Talenti A, Powell J, Hemmink J D, Cook E A J, Wragg D, Jayaraman S, Paxton E, Ezeasor C, Obishakin E T, Agusi E R, Tijjani A, Amanyire W, Muhanguzi D, Marshall K, Fisch A, Ferreira B R, Qasim A, Chaudhry U, Wiener P, Toye P, Morrison L J, Connelley T, Prendergast J G D
The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
The International Livestock Research Institute, PO Box 30709, Nairobi, Kenya.
Nat Commun. 2022 Feb 17;13(1):910. doi: 10.1038/s41467-022-28605-0.
Despite only 8% of cattle being found in Europe, European breeds dominate current genetic resources. This adversely impacts cattle research in other important global cattle breeds, especially those from Africa for which genomic resources are particularly limited, despite their disproportionate importance to the continent's economies. To mitigate this issue, we have generated assemblies of African breeds, which have been integrated with genomic data for 294 diverse cattle into a graph genome that incorporates global cattle diversity. We illustrate how this more representative reference assembly contains an extra 116.1 Mb (4.2%) of sequence absent from the current Hereford sequence and consequently inaccessible to current studies. We further demonstrate how using this graph genome increases read mapping rates, reduces allelic biases and improves the agreement of structural variant calling with independent optical mapping data. Consequently, we present an improved, more representative, reference assembly that will improve global cattle research.
尽管欧洲的牛只占全球的8%，但欧洲品种却主导着当前的遗传资源。这对其他重要的全球牛品种的研究产生了不利影响，尤其是非洲的牛品种，尽管它们对非洲大陆的经济具有不成比例的重要性，但基因组资源却特别有限。为了缓解这个问题，我们生成了非洲品种的基因组组装，并将其与294个不同牛种的基因组数据整合到一个包含全球牛多样性的图形基因组中。我们展示了这个更具代表性的参考基因组组装如何包含当前赫里福德基因组序列中缺少的额外116.1兆字节（4.2%）的序列，因此当前的研究无法获取这些序列。我们进一步证明了使用这个图形基因组如何提高读段映射率、减少等位基因偏差，并改善结构变异检测与独立光学映射数据的一致性。因此，我们提出了一个改进的、更具代表性的参考基因组组装，这将改善全球牛的研究。
