Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

First author: Silong Sun; Affiliations: China Agricultural University (中国农业大学): Beijing, China

Corresponding author: Jinsheng Lai (赖锦盛)

Maize is an important crop with a high level of genome diversity and heterosis. The genome sequence of a typical female line, B73, was previously released. Here, we report a de novo genome assembly of a corresponding male representative line, Mo17. More than 96.4% of the 2,183 Mb assembled genome can be accounted for by 362 scaffolds in ten pseudochromosomes with 38,620 annotated protein-coding genes. Comparative analysis revealed large gene-order and gene structural variations: approximately 10% of the annotated genes were mutually (互相地) nonsyntenic, and more than 20% of the predicted genes had either large-effect mutations or large structural variations, which might cause considerable protein divergence between the two inbred lines. Our study provides a high-quality reference-genome sequence of an important maize germplasm, and the intraspecific gene order and gene structural variations identified should have implications for heterosis and genome evolution.

玉米是一个具有高度基因组多态性和杂种优势的重要作物。经典的雌性株系B73的基因组序列已经公布。本文报道了对应雄性代谢株系Mo17的从头组装基因组。在2,183 Mb的组装基因组中，大约96.4%序列都集中在10个假染色体，共362个scaffold上，同时注释出的蛋白编码基因共38,620个。比较基因组分析显示在B73和Mo17基因组之间存在大量的基因顺序、基因结构变异，大约10%的注释基因在这两个基因组之间不存在共线性，并且超过20%的预测基因要么具有影响大的突变，或是大的结构变异，可能导致了这两个自交系之间相当大的蛋白分化。本文的研究提高了一个重要玉米种质的高质量参考基因组，同时本文所鉴定的玉米种内基因顺序、基因结构变异对于杂种优势及基因组演化具有重要参考意义。

通讯：赖锦盛 (http://cab.cau.edu.cn/art/2017/6/9/art_27218_60.html)

个人简介：1987-1991年，福建农学院，学士；1991-1993年，北京农业大学，农学院植物遗传育种系硕士；1993-1996年，中国农业大学，农学院植物遗传育种系博士；1996-1999年，美国新泽西州立大学，Waksman研究所博士后。

研究方向：玉米基因组学；玉米籽粒发育遗传调控；玉米胚乳基因印迹；玉米基因工程和分子育种。

doi: https://doi.org/10.1038/s41588-018-0182-0

Journal: Nature Genetics

Published date: 30 July, 2018

The maize W22 genome provides a foundation for functional genomics and transposon biology

First author: Nathan M. Springer; Affiliations: University of Minnesota (明尼苏达大学): Saint Paul, USA

Corresponding author: Thomas P. Brutnell 

The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline (使简单化) 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 (亚硫酸氢盐测序) 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.

自二十世纪中旬玉米W22自交系基因被用作玉米遗传学研究的平台。为了能够更加方便的研究玉米基因组，作者对W22基因组进行了测序和从头组装。研究显示，与B73基因组相比存在多个尺度的结构异质性，包括转座子组成、拷贝数变异及单核苷酸多样性。W22基因组的测序组装使得在正向、方向遗传学试验中数千个Mutator和Dissociation转座子元件的正确插入得到保证。利用RNA-seq鉴定开放阅读框、核酸酶敏感性差异谱鉴定开放染色质位点及亚硫酸氢盐测序鉴定DNA甲基化谱，作者对基因组进行了注释。综上，本文研究结果为玉米功能基因组的研究提供了参考基因组，同时为玉米泛基因组的研究提供了基础。

doi: https://doi.org/10.1038/s41588-018-0158-0

Journal: Nature Genetics

Published date: 30 July, 2018

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