The transcriptional landscape of Populus pattern/effector-triggered immunity and how PagWRKY18 involved in it.

Plants trigger a robust immune response by activating massive transcriptome reprogramming through crosstalk between PTI and ETI. However, how PTI and ETI contribute to the quantitative or/and qualitative output of immunity and how they work together when both are being activated were unclear. In this study, we performed a comprehensive overview of pathogen-triggered transcriptomic reprogramming by analyzing temporal changes in the transcriptome up to 144 h after Colletotrichum gloeosporioides inoculated in Populus. Moreover, we constructed a hierarchical gene regulatory network of PagWRKY18 and its potential target genes to explore the underlying regulatory mechanisms of PagWRKY18 that are not yet clear. Interestingly, we confirmed that PagWRKY18 protein can directly bind the W-box elements in the promoter of a transmembrane leucine-rich repeat receptor-like kinase, PagSOBIR1 gene, to trigger PTI. At the same time, PagWRKY18 functions in disease tolerance by modulation of ROS homeostasis and induction of cell death via directly targeting PagGSTU7 and PagPR4 respectively. Furthermore, PagPR4 can interact with PagWRKY18 to inhibit the expression of PagPR4 genes, forming a negative feedback loop. Taken together, these results suggest that PagWRKY18 may be involved in regulating crosstalk between PTI and ETI to activate a robust immune response and maintain intracellular homeostasis.

High-quality maple genome reveals duplication-facilitated leaf color diversity.

Acer truncatum is a horticultural tree species with individuals that display either yellow or red leaves in autumn, giving it high ornamental and economic value. 'Lihong' of A. truncatum is an excellent cultivar due to its characteristic of having autumn leaves that turn a bright and beautiful shade of red, while its closely related cultivar 'Bunge' does not. However, the molecular mechanism underlying the color change in the cultivar 'Lihong' is still unclear. Here, we assembled a high-quality genome sequence of Acer truncatum 'Lihong' (genome size = 688 Mb, scaffold N50 = 9.14 Mb) with 28,438 protein-coding genes predicted. Through comparative genomic analysis, we found that 'Lihong' had experienced more tandem duplication events although it's a high degree of collinearity with 'Bunge'. Especially, the expansion of key enzymes in the anthocyanin synthesis pathway was significantly uneven between the two varieties, with 'Lihong' genome containing a significantly higher number of tandem/dispersed duplication key genes. Further transcriptomic, metabolomic, and molecular functional analyses demonstrated that several UFGT genes, mainly resulting from tandem/dispersed duplication, followed by the promoter sequence variation, may contribute greatly to the leaf color phenotype, which provides new insights into the mechanism of divergent anthocyanin accumulation process in the 'Lihong' and 'Bunge' with yellow leaves in autumn. Further, constitutive expression of two UFGT genes, which showed higher expression in 'Lihong', elevated the anthocyanin content. We proposed that the small-scale duplication events could contribute to phenotype innovation.

Merit of integrating in situ transcriptomics and anatomical information for cell annotation and lineage construction in single-cell analyses of Populus.

Cell type annotation and lineage construction are two of the most critical tasks conducted in the analyses of single-cell RNA sequencing (scRNA-seq). Four recent scRNA-seq studies of differentiating xylem propose four models on differentiating xylem development in Populus. The differences are mostly caused by the use of different strategies for cell type annotation and subsequent lineage interpretation. Here, we emphasize the necessity of using in situ transcriptomes and anatomical information to construct the most plausible xylem development model.