Systemic paralogy and function of retinal determination network homologs in arachnids

Arachnids are important components of cave ecosystems and display many
examples of troglomorphisms, such as blindness, depigmentation, and
elongate appendages. Little is known about how the eyes of arachnids are
specified genetically, let alone the mechanisms for eye reduction and loss
in troglomorphic arachnids. Additionally, paralogy of Retinal
Determination Gene Network (RDGN) homologs in spiders has convoluted
functional inferences extrapolated from single-copy homologs in
pancrustacean models. Here, we investigated a sister species pair of
Israeli cave whip spiders (Arachnopulmonata, Amblypygi, Charinus) of which
one species has reduced eyes. We generated the first embryonic
transcriptomes for Amblypygi, and discovered that several RDGN homologs
exhibit duplications. We show that paralogy of RDGN homologs is systemic
across arachnopulmonates (arachnid orders that bear book lungs), rather
than being a spider-specific phenomenon. A differential gene expression
(DGE) analysis comparing the expression of RDGN genes in field-collected
embryos of both species identified candidate RDGN genes involved in the
formation and reduction of eyes in whip spiders. To ground bioinformatic
inference of expression patterns with functional experiments, we
interrogated the function of three candidate RDGN genes identified from
DGE in a spider, using RNAi in the spider Parasteatoda tepidariorum. We
provide functional evidence that one of these paralogs, sine oculis/Six1 A
(soA), is necessary for the development of all arachnid eye types. Our
results support the conservation of at least one RDGN component across
Arthropoda and establish a framework for investigating the role of gene
duplications in arachnid eye diversity.