Copy number variations (CNVs) are an important type of structural variations in the genome that usually affect gene expression levels by gene dosage effect. Understanding CNVs as part of genome evolution may provide insights into the genetic basis of important agricultural traits and contribute to the crop breeding in the future. While available methods to detect CNVs utilizing next-generation sequencing technology have helped shed light on prevalence and effects of CNVs, the complexity of crop genomes poses a major challenge and requires development of additional tools. Here, we generated genomic and transcriptomic data of 93 rice (Oryza sativa L.) accessions and developed a comprehensive pipeline to call CNVs in this large-scale dataset. We analyzed the correlation between CNVs and gene expression levels and found that approximately 13% of the identified genes showed a significant correlation between their expression levels and copy numbers. Further analysis showed that about 36% of duplicate pairs were involved in pseudogenetic events while only 5% of them showed functional differentiation. Moreover, the offspring copy mainly contributed to the expression levels and seemed more likely to become a pseudogene, whereas the parent copy tended to maintain the function of ancestral gene. We provide a high-accuracy CNV dataset that will contribute to functional genomics studies and molecular breeding in rice. We also showed that gene dosage effect of CNVs in rice is not exponential or linear. Our work demonstrates that the evolution of duplicated genes is asymmetric in both expression levels and gene fates, shedding a new insight into the evolution of duplicated genes.

中文翻译：

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全基因组拷贝数变异的调查显示，水稻中重复基因的不对称进化。

拷贝数变异（CNV）是基因组中结构变异的一种重要类型，通常通过基因剂量效应影响基因表达水平。将CNV理解为基因组进化的一部分，可以提供对重要农业性状遗传基础的见识，并为将来的作物育种做出贡献。尽管利用下一代测序技术检测CNV的可用方法有助于阐明CNV的流行和影响，但农作物基因组的复杂性构成了重大挑战，需要开发其他工具。在这里，我们生成了93个水稻（Oryza sativa L.）登录号的基因组和转录组数据，并开发了一个综合管道以在此大规模数据集中调用CNV。我们分析了CNV与基因表达水平之间的相关性，发现大约13％的已鉴定基因在其表达水平和拷贝数之间显示出显着的相关性。进一步的分析表明，约有36％的重复对参与假基因事件，而只有5％的人显示出功能分化。而且，后代拷贝主要促进表达水平，并且似乎更可能成为假基因，而亲代拷贝倾向于维持祖先基因的功能。我们提供了高精度的CNV数据集，将有助于水稻的功能基因组学研究和分子育种。我们还表明，CNV在水稻中的基因剂量效应不是指数或线性的。