Genomic resources and toolkits for developmental study of whip spiders (Amblypygi) provide insights into arachnid genome evolution and antenniform leg patterning

Abstract

Background: The resurgence of interest in the comparative developmental study of chelicerates has led to important insights, such as the discovery of a genome duplication shared by spiders and scorpions, inferred to have occurred in the most recent common ancestor of Arachnopulmonata (a clade comprising the five arachnid orders that bear book lungs). Nonetheless, several arachnid groups remain understudied in the context of development and genomics, such as the order Amblypygi (whip spiders). The phylogenetic position of Amblypygi in Arachnopulmonata posits them as an interesting group to test the incidence of the proposed genome duplication in the common ancestor of Arachnopulmonata, as well as the degree of retention of duplicates over 450 Myr. Moreover, whip spiders have their first pair of walking legs elongated and modified into sensory appendages (a convergence with the antennae of mandibulates), but the genetic patterning of these antenniform legs has never been investigated. Results: We established genomic resources and protocols for cultivation of embryos and gene expression assays by in situ hybridization to study the development of the whip spider Phrynus marginemaculatus. Using embryonic transcriptomes from three species of Amblypygi, we show that the ancestral whip spider exhibited duplications of all ten Hox genes. We deploy these resources to show that paralogs of the leg gap genes dachshund and homothorax retain arachnopulmonate-specific expression patterns in P. marginemaculatus. We characterize the expression of leg gap genes Distal-less, dachshund-1/2 and homothorax-1/2 in the embryonic antenniform leg and other appendages, and provide evidence that allometry, and by extension the antenniform leg fate, is specified early in embryogenesis. Conclusion: This study is the first step in establishing P. marginemaculatus as a chelicerate model for modern evolutionary developmental study, and provides the first resources sampling whip spiders for comparative genomics. Our results suggest that Amblypygi share a genome duplication with spiders and scorpions, and set up a framework to study the genetic specification of antenniform legs. Future efforts to study whip spider development must emphasize the development of tools for functional experiments in P. marginemaculatus.

Widespread retention of ohnologs in key developmental gene families following whole genome duplication in arachnopulmonates

“…The absence of a second copy of pb in both Charinus acosta and Euphrynichus bacillifer , which are distantly related within Amblypygi, suggests a loss in the common ancestor of amblypygids. Gainett and Sharma (2020) also recovered a single copy of pb in Phrynus marginemaculatus , but two copies in Charinus israelensis . However, one of these had an incomplete homeodomain (32 aa) that was identical to the other C-isr protein sequence; we are hesitant about its status as a duplicate.…”

“…Although synteny analysis remains the gold standard for the identification of ohnologs, the required chromosome-level genomic assemblies remain relatively scarce. Work on the P. tepidariorum, C. sculpturatus and M. martensii genomes has been complemented by targeted studies of individual gene families and transcriptomic surveys (Schwager et al 2007; Sharma et al 2012; Leite et al 2018; Gainett and Sharma 2020). Combined with phylogenetic analyses, the identification of duplications can provide evidence of WGD events and their timing in arachnid evolution.…”

Phylogenomic Resolution of Sea Spider Diversification through Integration of Multiple Data Classes

“…We surveyed these transcriptomes for the presence of Hox genes, which reliably exhibit duplicates in embryonic transcriptomes of WGD taxa ( Sharma, Schwager, et al. 2014 ; Gainett and Sharma 2020 ) and a subset of which has been shown to be expressed in canonical Hox-like domains in the protonymphon stage of sea spiders ( Jager et al. 2006 ).…”

“…We used the conserved homeodomain sequences of all Hox genes of the spider Parasteatoda tepidariorum to retrieve Hox sequences from new libraries, using tBLASTn searches. Putative A. hentzi and sea spider Hox homologs were added to multiple sequence alignments recently generated by us ( Gainett and Sharma 2020 ), in addition to all available sea spider Hox sequences previously generated using RACE PCR ( Manuel et al. 2006 ).…”

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions

“…2018 ). Moreover, exploratory analyses of gene trees and embryonic gene expression patterns in spiders, scorpions, and harvestmen have shown that the duplicated copies of arachnopulmonate leg-patterning genes also retain expression domains that reflect the evolutionary history of shared WGD ( Gainett and Sharma 2020 ; Nolan et al. 2020 ).…”