Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies
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…
Daphnia magna, a frequently utilized model organism in ecological genomics, ecotoxicology, and evolutionary biology, has had its genome assembly improved. This significant update resolves discrepancies in previous scaffolding arrangements. The new assembly, the first chromosome-level one based on PacBio HiFi sequencing, spans 184.38 Mb with a scaffold N50 of 12.4 Mb.
Eight out of ten chromosomal scaffolds are composed mainly of two contigs, each representing one chromosome arm. Eleven of the 20 telomeric regions are fully resolved. By employing a genomic map and comparative genomics, the team was able to not only fix previous assembly issues but also demonstrate that some scaffolding errors followed a systematic pattern, likely due to mis-joins during Hi-C scaffolding.
Furthermore, expression profiles for annotated genes, derived from multiple D. magna RNA-seq datasets, are provided. This new genomic and transcriptomic resource facilitates comparative genomic studies on genome architecture, structural variation, and gene family evolution in this crucial model organism.
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