Satheesh Viswanathan, Fan Wenwen, Chu Jie, Cho Jungnam
National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences (CEMPS), Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
University of Chinese Academy of Sciences, Shanghai, 200032, China.
Genes Genomics. 2021 Mar;43(3):289-294. doi: 10.1007/s13258-021-01040-z. Epub 2021 Feb 8.
Unlike peoples' belief that transposable elements (TEs) are "junk DNAs" or "genomic parasites", TEs are essential genomic elements that bring about genetic diversity and enable evolution of a species. In fact, transposons are major constituent of chromosome in crop genomes, particularly in major cereal crops, the primary type of which is long terminal repeat (LTR) retrotransposon. Since TE mobilization can be controlled by specific environmental stimulation and as the result can generate novel genetic variations, it has been suggested that controlled mobilization of TEs can be a plausible method for crop breeding. To achieve this goal, series of sequencing techniques have been recently established to identify TEs that are active in mobility. These methods target and detect extrachromosomal DNAs (ecDNAs), which are final products of integration. The newly identified TEs by these methods exhibit strong transpositional activity which can generate novel genetic diversity and provide useful breeding resources.
In this mini review, we summarize and introduce ALE-seq, mobilome-seq, and VLP DNA-seq techniques employed to detect active TEs in plants.
与人们认为转座元件（TEs）是“垃圾DNA”或“基因组寄生虫”的观点不同，TEs是重要的基因组元件，可带来遗传多样性并推动物种进化。事实上，转座子是作物基因组中染色体的主要组成部分，尤其是在主要谷类作物中，其主要类型是长末端重复序列（LTR）反转录转座子。由于TE的移动可受特定环境刺激控制，结果能产生新的遗传变异，因此有人提出，对TE进行可控移动可能是一种可行的作物育种方法。为实现这一目标，最近建立了一系列测序技术来鉴定具有活跃移动性的TEs。这些方法针对并检测染色体外DNA（ecDNAs），它们是整合的最终产物。通过这些方法新鉴定出的TEs表现出很强的转座活性，可产生新的遗传多样性并提供有用的育种资源。
在本综述中，我们总结并介绍了用于检测植物中活跃TEs的ALE-seq、移动基因组测序（mobilome-seq）和病毒样颗粒DNA测序（VLP DNA-seq）技术。
