经过改进的大鼠参考基因组有助于发现实验大鼠的遗传多样性。
A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.
作者信息
de Jong Tristan V, Pan Yanchao, Rastas Pasi, Munro Daniel, Tutaj Monika, Akil Huda, Benner Chris, Chen Denghui, Chitre Apurva S, Chow William, Colonna Vincenza, Dalgard Clifton L, Demos Wendy M, Doris Peter A, Garrison Erik, Geurts Aron M, Gunturkun Hakan M, Guryev Victor, Hourlier Thibaut, Howe Kerstin, Huang Jun, Kalbfleisch Ted, Kim Panjun, Li Ling, Mahaffey Spencer, Martin Fergal J, Mohammadi Pejman, Ozel Ayse Bilge, Polesskaya Oksana, Pravenec Michal, Prins Pjotr, Sebat Jonathan, Smith Jennifer R, Solberg Woods Leah C, Tabakoff Boris, Tracey Alan, Uliano-Silva Marcela, Villani Flavia, Wang Hongyang, Sharp Burt M, Telese Francesca, Jiang Zhihua, Saba Laura, Wang Xusheng, Murphy Terence D, Palmer Abraham A, Kwitek Anne E, Dwinell Melinda R, Williams Robert W, Li Jun Z, Chen Hao
机构信息
Department of Pharmacology, Addiction Science, and Toxicology, University of Tennessee Health Science Center, Memphis, TN, USA.
Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA.
出版信息
bioRxiv. 2023 Sep 28:2023.04.13.536694. doi: 10.1101/2023.04.13.536694.
The seventh iteration of the reference genome assembly for -mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold and increases contiguity by 290-fold compared to its predecessor. Gene annotations are now more complete, significantly improving the mapping precision of genomic, transcriptomic, and proteomics data sets. We jointly analyzed 163 short-read whole genome sequencing datasets representing 120 laboratory rat strains and substrains using mRatBN7.2. We defined ~20.0 million sequence variations, of which 18.7 thousand are predicted to potentially impact the function of 6,677 genes. We also generated a new rat genetic map from 1,893 heterogeneous stock rats and annotated transcription start sites and alternative polyadenylation sites. The mRatBN7.2 assembly, along with the extensive analysis of genomic variations among rat strains, enhances our understanding of the rat genome, providing researchers with an expanded resource for studies involving rats.
-mRatBN7.2-参考基因组组装的第七次迭代纠正了许多错放的片段，与前一版本相比，将碱基水平的错误减少了约9倍，并将连续性提高了290倍。基因注释现在更加完整，显著提高了基因组、转录组和蛋白质组数据集的映射精度。我们使用mRatBN7.2联合分析了代表120个实验大鼠品系和亚品系的163个短读长全基因组测序数据集。我们定义了约2000万个序列变异，其中18700个预计可能影响6677个基因的功能。我们还从1893只异质种群大鼠中生成了一个新的大鼠遗传图谱，并注释了转录起始位点和可变聚腺苷酸化位点。mRatBN7.2组装以及对大鼠品系间基因组变异的广泛分析，增强了我们对大鼠基因组的理解，为研究大鼠的研究人员提供了更丰富的资源。
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