RDGN）同源物的旁系同源物，这些同源物参与了许多其他两侧性群体的眼睛图案。拟议的工作将使用一个比较框架来询问蛛形纲动物眼睛的发展，该框架对三个关键的蛛形纲动物进行了采样，旨在建立一个比较平台，将独立进化的谱系纳入洞穴生物学研究，以及了解基因组复制后paradion功能的进化。除了建立研究节肢动物发育的新模型系统外，这项研究还将建立新的基因组资源和工具包，用于破译从自然进化的洞穴系统推断的发育过程的进化。生物科学局的这项研究奖由综合和有机系统司的发育系统和EDGE计划资助，该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

Cave habitats are remarkable environments for the study of biological adaptations and morphological convergence. One compelling trait that has repeatedly evolved in cave-dwelling organisms is loss of the eyes. Predatory arthropods like arachnids (e.g., spiders and harvestmen) play an important role in cave ecosystems and the group includes many examples of cave-adapted blind species. However, remarkably little is known about how arachnid eyes develop, much less how these eyes are lost in cave-specialized arachnids. This binational project brings together a US-Israeli team to advance understanding the evolutionary developmental biology of arachnid eyes. To examine how eyes are lost in cave-adapted arachnids, embryonic development will be compared for a sister-species pair in each of three arachnid orders (spiders, whip spiders, and harvestmen) that will be collected through intensive fieldwork campaigns; in each pair, a surface species bears eyes and its sister species is blind. To determine the genomic basis for eye degeneration, high-quality reference genomes will be established for these six species, together with profiling of gene expression using parallelized short read sequencing. To validate predictions of key genes putatively underlying cave adaptations that are inferred from genomic datasets, gene silencing screens will be performed in two model arachnid species, with the goal of establishing a direct link between patterns observed in nature and functional datasets in the laboratory. By comparison to better-studied vertebrate and pancrustacean (e.g., insects; isopod crustaceans) models, eye development in Chelicerata remains poorly studied. With respect to the developmental genetics of arachnid eyes, no datasets are available beyond in situ hybridization assays; even the morphogenesis of arachnid eyes remains underexplored from the perspective of modern imaging toolkits, relative to vertebrate and pancrustacean counterparts. Yet, the arachnid eye is of interest from the standpoint of comparative biology for two reasons. First, in contrast to the main pair of compound (faceted) eyes of pancrustaceans, arachnids bear multiple eye pairs broadly divided into two types of ocelli, which are structurally and functionally distinct from each other. A further complexity of arachnids is that a subset of orders that includes lineages like scorpions and spiders has undergone a shared genome duplication, resulting in numerous paralogs of retinal determinal gene network (RDGN) homologs, which are involved in patterning eyes of many other bilaterian groups. The proposed work will interrogate the development of arachnid eyes using a comparative framework that samples three key arachnid orders, toward establishing a comparative platform incorporating independently evolving lineages for study of cave biology, as well as for understanding the evolution of paralog function after genome duplication. Beyond establishing new model systems for study of arthropod development, this research will establish new genomic resources and toolkits for deciphering the evolution of developmental processes inferred from naturally evolving cave systems.This research award from the Directorate of Biological Sciences is funded by the Developmental Systems and EDGE Programs within the Division of Integrative and Organismal Systems, and by the Evolutionary Processes Program within the Division of Environmental Biology.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.