Genomic expansion in the dark: A repeat-rich genome of a cave-dwelling remipede sheds light on the evolution of the hexapod sister group.

Remipedes are blind, venomous crustaceans found exclusively in anchialine cave ecosystems, a subterranean environment lacking light and oxygen. These creatures hold a crucial position in the phylogenomics of Pancrustacea, serving as the sister group to Hexapoda. Despite their enigmatic nature and the challenges posed by their cave-dwelling habitat, scientists have recently unveiled a highly refined genome of the remipede species, Xibalbanus tulumensis.

This genome, spanning an impressive 8.05 Gb across 30 chromosome-scale scaffolds, marks one of the largest arthropod genomes ever reported.

The protein-coding gene repertoire within this genome is remarkably conserved, with over 97% of arthropod orthologs identified. Additionally, microRNA surveys suggest a high degree of completeness, at 94%, when compared to other pancrustacean genomes. The expansion of this genome is primarily attributed to the proliferation of intronic and repetitive elements, making up approximately 71% of its total structure.

When examining comparative genomic analyses, it becomes evident that gene family turnover is predominant, with only a limited number of families exhibiting lineage-specific expansions or contractions.

Among the venom-associated gene families, a distinct remipede-specific set known as Xibalbins was identified. Furthermore, substantial expansion and episodic positive selection were observed in other venom-associated gene families. This genomic study also uncovered the remnants of ancient fusion-with-mixing events that connect Pancrustacea and Allotriocarida, with notable similarities in the chromosome architecture of remipedes and basal insect orders.

This groundbreaking research provides the first genomic framework for Remipedia, illuminating a highly expanded and repeat-rich genome that retains deep phylogenetic signals in its architecture, despite the species' adaptation to an atypical environment.