Li Xukai, Guo Kai, Zhu Xiaobo, Chen Peng, Li Ying, Xie Guosheng, Wang Lingqiang, Wang Yanting, Persson Staffan, Peng Liangcai
Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, 430070, People's Republic of China.
BMC Genomics. 2017 Jan 9;18(1):55. doi: 10.1186/s12864-016-3454-z.
Transposable elements (TEs) are prominent features in many plant genomes, and patterns of TEs in closely related rice species are thus proposed as an ideal model to study TEs roles in the context of plant genome evolution. As TEs may contribute to improved rice growth and grain quality, it is of pivotal significance for worldwide food security and biomass production.
We analyzed three cultivated rice species and their closest five wild relatives for distribution and content of TEs in their genomes. Despite that the three cultivar rice species contained similar copies and more total TEs, their genomes contained much longer TEs as compared to their wild relatives. Notably, TEs were largely depleted from genomic regions that corresponded to genes in the cultivated species, while this was not the case for their wild relatives. Gene ontology and gene homology analyses revealed that while certain genes contained TEs in all the wild species, the closest homologs in the cultivated species were devoid of them. This distribution of TEs is surprising as the cultivated species are more distantly related to each other as compared to their closest wild relative. Hence, cultivated rice species have more similar TE distributions among their genes as compared to their closest wild relatives. We, furthermore, exemplify how genes that are conferring important rice traits can be regulated by TE associations.
This study demonstrate that the cultivation of rice has led to distinct genomic distribution of TEs, and that certain rice traits are closely associated with TE distribution patterns. Hence, the results provide means to better understand TE-dependent rice traits and the potential to genetically engineer rice for better performance.
转座元件（TEs）是许多植物基因组的显著特征，因此，近缘水稻物种中的TEs模式被认为是研究TEs在植物基因组进化背景下作用的理想模型。由于TEs可能有助于改善水稻生长和籽粒品质，这对全球粮食安全和生物质生产具有至关重要的意义。
我们分析了三种栽培稻及其最亲近的五个野生近缘种基因组中TEs的分布和含量。尽管这三种栽培稻含有相似数量且总数更多的TEs，但与它们的野生近缘种相比，其基因组中的TEs长得多。值得注意的是，在栽培物种中，TEs在与基因对应的基因组区域大量缺失，而其野生近缘种并非如此。基因本体论和基因同源性分析表明，虽然某些基因在所有野生种中都含有TEs，但在栽培物种中最接近的同源基因却没有。这种TEs的分布令人惊讶，因为与它们最亲近的野生近缘种相比，栽培物种之间的亲缘关系更远。因此，与它们最亲近的野生近缘种相比，栽培稻物种在其基因之间具有更相似的TEs分布。此外，我们举例说明了赋予水稻重要性状的基因是如何通过与TEs的关联来调控的。
本研究表明，水稻的栽培导致了TEs在基因组中的不同分布，并且某些水稻性状与TEs分布模式密切相关。因此，这些结果为更好地理解依赖TEs的水稻性状以及通过基因工程改造水稻以获得更好性能的潜力提供了方法。
