Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies
- 1University of Basel
Abstract
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.
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BibTeX
@misc{angst2026chromosomescale,
title = {{Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies}},
author = {P. Angst and P. D. Fields and C. R. Haag and D. Ebert},
howpublished = {bioRxiv},
year = {2026},
month = sep,
doi = {10.64898/2026.09.03.749101},
url = {https://www.biorxiv.org/content/10.64898/2026.09.03.749101v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Chromosome-scale Daphnia magna genome assembly resolves scaffolding discrepancies
AU - P. Angst
AU - P. D. Fields
AU - C. R. Haag
AU - D. Ebert
PY - 2026
DA - 2026/09/03
PB - bioRxiv
DO - 10.64898/2026.09.03.749101
UR - https://www.biorxiv.org/content/10.64898/2026.09.03.749101v1
AB - 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.
ER -