An exceptionally large and repetitive genome in the cave-dwelling shrimp Troglocaris planinensis

Abstract

Introduction: Genomic resources for subterranean crustaceans remain scarce, limiting investigation of the molecular basis of adaptation to light-deprived environments. Troglocaris planinensis is a stygobiont freshwater shrimp endemic to the Dinaric Karst that lacks nuclear genomic resources and displays typical cave-associated traits, including loss of pigmentation and visual system regression. This study aimed to generate the first draft nuclear genome of T. planinensis and characterize its genome size, repetitive content and gene-space completeness. Materials and methods: Illumina sequencing was used to generate a de novo draft genome assembly with the St. Petersburg genome assembler (SPAdes). Genome size was estimated using k-mer- and coverage-based approaches and compared with available crustacean genomes. The repeat landscape was characterized with RepeatModeler2, RepeatMasker, and RepeatExplorer2. Assembly completeness was assessed at the exon level using evolutionarily conserved decapod genes. Results: The genome of T. planinensis was estimated at 9.9–12.1 Gb, making it exceptionally large compared with other Atyidae. Approximately 90% of the genome consisted of repetitive sequence. Class I mobile elements represented the most abundant class of repeats, while nearly 20% of the genome comprised uncharacterized repeats. The large and repetitive genome prevented the generation of a highly contiguous assembly and annotation of complete gene models. Nevertheless, the draft assembly recovered approximately 90% evolutionarily conserved decapod exons. Conclusions: T. planinensis possesses an exceptionally large, repeat-rich genome, providing the first evidence of genome gigantism in Atyidae. Despite its fragmentation, the draft assembly captures most conserved coding regions and provides a genomic resource for investigating the molecular evolution of this subterranean crustacean.