Department of Plant Genetics, Breeding and Biotechnology, Faculty of Horticulture, Biotechnology and Landscape Architecture, Warsaw University of Life Sciences, Warsaw, Poland.
Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland.
Plant Sci. 2018 Mar;268:18-29. doi: 10.1016/j.plantsci.2017.12.003. Epub 2017 Dec 12.
Cyst-forming plant-parasitic nematodes are pests threatening many crops. By means of their secretions cyst nematodes induce the developmental and metabolic reprogramming of host cells that lead to the formation of a syncytium, which is the sole food source for growing nematodes. The in depth micro RNA (miRNA) dynamics in the syncytia induced by Globodera rostochiensis in tomato roots was studied. The miRNAomes were obtained from syncytia covering the early and intermediate developmental stages, and were the subject of differential expression analysis. The expression of 1235 miRNAs was monitored. The fold change (logFC) ranged from -7.36 to 8.38, indicating that this transcriptome fraction was very variable. Moreover, we showed that the DE (differentially expressed) miRNAs do not fully overlap between the selected time points, suggesting infection stage specific regulation by miRNA. The correctness of RNA-seq expression profiling was confirmed by qRT-PCR (quantitative Real Time Polymerase Chain Reaction) for seven miRNA species. Down- and up-regulated miRNA species, including their isomiRs, were further used to identify their potential targets. Among them there are a large number of transcription factors linked to different aspects of plant development belonging to gene families, such as APETALA2 (AP2), SQUAMOSA (MADS-box), MYB, GRAS, and AUXIN RESPONSE FACTOR (ARF). The substantial portion of potential target genes belong to the NB-LRR and RLK (RECEPTOR-LIKE KINASE) families, indicating the involvement of miRNA mediated regulation in defense responses. We also collected the evidence for target cleavage in the case of 29 miRNAs using one of three alternative methods: 5' RACE (5' Rapid Amplification of cDNA Ends), a search of tasiRNA within our datasets, and the meta-analysis of tomato degradomes in the GEO (Gene Expression Omnibus) database. Eight target transcripts showed a negative correlation with their respective miRNAs at two or three time points. These results indicate a large regulatory potential for miRNAs in tuning the development and defense responses.
形成孢囊的植物寄生线虫是威胁许多作物的害虫。通过分泌液，胞囊线虫诱导宿主细胞的发育和代谢重编程，导致合胞体的形成，这是生长线虫的唯一食物来源。本研究深入研究了根结线虫在番茄根系中诱导的合胞体中的 microRNA（miRNA）动态。从早期和中期发育阶段的合胞体中获得 miRNAome，并进行差异表达分析。监测了 1235 个 miRNA 的表达。倍数变化（logFC）范围为-7.36 至 8.38，表明该转录组部分非常多变。此外，我们表明，选择的时间点之间的 DE（差异表达）miRNA 不完全重叠，表明 miRNA 具有感染阶段特异性调节作用。通过对七个 miRNA 物种进行 qRT-PCR（定量实时聚合酶链反应）验证了 RNA-seq 表达谱的正确性。下调和上调的 miRNA 物种，包括它们的 isomiRs，进一步用于鉴定它们的潜在靶标。其中有大量与植物发育的不同方面相关的转录因子，属于基因家族，如 APETALA2（AP2）、SQUAMOSA（MADS 盒）、MYB、GRAS 和 AUXIN RESPONSE FACTOR（ARF）。大量潜在靶基因属于 NB-LRR 和 RLK（受体样激酶）家族，表明 miRNA 介导的调节参与了防御反应。我们还使用三种替代方法中的一种收集了 29 个 miRNA 的靶标切割证据：5' RACE（5'快速扩增 cDNA 末端）、我们数据集内 tasiRNA 的搜索以及 GEO（基因表达综合数据库）数据库中番茄降解组的荟萃分析。在两个或三个时间点，有 8 个靶转录本与各自的 miRNA 呈负相关。这些结果表明 miRNA 具有调节发育和防御反应的巨大调控潜力。
