The rich genetic diversity in Oryza sativa and Oryza rufipogon serves as the main sources in rice breeding. Large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the O. sativa japonica Nipponbare reference genome. Here we constructed a pan-genome dataset of the O. sativa-O. rufipogon species complex through deep sequencing and de novo assembly of 66 divergent accessions. Intergenomic comparisons identified 23 million sequence variants in the rice genome. This catalog of sequence variations includes many known quantitative trait nucleotides and will be helpful in pinpointing new causal variants that underlie complex traits. In particular, we systemically investigated the whole set of coding genes using this pan-genome data, which revealed extensive presence and absence of variation among rice accessions. This pan-genome resource will further promote evolutionary and functional studies in rice.

中文翻译：

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泛基因组分析强调了栽培稻和野生稻中基因组变异的程度。

水稻和芸苔中丰富的遗传多样性是水稻育种的主要来源。已经进行了大规模的重测序以发现水稻中的等位基因变体，但是通过将短序列读段直接定位到稻粳稻日本晴参考基因组上常常丢失了许多遗传变异信息。在这里，我们构建了一个O. sativa-O的全基因组数据集。rufipogon物种通过深度测序和从头组装66个不同种质而复杂化。基因组间的比较确定了水稻基因组中的2300万个序列变体。该序列变异目录包括许多已知的数量性状核苷酸，将有助于查明构成复杂性状的新因果变异。尤其是，我们使用这一全基因组数据系统地研究了整个编码基因，揭示了水稻种质间广泛存在和不存在变异。这种泛基因组资源将进一步促进水稻的进化和功能研究。