Haplotype-resolved genome assemblies of the Friesian horse and the Dutch Warmblood horse using the trio-binning method

We performed nanopore sequencing (R10.4, Q20+) of an F1 cross between a Dutch Warmblood horse and a Friesian horse to create two breed-specific reference assemblies using trio binning. Triocanu was used to bin the nanopore reads (80X) of the F1 cross using the short reads (50X) of the parents. Then, we used Flye and RagTag software to create and scaffold both assemblies. Scaffolded assemblies were validated with breed-specific linkage maps based on 70K genotypes. This resulted in two high-quality, haplotype-resolved reference assemblies (contig N50 was 35Mb and 37Mb and single copy gene completeness was 99.2% and 99.3%, for the Dutch Warmblood horse and Friesian horse, respectively).

本研究针对荷兰温血马与弗里斯兰马杂交获得的F1代群体开展纳米孔测序（Nanopore sequencing，采用R10.4测序化学版本，质控标准为Q20+），通过trio分箱法（trio binning）构建两个品种特异性参考基因组组装。具体流程如下：首先利用Triocanu工具，以亲本的50×覆盖度短读长测序数据为参考，对F1代的80×覆盖度纳米孔读长序列进行分箱；随后借助Flye与RagTag软件完成两种组装的构建与支架序列挂载；最后基于包含70K基因型分型的品种特异性连锁图谱对挂载后的组装结果进行验证。最终得到两个高质量单倍型解析参考基因组组装：荷兰温血马组装的重叠群N50（contig N50）为35Mb，单拷贝基因完整度达99.2%；弗里斯兰马组装的重叠群N50为37Mb，单拷贝基因完整度达99.3%。