From an economic point of view, Bovidae represent the most important family of the Ruminantia suborder. Thus, the mitochondrial and nuclear genomes of Bos taurus were among the first genomes to be sequenced after the sequencing of the human genomes. Over the millennia, the evolution of the genomes of the 3 main species belonging to the Bovidae family - B. taurus (BTA), Ovis aries (OAR), and Capra hircus (CHI) - has led to few chromosome rearrangements. Certainly, the availability and free access to the animal genomes significantly contributed to the improvement of animal genetics; however, some errors may exist due to the high automation in the genomic assembly construction process. In this work, some differences between the genomes of cattle, goat, and sheep highlighted by bioinformatics analysis have been verified by FISH, confirming that some errors persist even in the most recent genome assemblies. This type of approach has allowed us to detect a misassembly of a region belonging to BTA16 and to the homologues OAR12 and CHI16, a misassembly of a short tract in BTA22, OAR19, and CHI22, an incorrect mapping of a region of BTA21 and of CHI27 and OAR26, a discrepancy in the BTA26, OAR22, and CHI26 assemblies, a missed inversion in CHI1 compared to BTA1 and OAR1, and the exact assembly of a region of about 7 Mb in OAR10 and CHI12. Incorrect positioning of genomic tracts can cause unintended consequences in genetic analyses, especially when the data represent a starting point for the construction of genetic tools. In the new genomic assemblies published after the conclusion of our experiments, however, the accuracy in the construction of animal assemblies has been much improved, even if the new assemblies present more extended unmapped portions than the previous versions. The gap could be filled by comparative analyses between similar species or FISH.

中文翻译：

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FISH鉴定牛科基因组组装中的一些错误

从经济角度来看，牛科是反刍动物亚目中最重要的科。因此，Bos taurus 的线粒体和核基因组是继人类基因组测序后最早被测序的基因组之一。几千年来，属于牛科的 3 个主要物种——金牛座 (BTA)、白羊座 (OAR) 和山羊座 (CHI)——的基因组进化导致很少的染色体重排。当然，动物基因组的可获得性和免费获取极大地促进了动物遗传学的改进；然而，由于基因组组装构建过程的高度自动化，可能存在一些错误。在这项工作中，生物信息学分析突出显示的牛、山羊和绵羊基因组之间的一些差异已被 FISH 验证，确认即使在最近的基因组组装中也存在一些错误。这种类型的方法使我们能够检测到属于 BTA16 的区域以及同源物 OAR12 和 CHI16 的错误组装，BTA22、OAR19 和 CHI22 中的短区域的错误组装，BTA21 和 CHI27 区域的错误映射和 OAR26，BTA26、OAR22 和 CHI26 组装中的差异，与 BTA1 和 OAR1 相比，CHI1 中丢失的反转，以及 OAR10 和 CHI12 中约 7 Mb 区域的精确组装。基因组区域的错误定位可能会在遗传分析中导致意想不到的后果，尤其是当数据代表构建遗传工具的起点时。然而，在我们的实验结束后发表的新基因组组装中，动物组件构建的准确性已大大提高，即使新组件比以前的版本存在更多扩展的未映射部分。可以通过相似物种或 FISH 之间的比较分析来填补这一空白。