Unraveling the evolutionary genomics of Arachnida: Phylogenetic relationships and venom complexity

Arachnology has long sought to resolve the evolutionary history of arachnids—an ancient and morphologically diverse lineage including spiders, scorpions, ticks, and mites. With over 110,000 described species, arachnids have radiated into a wide variety of ecological niches since their early terrestrial colonization in the Silurian period. Despite their abundance and diversity, the evolutionary relationships among arachnid orders remain deeply contested. Morphological and molecular studies have produced inconsistent phylogenetic trees, leaving the higher-level taxonomy of Arachnida under debate. Recent advances in genomics, particularly the availability of over a hundred chromosomal-level genomes, have begun to transform the field by providing unprecedented resolution into genetic relationships, developmental mechanisms, and adaptive strategies. However, this genomic coverage still accounts for only a small proportion of known diversity, signaling a substantial knowledge gap that must be addressed.The exploration of arachnid venoms adds another compelling dimension to their evolutionary story. Venoms in spiders and scorpions comprise complex mixtures of bioactive compounds—enzymes, small molecules, and disulfide-rich peptides (DRPs)—that have evolved for predation, defense, and ecological specialization. Comparative transcriptomic and proteomic analyses have begun to uncover the ancient evolutionary roots of DRPs and their ongoing diversification across arachnid lineages. Yet, many venom systems remain poorly characterized across groups, and much work is needed to integrate molecular, genomic, and functional data to fully understand the origins and diversification of these biochemical arsenals.This Research Topic aims to advance our understanding of arachnid phylogeny and venom evolution by integrating genomic, transcriptomic, and proteomic data across a broad taxonomic spectrum. It seeks to clarify the evolutionary relationships among arachnid lineages, reveal the genomic foundations of adaptation, and elucidate the genetic and biochemical diversification of venom systems. Particular attention will be given to genomic-scale phylogenetic reconstruction, molecular evolution of venom components, and the interplay between functional diversification and ecological adaptation. Through this collective endeavor, researchers will be better positioned to bridge phylogenetic inconsistencies and uncover the molecular innovations that shaped arachnid evolution. To gather further insights into arachnid evolution and venom biology, we welcome articles addressing, but not limited to, the following themes:o Genomic-based revisions of phylogenetic relationships within Arachnidao Phylogenetic inference at broad and fine taxonomic levels using novel genomic or multi-omic datao Comparative studies on venom gene families across venomous arachnidso Integration of transcriptomic and proteomic datasets for venom characterizationo Evolutionary origin and diversification of disulfide-rich peptides in arachnid venomso Functional genomics of venom adaptation and ecological specializationo Computational and bioinformatic pipelines for arachnid omics data integration Topic editors: Wai Lok So, Thomas C.N. LEUNG, Sean Tsz Sum Law Source: https://www.frontiersin.org/research-topics/84797/unraveling-the-evolutionary-genomics-of-arachnida-phylogenetic-relationships-and-venom-complexity