Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies
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Daphnia magna is a widely used model organism in ecological genomics, ecotoxicology, and evolutionary biology. While a few genome assemblies of this species of freshwater crustacean are available, disagreements in their chromosomal arrangements point toward scaffolding problems. We present the most contiguous chromosome-level genome assembly of D. magna , the first based on PacBio HiFi sequencing technology. The assembly spans 184.38 Mb and has a scaffold N50 of 12.4 Mb. Eight of ten chromosomal scaffolds consist of mainly two contigs, representing one chromosome arm each. Eleven of 20 telomeric regions are fully resolved. Using a genomic map and comparative genomics, we were able to not only resolve the problems of previous assemblies, but also to demonstrate that some of the scaffolding errors followed a systematic pattern, most likely resulting from mis-joins during Hi-C scaffolding. Additionally, we provide expression profiles for annotated genes derived from different D. magna RNA-seq datasets, enabling rapid assessment of predicted gene expression and identification of potential pseudogenes. The new genomic and transcriptomic resource enables comparative genomic studies on genome architecture, structural variation, and gene family evolution in this important model organism.
Significance Statement
Genome assemblies of different individuals of the same species vary as a result of natural genetic variation and assembly errors but distinguishing between these two sources of variation can be challenging. We generated an updated D. magna genome using long, highly-fidelity DNA sequences and a genetic map, revealing that previous assemblies contain systematic errors, including inverted chromosome arms likely due to mis-joins from the widely used Hi-C scaffolding method. The new genome enables identifying real genetic differences among the many already sequenced D. magna individuals from across the species range, allowing to investigate how natural selection shapes large-scale genetic variation, for example, involved in resistance to stressors and parasites.
