Nearly 200 plant genomes have been sequenced over the last two years, and new functions of plant microRNAs (miRNAs) have been revealed. Therefore, timely update of the plant miRNA databases by incorporating miRNAs from the newly sequenced species and functional information is required to provide useful resources for advancing plant miRNA research. Here we report the update of PmiREN2.0 (https://pmiren.com/) with an addition of 19 363 miRNA entries from 91 plants, doubling the amount of data in the original version. Meanwhile, abundant regulatory information centred on miRNAs was added, including predicted upstream transcription factors through binding motifs scanning and elaborate annotation of miRNA targets. As an example, a genome-wide regulatory network centred on miRNAs was constructed for Arabidopsis. Furthermore, phylogenetic trees of conserved miRNA families were built to expand the understanding of miRNA evolution across the plant lineages. These data are helpful to deduce the regulatory relationships concerning miRNA functions in diverse plants. Beside the new data, a suite of design tools was incorporated to facilitate experimental practice. Finally, a forum named ‘PmiREN Community’ was added for discussion and resource and new discovery sharing. With these upgrades, PmiREN2.0 should serve the community better and accelerate miRNA research in plants.

中文翻译：

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PmiREN2.0：从数据注释到植物microRNA的功能探索

在过去的两年里，近 200 个植物基因组被测序，植物 microRNAs (miRNAs) 的新功能已经被揭示。因此，需要通过整合来自新测序物种的 miRNA 和功能信息来及时更新植物 miRNA 数据库，为推进植物 miRNA 研究提供有用的资源。在这里，我们报告了 PmiREN2.0 (https://pmiren.com/) 的更新，增加了来自 91 个植物的 19 363 个 miRNA 条目，使原始版本的数据量翻了一番。同时，增加了以 miRNA 为中心的丰富调控信息，包括通过结合基序扫描预测的上游转录因子和 miRNA 靶标的精细注释。例如，为拟南芥构建了一个以 miRNA 为中心的全基因组调控网络。此外，建立了保守的 miRNA 家族的系统发育树，以扩展对跨植物谱系的 miRNA 进化的理解。这些数据有助于推断不同植物中miRNA功能的调控关系。除了新数据之外，还结合了一套设计工具以促进实验实践。最后，增加了一个名为“PmiREN Community”的论坛，用于讨论和资源和新发现的共享。通过这些升级，PmiREN2.0 应该可以更好地服务于社区并加速植物中的 miRNA 研究。一套设计工具被纳入以促进实验实践。最后，增加了一个名为“PmiREN Community”的论坛，用于讨论和资源和新发现的共享。通过这些升级，PmiREN2.0 应该可以更好地服务于社区并加速植物中的 miRNA 研究。一套设计工具被纳入以促进实验实践。最后，增加了一个名为“PmiREN Community”的论坛，用于讨论和资源和新发现的共享。通过这些升级，PmiREN2.0 应该可以更好地服务于社区并加速植物中的 miRNA 研究。