A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae - Phoxinus phoxinus) provide evidence of haplotype diversity

Abstract

In this study we present an in-depth analysis of the Eurasian Minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 25) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C). We achieved a haploid length of 940 Mbp for haplome one and 929 Mbp for haplome two with high N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, indicating a highly complete genome.We detected notable heterozygosity (1.43%) and a high repeat content (approximately 54%), primarily consisting of DNA transposons, which contribute to genome rearrangements and variations. We found substantial structural variations within the genome, including insertions, deletions, inversions, and translocations. These variations affect genes enriched in functions such as dephosphorylation, developmental pigmentation, phagocytosis, immunity, and stress response.Protein annotation identified 30,980 mRNAs and 23,497 protein-coding genes with a high completeness score, providing further support for our genome’s high contiguity. We performed a gene family evolution analysis by comparing our proteome to ten other teleost species, which identified immune system gene families that prioritise histone-based disease prevention over NLR-based immune responses.Additionally, demographic analysis indicates historical fluctuations in the effective population size ofP. phoxinus, likely correlating with past climatic changes.This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genusPhoxinusand highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterised by high heterozygosity.