Small RNA-mediated gene silencing contributes to plant immunity. The secondary small interfering RNA (siRNA) pathway promotes defense by silencing target genes in invading fungal and oomycete pathogens. Many secondary siRNAs are derived from transcripts potentially encoding pentatricopeptide repeat (PPR) proteins. Here, we report that siRNA production is an ancient function of a conserved clade of
PPR
genes that undergo extensive within-species diversification. In
Arabidopsis thaliana
, siRNA-source
PPR
s are physically clustered on Chromosome 1. These sequences are diversified through gene duplication followed by sequence diversification and accumulation of high-impact variations including pseudogenization, leading to the accumulation of a diverse siRNA pool. These features are consistent with the engagement of
PPR
-siRNAs in a co-evolutionary arms race with the pathogens. This study defines siRNA-producing
PPR
s as a class of defense genes and highlights the potential of
PPR
-siRNA-based engineering as a strategy to enhance disease resistance.
Li Feng, Yingnan Hou, AmirAli Toghani et al.· Nature Communications· 1 citation
Plant development and stress responses are coordinated through phytohormone-mediated gene networks, yet resolving their spatiotemporal crosstalk remains challenging. Here, we generate a single-nucleus transcriptomic atlas of Arabidopsis seedlings, capturing early (0.5 h, 3 h) responses to 9 hormones across ~500,000 nuclei, including auxin, cytokinin, ABA, gibberellin, strigolactone, brassinosteroid, ethylene, JA, and SA. Within this window, most hormones showed rapid and cell-type-specific responses, whereas JA, SA, ABA showed more sustained and convergent responses by 3 h. Co-directional transcriptomic overlap was strongest at 0.5 h, while the JA-, SA-, and ABA-related responses showed the highest overlap at 3 h. Pathway-level analysis indicated asymmetric relationships among JA, SA, and ABA across biosynthetic and catabolic layers. Spatially, transcriptomic response overlap separated shoots from other tissues, with guard cells as shoot-side outliers showing weak JA–SA–ABA overlap. We further identified an SA-induced guard-cell-specific MYB60-centered module linked to ABA-associated stomatal regulators, suggesting a circuit that may fine-tune stomatal dynamics. Together, this atlas provides a high-resolution view of phytohormone response dynamics and interactions. Here the authors describe cell-type-specific responses of Arabidopsis seedlings to nine phytohormones. They characterize transcriptional crosstalk among them, and identify a guard-cell MYB60 module linked to stomatal regulation.
Zhijian Liu, Zhuowen Li, Yuzhuo Wang et al.· Nature Communications· 0 citations
The roles and molecular mechanisms of diverse RNA types, the roles of RNA structures and modifications in regulatory processes, and the translational application of RNA-based strategies for improving agronomic traits are discussed.
Yijun Qi, Yue-Qin Chen, Hongwei Guo et al.· Science China Life Sciences· 0 citations