State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China.
Plant Commun. 2023 Jan 9;4(1):100429. doi: 10.1016/j.xplc.2022.100429. Epub 2022 Sep 7.
Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However, the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood. In this study, a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato, an emerging AMS model. The annotation of the tomato genome was improved by a multiple-platform sequencing strategy. A total of 3,174 protein-coding genes were upregulated during AMS, 42% of which were alternatively spliced. Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms. Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants. However, these orthogroups were absent or not induced in monocots and/or non-AMS hosts, suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module. Additionally, we detected 587 lncRNAs, ten miRNAs, and 146 circRNAs that responded to AMS, which were incorporated to establish a tomato AMS-responsive, competing RNA-responsive endogenous RNA (ceRNA) network. Finally, a tomato symbiotic transcriptome database (TSTD, https://efg.nju.edu.cn/TSTD) was constructed to serve as a resource for deep deciphering of the AMS regulatory network. These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.
丛枝菌根共生 (AMS) 是一种广泛分布于陆生植物中的古老植物-真菌关系。共生结构的形成和双向养分交换需要众多基因的调控。然而，涉及不同类型调节 RNA 的植物 AMS 中 RNA 组学的全景仍知之甚少。在这项研究中，采用组合策略结合多种测序方法，以解析番茄（一种新兴的 AMS 模式植物）中 RNA 组学的全景。通过多平台测序策略对番茄基因组进行了注释改进。在 AMS 过程中，共鉴定到 3174 个上调表达的蛋白编码基因，其中 42%为可变剪接。比较转录组分析表明，在 8 种系统发育较远的被子植物中，有 24 个直系同源基因簇的基因被 AMS 一致诱导。另外还有 7 个直系同源基因簇在所有调查的双子叶 AMS 宿主植物中被 AMS 特异性诱导。然而，在单子叶植物和/或非 AMS 宿主中，这些直系同源基因簇缺失或不受诱导，表明除了保守的核心调控模块外，还存在一个不断进化的 AMS 响应网络。此外，我们还检测到 587 个 lncRNA、10 个 miRNA 和 146 个 circRNA 对 AMS 有响应，将它们整合建立了一个番茄 AMS 响应、竞争性 RNA 响应内源性 RNA（ceRNA）网络。最后，构建了一个番茄共生转录组数据库（TSTD，https://efg.nju.edu.cn/TSTD），作为深入解析 AMS 调控网络的资源。这些结果有助于阐明番茄 AMS 过程中 RNA 组学的重排，并提示在 AMS 过程中存在一个复杂而不断进化的 RNA 响应网络。
