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

First author:Silong Sun; Affiliations: China Agricultural University (中國農業大學): Beijing, China

Corresponding author:Jinsheng Lai(賴錦盛)

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 ade novogenome 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.

玉米是一個具有高度基因組多態性和雜種優勢的重要作物。經典的雌性株系B73基因組的序列已經公布。本文報道了對應雄性代謝株系Mo17的從頭組裝基因組。在2,183?Mb的組裝基因組中，大約96.4%序列都集中在10個假染色體，共362個scaffold上，同時注釋出的蛋白編碼基因共38,620個。比較基因組分析顯示在B73和Mo17基因組之間存在大量的基因順序、基因結構變異，大約10%的注釋基因在這兩個基因組之間不存在共線性，並且超過20%的預測基因要麼具有影響大的突變，或是大的結構變異，可能導致了這兩個自交系之間相當大的蛋白分化。本文的研究提高了一個重要玉米種質的高質量參考基因組，同時本文所鑒定的玉米種內基因順序、基因結構變異對於雜種優勢及基因組演化具有重要參考意義。

通訊：賴錦盛(http://cab.cau.edu.cn/art/2017/6/9/art_27218_60.html)

個人簡介：1987-1991年，福建農學院，學士；1991-1993年，北京農業大學，農學院植物遺傳育種系碩士；1993-1996年，中國農業大學，農學院植物遺傳育種系博士；1996-1999年，美國新澤西州立大學，Waksman研究所博士後。

研究方向：玉米基因組學；玉米籽粒發育遺傳調控；玉米胚乳基因印跡；玉米基因工程和分子育種。

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 (明尼蘇達大學): 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 (使簡單化) maize genome analyses, we have sequenced andde novoassembled 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 ofMutator(Mu) andDissociation(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 (亞硫酸氫鹽測序) 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.

自二十世紀中旬玉米W22自交系基因被用作玉米遺傳學研究的平台。為了能夠更加方便的研究玉米基因組，作者對W22基因組進行了測序和從頭組裝。研究顯示，與B73基因組相比存在多個尺度的結構異質性，包括轉座子組成、拷貝數變異及單核苷酸多樣性。W22基因組的測序組裝使得在正向、方向遺傳學試驗中數千個Mutator和Dissociation轉座子元件的正確插入得到保證。利用RNA-seq鑒定開放閱讀框、核酸酶敏感性差異譜鑒定開放染色質位點及亞硫酸氫鹽測序鑒定DNA甲基化譜，作者對基因組進行了注釋。綜上，本文研究結果為玉米功能基因組的研究提供了參考基因組，同時為玉米泛基因組的研究提供了基礎。

Journal:Nature Genetics

Published date: 30 July, 2018

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