High-quality genome assembly of Chironomus riparius and its population history in European populations

The aquatic midge Chironomus riparius is an established indicator taxon for the assessment of water quality as of the European Water Framework Directive. Here, we present a novel long-read genome assembly generated with PacBio HiFi and Hi-C sequencing, which achieves chromosome-scale resolution with an assembly size of 192 Mb, an N50 of 59 Mb, and a BUSCO completeness of 99.0%. Four chromosomes with their predicted centromeric regions and 10 unplaced scaffolds were assembled containing 15,439 protein-coding genes. Chromosome-level resolution in nonmodel species is often limited, posing challenges for population genomic studies that depend on high-quality reference genomes. Reanalyzing genomic data of natural C. riparius populations, we demonstrate the improved accuracy of population genomic estimators based on the high-quality reference genome. The high contiguity and completeness of the assembly enhanced demographic inference with Sequential Markovian Coalescent (MSMC2) modeling. Our results suggest that population divergence began in an ancestral lineage during the late Pleistocene to early Holocene, consistent with paleoclimate records from Central Europe.