Supporting data for "A chromosome-level, haplotype-resolved genome assembly and annotation for the Eurasian minnow (Leuciscidae: <i>Phoxinus phoxinus</i>) provide evidence of haplotype diversity"

In this study we present an in-depth analysis of the Eurasian minnow (<i>Phoxinus phoxinus</i>) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).<br>We achieved a haploid size of 940 Megabase pairs (Mbp) for haplome one and 929 Mbp for haplome two with high scaffold N50 values of 36.4 Mb and 36.6 Mb and BUSCO scores of 96.9% and 97.2%, respectively, indicating a highly complete genome assembly.<br>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.<br>In the annotation of protein-coding genes, 30,980 mRNAs and 23,497 protein-coding genes were identified with a high completeness score, which further underpins the high contiguity of our genome assemblies. 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.<br>Additionally, demographic analysis indicates historical fluctuations in the effective population size of <i>P. phoxinus</i>, likely correlating with past climatic changes.<br>This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus <i>Phoxinus</i> and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterised by high heterozygosity.本研究针对欧亚鱥（*Phoxinus phoxinus*）的基因组开展深入解析，重点剖析其遗传多样性、结构变异与演化适应特征。 本研究整合高保真（HiFi）长读长测序数据与染色质构象捕获（Hi-C）数据，构建了注释完成的单倍型分型染色体水平基因组组装（2n=50）。 其中单倍型组1的单倍体基因组大小为940兆碱基对（Megabase pairs, Mbp），单倍型组2为929 Mbp；两条单倍型的支架N50值分别为36.4 Mb与36.6 Mb，BUSCO（Benchmarking Universal Single-Copy Orthologs）评估值分别为96.9%与97.2%，表明本研究获得的基因组组装完整性极佳。 本研究检测到该物种显著的杂合率（1.43%）与较高的重复序列占比（约54%），其中重复序列主要由DNA转座子构成，这类转座子可介导基因组重排与变异。此外，基因组内存在大量结构变异，包括插入、缺失、倒位与易位；这些变异会影响功能富集于去磷酸化、发育色素沉着、吞噬作用、免疫与应激响应的基因。 在蛋白编码基因注释环节，本研究共鉴定出30980条mRNA与23497个蛋白编码基因，且完整性评分较高，进一步佐证了本研究基因组组装的高连续性。本研究将所获得的蛋白质组与其他10种硬骨鱼物种进行比较，开展基因家族演化分析，结果发现免疫系统基因家族更倾向于采用基于组蛋白的疾病防御机制，而非基于NLR（Nod-like receptor，核苷酸结合寡聚化结构域样受体）的免疫应答通路。 此外，种群历史动态分析结果显示，欧亚鱥的有效种群大小曾出现历史波动，这一现象大概率与过去的气候变化存在关联。 本研究获得的注释完成且经过单倍型分型的参考基因组，为解析鱥属（*Phoxinus*）内的分类学复杂性提供了关键资源，同时也凸显了单倍型分型组装对于理解高杂合性物种单倍型多样性的重要意义。