Haplotype-resolved genome of a dry-preservable cell line reveals chromosome evolution and DNA damage

Anhydrobiosis, the ability to survive extreme desiccation, occurs in diverse organisms and provides a framework for understanding how cells preserve genome integrity under severe water loss. In insects, this phenotype is rare, and mechanistic studies have focused on the chironomid midge Polypedilum vanderplanki and its cultured cell line, Pv11. Previous genomic resources for this system were limited by the use of mixed insect and cell-line DNA. Here, we generated a high-quality chromosome-level, haplotype-resolved assembly from a clonal Pv11 line. Chromosome 4 showed markedly elevated heterozygosity and haplotype-specific genes. Comparative gene synteny with other chironomids revealed extensive intrachromosomal rearrangement, but largely conserved broad chromosome identity across subfamily lineages. Finally, genome-wide mapping of DNA double-strand breaks by sBLISS showed that breaks during trehalose pretreatment accumulate preferentially near highly expressed transcription start sites. Together, these results provide a haplotype-resolved genomic framework for linking chromosome evolution, regulatory chromatin, and genome integrity during entry into anhydrobiosis.