DOI: 10.5061/dryad.xgxd254d1
title: Systemic paralogy and function of retinal determination network homologs in arachnids

description: 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.
description: README file for "Systemic paralogy and function of retinal
 determination network homologs in arachnids" BMC
 Genomics<br>
 https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-020-07149-x<br> Gainett, G., Ballesteros, J.A., Kanzler, C.R. et al. Systemic paralogy and function of retinal determination network homologs in arachnids. BMC Genomics 21, 811 (2020). https://doi.org/10.1186/s12864-020-07149-x Contact information:<br> Guilherme Gainett: guilherme.gainett@wisc.edu<br> Jesús Ballesteros: ballesterosc@wisc.edu This dataset includes the following: Additional file 3:<br> Video S1: Time-lapse imaging of a postembryo ~ 24 h after hatching of Parasteatoda tepidariorum from the dH2O-injected treatment (negative control). Pictures were taken every 30 min, in a room at 22 °C. Normal molting time after hatching is ~ 48 h at 26 °C. Video S2: Time-lapse imaging of a postembryo ~ 24 h after hatching of Parasteatoda tepidariorum from the Ptep-soA-injected treatment. Pictures were taken every 30 min, in a room at 22 °C. Normal molting time after hatching is ~ 48 h at 26 °C. (.zip). Additional file 4:<br> Dataset S1: Dataset of the orthology analyses. Alignments and sequences of Charinus RDGN genes identified in this study and gene trees in Newick format; alignments of opsins and arrestins. (.zip).  Additional file 5:<br> Dataset S2: Dataset for the differential gene expression analyses. DESeq2 dataset (DESeq (dds); filtered for padj &gt; 0.5) of the DGE analysis of Comparison 1, 2.1 and 2.2 (see “Material and Methods” for explanation). run_ddseq2.r: custom R script used to run all three analysis. (.zip).  Additional file 6:<br> Dataset S3: Dataset for the GOseq enrichment analyses. This folder contains the complete GOseq results of enriched/depleted (FDR ≤ 0.05) GO terms of up- (Log2FC &gt; 1) and down-regulated (Log2FC &lt; 1) genes in Comparisons 1, 2.1 and 2.2. The twelve spreadsheets (.xls) are named as follows: Comparison#,_UP/DOWN_enriched/depleted. (.zip).  Additional file 7:<br> Dataset S4. (a): High resolution Additional file 1 Fig. S14. (b): Spreadsheets with the raw counts and sum of counts used to generate the distribution bar plots of the Ptep-soA RNAi experiment. (c) raw counts and sum of counts used to generate the distribution bar plots of the effects of Ptep-soA RNAi per eye type. (d) Primer sequences for the amplified fragments of Ptep-soA, Ptep-otdB and Ptep-OptixB. (.zip).