A cattle graph genome incorporating global breed diversity.
A cattle graph genome incorporating global breed diversity.
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DOI：
10.1038/s41467-022-28605-0
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发表时间：
2022-02-17
影响因子：
16.6
通讯作者：
Prendergast JGD
中科院分区：
文献类型：
--
作者：
Talenti A;Powell J;Hemmink JD;Cook EAJ;Wragg D;Jayaraman S;Paxton E;Ezeasor C;Obishakin ET;Agusi ER;Tijjani A;Amanyire W;Muhanguzi D;Marshall K;Fisch A;Ferreira BR;Qasim A;Chaudhry U;Wiener P;Toye P;Morrison LJ;Connelley T;Prendergast JGD
尽管只有8%的牛在欧洲被发现，但欧洲品种主导了目前的遗传资源。这对其他重要的全球牛品种的牛研究产生了不利影响，特别是来自非洲的牛品种，尽管它们对非洲大陆的经济具有不成比例的重要性，但其基因组资源特别有限。为了缓解这个问题，我们已经生成了非洲品种的集合，这些集合已经与294种不同牛的基因组数据整合到一个包含全球牛多样性的图基因组中。我们说明了这个更具代表性的参考组件如何包含额外的116.1 Mb（4.2%）的序列，从当前的赫里福德序列中缺失，因此无法进入当前的研究。我们进一步证明了如何使用这个图基因组增加读取映射率，减少等位基因的偏见，并提高了结构变异调用与独立的光学映射数据的协议。因此，我们提出了一个改进的，更有代表性的，参考大会，将改善全球牛的研究。牛参考基因组是宝贵的资源，但目前严重偏向欧洲品种。在这里，作者将非洲品种的组件整合到一个更具代表性的牛基因组图中，以捕捉全球品种多样性。
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. Cattle reference genomes are valuable resources but are currently heavily biased towards European breeds. Here the authors integrate assemblies for African breeds into a more representative cattle graph genome capturing global breed diversity.
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影响因子：
64.8
作者：
Armstrong J;Hickey G;Diekhans M;Fiddes IT;Novak AM;Deran A;Fang Q;Xie D;Feng S;Stiller J;Genereux D;Johnson J;Marinescu VD;Alföldi J;Harris RS;Lindblad-Toh K;Haussler D;Karlsson E;Jarvis ED;Zhang G;Paten B
通讯作者：
Paten B
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.
影响因子：
2.6
作者：
Challis, Richard;Richards, Edward;Blaxter, Mark
通讯作者：
Blaxter, Mark
影响因子：
4.5
作者：
Gunther, Torsten;Nettelblad, Carl
通讯作者：
Nettelblad, Carl
影响因子：
12.3
作者：
Crysnanto, Danang;Pausch, Hubert
通讯作者：
Pausch, Hubert