European maize genomes highlight intraspecies variation in repeat and gene content
European maize genomes highlight intraspecies variation in repeat and gene content
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DOI：
10.1038/s41588-020-0671-9
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发表时间：
2020-07-27
期刊：
影响因子：
30.8
通讯作者：
Mayer, Klaus F. X.
中科院分区：
文献类型：
--
作者：
Haberer, Georg;Kamal, Nadia;Mayer, Klaus F. X.
通过对4个欧洲硬粒玉米品系的基因组从头组装以及与美国玉米带基因组的比较，研究了玉米基因组重复序列和基因含量的种内变异动态，玉米的多样性是现代杂种优势模式和杂交育种的基础。从历史上看，美国农民利用这种变异性，从凹痕和燧石种质库的混合物中建立了今天高产的玉米带自交系。在这里，我们报告从头基因组序列的四个欧洲火石线组装到假分子与支架N50范围从6.1到10.4 Mb。与两个美国玉米带系的比较分析解释了两个种质之间的显著差异。虽然整体同线顺序和统一的基因注释显示只有适度的泛基因组差异，全基因组比对描绘的核心和非核心基因组，异染色质旋钮和orthopathic长末端重复反转录转座子的分析揭示了玉米基因组的动态。弗林特库的高质量基因组序列补充了玉米泛基因组，并为在基因组规模上研究玉米改良和加强现代杂交育种提供了重要工具。
De novo genome assemblies of four European flint maize lines and comparison with two US Corn Belt genomes provide insights into the dynamics of intraspecies variation in repeat and gene content in maize genomes.The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today's highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.