Oriowo Temitope Opeyemi, Chrysostomakis Ioannis, Martin Sebastian, Kukowka Sandra, Brown Thomas, Winkler Sylke, Myers Eugene W, Böhne Astrid, Stange Madlen
Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, 53113 Bonn, Germany.
Max Planck Institute of Molecular Cell Biology and Genetics, Sequencing and Genotyping, 01307 Dresden, Germany.
Gigascience. 2025 Jan 6;14. doi: 10.1093/gigascience/giae116.
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 = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).
We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 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. 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. In the annotation of protein-coding genes, 30,980 messenger RNAs 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 10 other teleost species, which identified immune system gene families that prioritize histone-based disease prevention over NB-LRR-related-based immune responses. Additionally, demographic analysis indicates historical fluctuations in the effective population size of P. phoxinus, likely correlating with past climatic changes.
This annotated, phased reference genome provides a crucial resource for resolving the taxonomic complexity within the genus Phoxinus and highlights the importance of haplotype-phased assemblies in understanding haplotype diversity in species characterized by high heterozygosity.
在本研究中，我们对欧亚米诺鱼（Phoxinus phoxinus）的基因组进行了深入分析，突出了其遗传多样性、结构变异和进化适应性。我们通过整合高保真（HiFi）长读长和染色体构象捕获数据（Hi-C），生成了一个注释的单倍型定相、染色体水平的基因组组装（2n = 50）。
我们获得了单倍体1的单倍型大小为940兆碱基对（Mbp），单倍体2的单倍型大小为929 Mbp，支架N50值分别为36.4 Mb和36.6 Mb，BUSCO得分分别为96.9%和97.2%，表明基因组组装高度完整。我们检测到显著的杂合性（1.43%）和高重复含量（约54%），主要由DNA转座子组成，这些转座子导致基因组重排和变异。我们在基因组中发现了大量的结构变异，包括插入、缺失、倒位和易位。这些变异影响了在去磷酸化、发育色素沉着、吞噬作用、免疫和应激反应等功能中富集的基因。在蛋白质编码基因的注释中，鉴定出30,980个信使RNA和23,497个蛋白质编码基因，完整性得分很高，这进一步证明了我们基因组组装的高连续性。我们通过将我们的蛋白质组与其他10种硬骨鱼物种进行比较，进行了基因家族进化分析，确定了优先基于组蛋白的疾病预防而非基于NB-LRR相关免疫反应的免疫系统基因家族。此外，种群统计学分析表明欧亚米诺鱼有效种群大小的历史波动，可能与过去的气候变化相关。
这个注释的、定相的参考基因组为解决米诺鱼属内的分类复杂性提供了关键资源，并突出了单倍型定相组装在理解以高杂合性为特征的物种中的单倍型多样性方面的重要性。
