Landscape and evolutionary dynamics of Helitron transposons in plant genomes as well as construction of online database HelDB
Landscape and evolutionary dynamics of Helitron transposons in plant genomes as well as construction of online database HelDB
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DOI：
10.1111/jse.12929
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发表时间：
2022-11
影响因子：
3.7
通讯作者：
Shu-Fen Li;Xinying Zhang;Long-Long Yang-Long;K. Jia;Jia-Rong Li;Li-Na Lan;Yulan Zhang;Ning Li
中科院分区：
文献类型：
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作者：
Shu-Fen Li;Xinying Zhang;Long-Long Yang-Long;K. Jia;Jia-Rong Li;Li-Na Lan;Yulan Zhang;Ning Li
Helitron 转座子由于其捕获基因和调控元件的能力，在宿主基因组进化中发挥着重要作用。在这项研究中，我们开发了一个管道，可以从 358 种植物和 178 种动物的高质量基因组中系统地识别和注释 Helitron。所有这些数据都被组织到 HelDB 中，这是一个可以通过用户友好的 Web 界面和相关软件来探索 Helitrons 的数据库。基于这些数据，进一步分析表明，Helitrons的数量或累积长度与基因组大小呈正相关。植物中的Helitron经历了两次膨胀期，第一次发生在20-30Ma，峰值在大约24Ma。第二次扩张发生在过去 400 万年里。扩张可能是由于古地理环境的刺激。对十字花科和茄科植物中Helitrons基因捕获的详细研究表明，捕获的基因表现出不同的功能。有趣的是，在大多数物种中，这些捕获的基因丰富了金属离子结合功能。这种现象可能是由于 Helitron 转座所需的二价金属离子需要与 Rep 结构域结合所致。这项研究提高了我们对植物中 Helitron 转座子的景观和进化的认识，并为此类转座子的进一步功能研究铺平了道路。
Helitron transposons play an important role in host genome evolution due to their ability to capture genes and regulatory elements. In this study, we developed a pipeline to identify and annotate Helitrons systematically from 358 plant and 178 animal high‐quality genomes. All these data were organized into HelDB, a database where Helitrons can be explored with a user‐friendly Web interface and related software. Based on these data, further analysis showed that the number or the cumulative length of Helitrons is positively correlated with genome size. Helitrons had experienced two expansion periods in plants, with the first occurring 20–30 Ma and peaking at approximately 24 Ma. The second expansion occurred in the last 4 million years. The expansions might be due to stimulation of paleogeographic environment. Detailed investigation of gene capture by Helitrons in Brassicaceae and Solanaceae plants showed that the captured genes showed diverse functions. Interestingly, metal ion binding function was enriched in these captured genes in most species. This phenomenon might be due to the need for binding of divalent metal ions to the Rep domain required for Helitron transposition. This study improves our knowledge of the landscape and evolution of Helitron transposons in plants and paves a way for further functional studies of this kind of transposable element.