The maize W22 genome provides a foundation for functional genomics and transposon biology
The maize W22 genome provides a foundation for functional genomics and transposon biology
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DOI：
10.1038/s41588-018-0158-0
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发表时间：
2018-09-01
期刊：
影响因子：
30.8
通讯作者：
Brutnell, Thomas P.
中科院分区：
文献类型：
--
作者：
Springer, Nathan M.;Anderson, Sarah N.;Brutnell, Thomas P.
自世纪中期以来，玉米W22自交系一直充当玉米遗传学的平台。为了简化玉米基因组分析，我们使用短读测序技术对W22参考基因组进行了测序和从头组装。我们发现，B73参考基因组在多个尺度上存在显着的结构异质性，从转座子组成和拷贝数变异到单核苷酸多态性。该参考基因组的产生使得能够准确放置数千个突变子（Mu）和解离（Ds）转座因子插入，用于反向和正向遗传学研究。已使用RNA-seq分析、差异核酸酶敏感性分析和亚硫酸氢盐测序分别绘制开放阅读框、开放染色质位点和DNA甲基化谱来实现基因组的注释。总的来说，这里开发的资源将W22整合为功能基因组学的社区参考基因组，并为玉米泛基因组提供基础。
The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.