Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel.
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DOI：
10.1186/s13059-022-02602-4
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发表时间：
2022-02-21
期刊：
影响因子：
12.3
通讯作者：
Fitzgerald T
中科院分区：
文献类型：
--
作者：
Leger A;Brettell I;Monahan J;Barton C;Wolf N;Kusminski N;Herder C;Aadepu N;Becker C;Gierten J;Hammouda OT;Hasel E;Lischik C;Lust K;Sokolova N;Suzuki R;Tavhelidse T;Thumberger T;Tsingos E;Watson P;Welz B;Naruse K;Loosli F;Wittbrodt J;Birney E;Fitzgerald T
青鳉是一种成熟的脊椎动物模式系统，具有悠久的遗传学研究历史，并有多个高质量的参考基因组可用于几个近交系。青鳉对野生近亲繁殖有很高的耐受性，因此可以从野生个体建立近交系。我们利用这一特点，创建一个近交系面板资源：青鳉近交清须-卡尔斯鲁厄（MIKK）面板。这组80个近等基因近交系含有大量遗传变异，从原始野生种群遗传。我们使用Oxford Nanopore Technologies（ONT）长读段数据来进一步研究MIKK面板的子集的基因组和表观基因组景观。纳米孔测序使我们能够识别各种各样的高质量的结构变体，我们目前的结果和方法使用泛基因组图表示12个单独的青鳉线。这种基于图的参考MIKK面板基因组揭示了MIKK面板品系和标准线性参考基因组之间的新差异。我们发现额外的MIKK小组特定的基因组内容，将从线性参考比对方法中丢失。我们还能够识别和量化每条线中重复元件的存在。最后，我们研究了细胞系特异性CpG甲基化，并在这12个细胞系中进行了差异DNA甲基化分析。我们使用长和短读段序列技术对MIKK面板基因组进行了详细分析，创建了MIKK面板特定的泛基因组参考数据集，允许使用标准方法研究难以实现的新变异类型。在线版本包含补充材料，可通过10.1186/s13059 - 022 - 02602 - 4获得。
The teleost medaka (Oryzias latipes) is a well-established vertebrate model system, with a long history of genetic research, and multiple high-quality reference genomes available for several inbred strains. Medaka has a high tolerance to inbreeding from the wild, thus allowing one to establish inbred lines from wild founder individuals. We exploit this feature to create an inbred panel resource: the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel. This panel of 80 near-isogenic inbred lines contains a large amount of genetic variation inherited from the original wild population. We use Oxford Nanopore Technologies (ONT) long read data to further investigate the genomic and epigenomic landscapes of a subset of the MIKK panel. Nanopore sequencing allows us to identify a large variety of high-quality structural variants, and we present results and methods using a pan-genome graph representation of 12 individual medaka lines. This graph-based reference MIKK panel genome reveals novel differences between the MIKK panel lines and standard linear reference genomes. We find additional MIKK panel-specific genomic content that would be missing from linear reference alignment approaches. We are also able to identify and quantify the presence of repeat elements in each of the lines. Finally, we investigate line-specific CpG methylation and performed differential DNA methylation analysis across these 12 lines. We present a detailed analysis of the MIKK panel genomes using long and short read sequence technologies, creating a MIKK panel-specific pan genome reference dataset allowing for investigation of novel variation types that would be elusive using standard approaches. The online version contains supplementary material available at 10.1186/s13059-022-02602-4.
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DOI：
10.1093/bioinformatics/btx346
发表时间：
2017-10-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gel B;Serra E
通讯作者：
Serra E
影响因子：
12.3
作者：
Garg S
通讯作者：
Garg S
DOI：
10.1146/annurev-genom-120219-080406
发表时间：
2020-08-31
影响因子：
8.7
作者：
Eizenga JM;Novak AM;Sibbesen JA;Heumos S;Ghaffaari A;Hickey G;Chang X;Seaman JD;Rounthwaite R;Ebler J;Rautiainen M;Garg S;Paten B;Marschall T;Sirén J;Garrison E
通讯作者：
Garrison E
影响因子：
16.6
作者：
Golicz, Agnieszka A.;Bayer, Philipp E.;Barker, Guy C.;Edger, Patrick P.;Kim, HyeRan;Martinez, Paula A.;Chan, Chon Kit Kenneth;Severn-Ellis, Anita;McCombie, W. Richard;Parkin, Isobel A. P.;Paterson, Andrew H.;Pires, J. Chris;Sharpe, Andrew G.;Tang, Haibao;Teakle, Graham R.;Town, Christopher D.;Batley, Jacqueline;Edwards, David
通讯作者：
Edwards, David
影响因子：
3.3
作者：
Chalopin D;Naville M;Plard F;Galiana D;Volff JN
通讯作者：
Volff JN