De Novo Assembly of the Nearly Complete Fathead Minnow Reference Genome Reveals a Repetitive But Compact Genome.

The fathead minnow (FHM) is a widely used model organism in environmental toxicology. The lack of a high-quality FHM reference genome, however, has severely hampered its uses in toxicogenomics. We present here the de novo assembly and annotation of the fathead minnow genome using long PacBio reads, Bionano and Hi-C scaffolding data, and large RNA-seq datasets from different tissues and life stages. The new annotated FHM reference genome has a scaffold N50 of 12.0 Mbps and a complete BUSCOs (Benchmarking Universal Single-Copy Orthologs) score of 95.1%. The completeness of annotation for the new reference genome is comparable to that of the zebrafish GRCz11 reference genome. The FHM genome, revealed to be highly repetitive and sharing extensive syntenic regions with the zebrafish genome, has a much more compact gene structure than the zebrafish genome. Particularly, comparative genomic analysis with zebrafish, mouse and human showed that FHM homologous genes are relatively conserved in exon regions but had strikingly shorter intron regions. The new FHM reference genome and annotation data, publicly available at the NCBI and the UCSC genome browser, provides an essential resource for aquatic toxicogenomic studies in ecotoxicology and public health. This article is protected by copyright. All rights reserved.