Immune-response (IR) genes have an important role in the defense against highly variable pathogens, and therefore, diversity in these genomic regions is essential for species’ survival and adaptation. Although current genome assemblies from Old World camelids are very useful for investigating genome-wide diversity, demography and population structure, they have inconsistencies and gaps that limit analyses at local genomic scales. Improved and more accurate genome assemblies and annotations are needed to study complex genomic regions like adaptive and innate IR genes. In this work, we improved the genome assemblies of the three Old World camel species – domestic dromedary and Bactrian camel, and the two-humped wild camel – via different computational methods. The newly annotated dromedary genome assembly CamDro3 served as reference to scaffold the NCBI RefSeq genomes of domestic Bactrian and wild camels. These upgraded assemblies were then used to assess nucleotide diversity of IR genes within and between species, and to compare the diversity found in immune genes and the rest of the genes in the genome. We detected differences in the nucleotide diversity among the three Old World camelid species and between IR gene groups, i.e., innate versus adaptive. Among the three species, domestic Bactrian camels showed the highest mean nucleotide diversity. Among the functionally different IR gene groups, the highest mean nucleotide diversity was observed in the major histocompatibility complex. The new camel genome assemblies were greatly improved in terms of contiguity and increased size with fewer scaffolds, which is of general value for the scientific community. This allowed us to perform in-depth studies on genetic diversity in immunity-related regions of the genome. Our results suggest that differences of diversity across classes of genes appear compatible with a combined role of population history and differential exposures to pathogens, and consequent different selective pressures.

中文翻译：

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基于新注释和参考引导组装的旧世界骆驼中功能不同的免疫反应基因组的核苷酸多样性。

免疫反应 (IR) 基因在抵御高度可变的病原体方面具有重要作用，因此，这些基因组区域的多样性对于物种的生存和适应至关重要。虽然目前旧世界骆驼科动物的基因组组装对于研究全基因组多样性、人口统计学和种群结构非常有用，但它们存在不一致和差距，限制了局部基因组规模的分析。需要改进和更准确的基因组组装和注释来研究复杂的基因组区域，如适应性和先天 IR 基因。在这项工作中，我们通过不同的计算方法改进了三种旧世界骆驼物种——家养单峰骆驼和双峰驼，以及两峰野生骆驼的基因组组装。新注释的单峰骆驼基因组组装 CamDro3 作为支架家养双峰驼和野生骆驼 NCBI RefSeq 基因组的参考。然后使用这些升级后的组件来评估物种内和物种之间 IR 基因的核苷酸多样性，并比较免疫基因和基因组中其余基因的多样性。我们检测到三个旧世界骆驼物种之间和 IR 基因组之间的核苷酸多样性差异，即先天性与适应性。在这三个物种中，家养双峰驼的平均核苷酸多样性最高。在功能不同的 IR 基因组中，在主要组织相容性复合物中观察到最高的平均核苷酸多样性。新的骆驼基因组组装在连续性和尺寸增加方面有了很大的改进，支架更少，这对科学界具有普遍价值。这使我们能够对基因组免疫相关区域的遗传多样性进行深入研究。我们的结果表明，不同类别基因的多样性差异似乎与种群历史和病原体接触差异以及随之而来的不同选择压力的综合作用相一致。