Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.
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DOI：
10.1101/gr.234096.117
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发表时间：
2018-04
期刊：
影响因子：
7
通讯作者：
Flicek P
中科院分区：
文献类型：
--
作者：
Thybert D;Roller M;Navarro FCP;Fiddes I;Streeter I;Feig C;Martin-Galvez D;Kolmogorov M;Janoušek V;Akanni W;Aken B;Aldridge S;Chakrapani V;Chow W;Clarke L;Cummins C;Doran A;Dunn M;Goodstadt L;Howe K;Howell M;Josselin AA;Karn RC;Laukaitis CM;Jingtao L;Martin F;Muffato M;Nachtweide S;Quail MA;Sisu C;Stanke M;Stefflova K;Van Oosterhout C;Veyrunes F;Ward B;Yang F;Yazdanifar G;Zadissa A;Adams DJ;Brazma A;Gerstein M;Paten B;Pham S;Keane TM;Odom DT;Flicek P
由于缺乏具有高质量基因组组装的相似系统发育结构的姐妹进化枝，阻碍了对灵长类和啮齿类中驱动谱系特异性进化的机制的理解。在这里，我们已经创建了Mus caroli和Mus pahari基因组的染色体水平组件。与小家鼠和褐家鼠基因组一起，这组啮齿动物基因组在分歧时间上与人科（人类-黑猩猩-大猩猩-猩猩）相似。通过比较鼠科和人科之间的进化动力学，我们确定了染色体改组的点状事件，形成了300万至600万年前的小家鼠和小家鼠的祖先核型，但在人科中不存在。人科显示之间的四倍和七倍的核苷酸变化率和功能营业额在中性和功能序列，这表明一个潜在的一致性的鼠科加速。我们匹配的高质量基因组组装系统揭示了特定类型的重复序列如何在相关物种中发挥谱系特异性作用。最近的LINE活动在更大程度上改造了蛋白质编码位点，在鼠科比人科，在物种水平上的功能后果，如生殖隔离。此外，我们以前所未有的分辨率绘制了Muridae特异性反转录转座子扩增图，揭示了单核苷酸突变如何将特定的SINE元件转化为Mus caroli中特异性的活性CTCF结合位点载体，从而产生了数千个新的物种特异性CTCF结合位点。我们的研究结果表明，比较匹配的基因组系统发育集将是一个越来越强大的战略，了解哺乳动物生物学。
Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.
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影响因子：
12.3
作者：
Bailey JA;Baertsch R;Kent WJ;Haussler D;Eichler EE
通讯作者：
Eichler EE
影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
14.9
作者：
Bailey TL;Johnson J;Grant CE;Noble WS
通讯作者：
Noble WS
DOI：
10.1126/science.aad5497
发表时间：
2016-03-04
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Chuong EB;Elde NC;Feschotte C
通讯作者：
Feschotte C
影响因子：
3.7
作者：
Chevret, Pascale;Robinson, Terence J.;Britton-Davidian, Janice
通讯作者：
Britton-Davidian, Janice