Systemic paralogy and function of retinal determination network homologs in arachnids

Guilherme Gainett*, Jesús A. Ballesteros*, Charlotte R. Kanzler, Jakob T. Zehms, John M. Zern, Shlomi Aharon, Efrat Gavish-Regev, Prashant P. Sharma

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Background: 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, duplication of Retinal Determination Gene Network (RDGN) homologs in spiders has convoluted functional inferences extrapolated from single-copy homologs in pancrustacean models. Results: We investigated a sister species pair of Israeli cave whip spiders, Charinus ioanniticus and C. israelensis (Arachnopulmonata, Amblypygi), of which one species has reduced eyes. We generated embryonic transcriptomes for both Amblypygi species, and discovered that several RDGN homologs exhibit duplications. We show that duplication 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 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. Conclusions: Our work establishes a foundation to investigate the genetics of troglomorphic adaptations in cave arachnids, and links differential gene expression to an arthropod eye phenotype for the first time outside of Pancrustacea. Our results support the conservation of at least one RDGN component across Arthropoda and provide a framework for identifying the role of gene duplications in generating arachnid eye diversity.

Original languageAmerican English
Article number811
JournalBMC Genomics
Issue number1
StatePublished - Dec 2020

Bibliographical note

Funding Information:
Fieldwork in Israel was supported by a National Geographic Society Expeditions Council grant no. NGS-271R-18 to J.A.B. Sequencing, reagents for molecular work, and access to computer clusters were funded by National Science Foundation grant no. IOS-1552610 and IOS-2016141 to P.P.S. G.G. was supported by a Wisconsin Alumni Research Foundation Fall Research Competition award. Funding agencies played no part in the design of the study, data collection, data analysis, data interpretation, or drafting of the manuscript.

Funding Information:
Microscopy was performed at the Newcomb Imaging Center, Department of Botany, University of Wisconsin-Madison. Sequencing was performed at the UW-Madison Biotechnology Center. Access to computing nodes for intensive tasks was provided by the Center for High Throughput Computing (CHTC) and the Bioinformatics Resource Center (BRC) of the University of Wisconsin?Madison. Comments from three anonymous reviewers substantially improved an earlier version of the manuscript.

Publisher Copyright:
© 2020, The Author(s).


  • Amblypygi
  • Cave blindness
  • Parasteatoda tepidariorum
  • RNAi
  • Six1
  • sine oculis


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