From candidate genes to omics: Unbiased approaches reshaping arthropod Evo-Devo

Drosophila melanogaster established the candidate-gene paradigm that shaped arthropod evolutionary developmental biology (Evo-Devo) for decades. Genome-wide methods-bulk RNA-seq, single-cell/single-nucleus transcriptomics, chromatin profiling (ATAC-seq, CUT&Tag/CUT&RUN), and 3D genome mapping (Hi-C)-now enable direct interrogation of gene regulatory networks (GRNs) in non-model arthropods. Here we review how these approaches have already uncovered lineage-restricted regulators, resolved cell-type trajectories, and mapped cis-regulatory landscapes across diverse clades. We then take a critical view of their scope and limitations: success depends on high-quality genomes and annotations, careful staging and replication, mitigation of dissociation and ambient-RNA artifacts, and robust cross-species mapping of orthology and cell-type homology. At the regulatory level, linking distal accessible sites to target genes remains a central challenge that often requires integrating chromatin and conformation data with functional perturbations. Progress in this field is further supported by the development and adaptation of enabling tools, such as low-input chemistries (e.g., CUT&Tag), single-nucleus and spatial workflows, and the availability of improved genome assemblies and computational frameworks for multi-omic integration. Ultimately, we argue that the integration of these techniques-especially perturbation with multi-omic data across diverse species-is the key to transforming descriptive regulatory 'maps' into a mechanistic understanding of evolution.