Reference genomes are essential in the analysis of genomic data. As the cost of sequencing decreases, multiple reference genomes are being produced within species to alleviate problems such as low mapping accuracy and reference allele bias in variant calling that can be associated with the alignment of divergent samples to a single reference individual. The latest reference sequence adopted by the scientific community for the analysis of cattle data is ARS_UCD1.2, built from the DNA of a Hereford cow (Bos taurus taurus—B. taurus). A complementary genome assembly, UOA_Brahman_1, was recently built to represent the other cattle subspecies (Bos taurus indicus—B. indicus) from a Brahman cow haplotype to further support analysis of B. indicus data. In this study, we aligned the sequence data of 15 B. taurus and B. indicus breeds to each of these references. The alignment of B. taurus individuals against UOA_Brahman_1 detected up to five million more single-nucleotide variants (SNVs) compared to that against ARS_UCD1.2. Similarly, the alignment of B. indicus individuals against ARS_UCD1.2 resulted in one and a half million more SNVs than that against UOA_Brahman_1. The number of SNVs with nearly fixed alternative alleles also increased in the alignments with cross-subspecies. Interestingly, the alignment of B. taurus cattle against UOA_Brahman_1 revealed regions with a smaller than expected number of counts of SNVs with nearly fixed alternative alleles. Since B. taurus introgression represents on average 10% of the genome of Brahman cattle, we suggest that these regions comprise taurine DNA as opposed to indicine DNA in the UOA_Brahman_1 reference genome. Principal component and admixture analyses using genotypes inferred from this region support these taurine-introgressed loci. Overall, the flagged taurine segments represent 13.7% of the UOA_Brahman_1 assembly. The genes located within these segments were previously reported to be under positive selection in Brahman cattle, and include functional candidate genes implicated in feed efficiency, development and immunity. We report a list of taurine segments that are in the UOA_Brahman_1 assembly, which will be useful for the interpretation of interesting genomic features (e.g., signatures of selection, runs of homozygosity, increased mutation rate, etc.) that could appear in future re-sequencing analysis of indicine cattle.

中文翻译：

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评估 UOA Bos indicus 组装中的 Bos taurus 基因渗入

参考基因组在基因组数据分析中必不可少。随着测序成本的降低，物种内正在产生多个参考基因组，以缓解一些问题，例如低映射准确性和变异调用中的参考等位基因偏差，这些问题可能与将不同样本与单个参考个体的比对相关联。科学界用于分析牛数据的最新参考序列是 ARS_UCD1.2，由赫里福德牛 (Bos taurus taurus-B. taurus) 的 DNA 构建而成。最近构建了一个互补基因组组装 UOA_Brahman_1，以代表来自婆罗门奶牛单倍型的其他牛亚种（Bos taurus indicus-B. indicus），以进一步支持对 B. indicus 数据的分析。在这项研究中，我们比对了 15 个 B. taurus 和 B. indicus 品种对这些参考中的每一个。与 ARS_UCD1.2 相比，B. taurus 个体与 UOA_Brahman_1 的比对检测到多达 500 万个单核苷酸变异 (SNV)。类似地，B. indicus 个体与 ARS_UCD1.2 的比对导致比对 UOA_Brahman_1 的多 150 万个 SNV。在与跨亚种的比对中，具有几乎固定的替代等位基因的 SNV 的数量也增加了。有趣的是，B. taurus 牛与 UOA_Brahman_1 的比对揭示了具有几乎固定的替代等位基因的 SNV 计数少于预期数量的区域。由于 B. taurus 基因渗入平均占婆罗门牛基因组的 10%，我们建议这些区域包含牛磺酸 DNA，而不是 UOA_Brahman_1 参考基因组中的 indicine DNA。使用从该区域推断的基因型进行的主成分和混合物分析支持这些牛磺酸渗入基因座。总体而言，标记的牛磺酸片段占 UOA_Brahman_1 组件的 13.7%。先前报道，位于这些片段内的基因在婆罗门牛中处于阳性选择之下，包括与饲料效率、发育和免疫有关的功能候选基因。我们报告了 UOA_Brahman_1 装配体中牛磺酸片段的列表，这将有助于解释有趣的基因组特征（例如，选择特征、纯合性运行、突变率增加等），这些特征可能在未来重新出现。印度牛的测序分析。总体而言，标记的牛磺酸片段占 UOA_Brahman_1 组件的 13.7%。先前报道，位于这些片段内的基因在婆罗门牛中处于阳性选择之下，包括与饲料效率、发育和免疫有关的功能候选基因。我们报告了 UOA_Brahman_1 装配体中牛磺酸片段的列表，这将有助于解释有趣的基因组特征（例如，选择特征、纯合性运行、突变率增加等），这些特征可能在未来重新出现。印度牛的测序分析。总体而言，标记的牛磺酸片段占 UOA_Brahman_1 组件的 13.7%。先前报道，位于这些片段内的基因在婆罗门牛中处于阳性选择之下，包括与饲料效率、发育和免疫有关的功能候选基因。我们报告了 UOA_Brahman_1 装配体中牛磺酸片段的列表，这将有助于解释有趣的基因组特征（例如，选择特征、纯合性运行、突变率增加等），这些特征可能在未来重新出现。印度牛的测序分析。并包括与饲料效率、发育和免疫有关的功能候选基因。我们报告了 UOA_Brahman_1 装配体中牛磺酸片段的列表，这将有助于解释有趣的基因组特征（例如，选择特征、纯合性运行、突变率增加等），这些特征可能在未来重新出现。印度牛的测序分析。并包括与饲料效率、发育和免疫有关的功能候选基因。我们报告了 UOA_Brahman_1 装配体中牛磺酸片段的列表，这将有助于解释有趣的基因组特征（例如，选择特征、纯合性运行、突变率增加等），这些特征可能在未来重新出现。印度牛的测序分析。