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  1. Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
    • Ran Li,
    • Mian Gong,
    • Xinmiao Zhang,
    • Fei Wang,
    • Zhenyu Liu,
    • Lei Zhang,
    • Qimeng Yang,
    • Yuan Xu,
    • Mengsi Xu,
    • Huanhuan Zhang,
    • Yunfeng Zhang,
    • Xuelei Dai,
    • Yuanpeng Gao,
    • Zhuangbiao Zhang,
    • Wenwen Fang,
    • Yuta Yang,
    • Weiwei Fu,
    • Chunna Cao,
    • Peng Yang,
    • Zeinab Amiri Ghanatsaman,
    • Niloufar Jafarpour Negari,
    • Hojjat Asadollahpour Nanaei,
    • Xiangpeng Yue,
    • Yuxuan Song,
    • Xianyong Lan,
    • Weidong Deng,
    • Xihong Wang,
    • Chuanying Pan,
    • Ruidong Xiang,
    • Eveline M. Ibeagha-Awemu,
    • Pat (J.S.) Heslop-Harrison,
    • Benjamin D. Rosen,
    • Johannes A. Lenstra,
    • Shangquan Gan,
    • and Yu Jiang
    Genome Res. March 2023 33: 463-477; Published in Advance April 3, 2023, doi:10.1101/gr.277372.12
    ..., and PDGFD) (Fig. 5E) with roles in sheep morphology. The stratified dSV of IRF2BP2 is a 1.4-kb domestication-associated insertion downstream from this gene (Fig. 5F), which is reported to affect fleece variation (Demars et al. 2017). For RXFP2, the dSV is a 1.8-kb domestication-associated insertion...
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  2. Resource: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
    • Ran Li,
    • Mian Gong,
    • Xinmiao Zhang,
    • Fei Wang,
    • Zhenyu Liu,
    • Lei Zhang,
    • Qimeng Yang,
    • Yuan Xu,
    • Mengsi Xu,
    • Huanhuan Zhang,
    • Yunfeng Zhang,
    • Xuelei Dai,
    • Yuanpeng Gao,
    • Zhuangbiao Zhang,
    • Wenwen Fang,
    • Yuta Yang,
    • Weiwei Fu,
    • Chunna Cao,
    • Peng Yang,
    • Zeinab Amiri Ghanatsaman,
    • Niloufar Jafarpour Negari,
    • Hojjat Asadollahpour Nanaei,
    • Xiangpeng Yue,
    • Yuxuan Song,
    • Xianyong Lan,
    • Weidong Deng,
    • Xihong Wang,
    • Chuanying Pan,
    • Ruidong Xiang,
    • Eveline M. Ibeagha-Awemu,
    • Pat (J.S.) Heslop-Harrison,
    • Benjamin D. Rosen,
    • Johannes A. Lenstra,
    • Shangquan Gan,
    • and Yu Jiang
    Genome Res. March 27, 2023 ; Published in Advance March 27, 2023, doi:10.1101/gr.277372.122
    ...(Gonzalez et al. 2013). Among the multiallelic variations, we identified one region affecting interferon (IFN) gene cluster (Fig. 2C). The IFN gene clusters are keymodulators of innate and adaptive immunity (Wittling et al. 2021). As there is no “truth-set” to benchmark SV calls in sheep, we manually...
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  3. Resource: Copy number variation of individual cattle genomes using next-generation sequencing
    • Derek M. Bickhart,
    • Yali Hou,
    • Steven G. Schroeder,
    • Can Alkan,
    • Maria Francesca Cardone,
    • Lakshmi K. Matukumalli,
    • Jiuzhou Song,
    • Robert D. Schnabel,
    • Mario Ventura,
    • Jeremy F. Taylor,
    • Jose Fernando Garcia,
    • Curtis P. Van Tassell,
    • Tad S. Sonstegard,
    • Evan E. Eichler,
    • and George E. Liu
    Genome Res. April 2012 22: 778-790; Published in Advance February 2, 2012, doi:10.1101/gr.133967.111
    ...to dermoid sinus (Hillbertz et al. 2007). The ‘‘wrinkled’’ skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs are caused by a duplication upstream of HAS2 (Olsson et al. 2011). The white coat color in pigs and sheep is caused by a duplication involving KIT and ASIP, respectively (Moller et...
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