Diverse roles of the CIPK gene family in transcription regulation and various biotic and abiotic stresses: A literature review and bibliometric study

Genome-wide characterization of the sunflower kinome: classification, evolutionary analysis and expression patterns under different stresses

Protein kinases play a significant role in plant responses to biotic and abiotic stresses, as well as in growth and development. While the kinome has been extensively investigated in crops such as Arabidopsis thaliana, soybean, common bean, and cotton, studies on protein kinases in sunflower remain limited. Our objective is to explore protein kinases in sunflower to bridge the research gap and enhance the understanding of their functions. We identified a total of 2,583 protein kinases from sunflower, which were classified into 22 families and 121 subfamilies. By comparing the subfamily members between sunflower and other species, we found that three subfamilies in sunflower-RLK-Pelle_CrRLK1L-1, RLK-Pelle_SD-2b, and RLK-Pelle_WAK-had undergone significant expansion. We then investigated the chromosomal distribution, molecular weight, isoelectric point, transmembrane domain, signal peptide, and structural and evolutionary diversity of the protein kinases. Through these studies, we have obtained a basic understanding of protein kinases in sunflower. To investigate the role of protein kinases in sunflower's response to biotic and abiotic stresses, we obtained 534 transcriptome datasets from various research groups, covering eight types of abiotic stress and two types of biotic stress. For the first time, we overcame the batch effects in the data and utilized a gene scoring system developed by our lab to perform a comprehensive analysis of multiple transcriptome datasets from different research groups. Ultimately, 73 key protein kinases were identified from numerous candidates, and functional annotation revealed that they are key members of signaling pathways such as ABA, MAPK, and SOS, actively participating in sunflower's response to biotic and abiotic stresses. In summary, through the exploration of protein kinases in sunflower, we have filled the gap in protein kinase research and provided a substantial amount of foundational data. By using the new scoring method to eliminate batch effects between transcriptome datasets, we achieved the first comprehensive analysis of large-scale transcriptome data. This method allows for a more thorough and detailed identification of key protein kinases that are widely regulated under various stress conditions, providing numerous candidate genes for sunflower stress resistance research.

TaCAMTA4 negatively regulates H2O2-dependent wheat leaf rust resistance by activating catalase 1 expression

Leaf rust, caused by Puccinia triticina Erikss. (Pt), is a serious disease threatening wheat (Triticum aestivum L.) production worldwide. Hydrogen peroxide (H2O2) triggered by Pt infection in resistant wheat cultivars cause oxidative damage directly to biomolecules or is activated by calcium signaling and mediates the hypersensitive response. Calmodulin-binding transcriptional activator 4 (TaCAMTA4) has been reported to negatively regulate wheat resistance to Pt. In this study, we found that TaCAMTA4 was induced by Pt race 165 in its compatible host harboring the Pt-resistant locus Lr26, TcLr26, and silencing of TaCAMTA4 increased local H2O2 accumulation and Pt resistance. Subcellular localization and autoactivation tests revealed that TaCAMTA4 is a nucleus-localized transcriptional activator. Furthermore, 4 DNA motifs recognized by TaCAMTA4 were identified by transcription factor-centered Y1H. Through analyzing the transcriptome database, 4 gene clusters were identified, each containing a different DNA motif on each promoter. Among them, the expression of catalase 1 (TaCAT1) with motif-1 was highly induced in the compatible interaction and was decreased when TaCAMTA4 was silenced. The results of electrophoretic mobility shift assay, ChIP-qPCR, and RT-qPCR further showed that TaCAMTA4 directly bound motif-1 in the TaCAT1 promoter. Furthermore, silencing of TaCAT1 resulted in enhanced resistance to Pt and increased local H2O2 accumulation in wheat, which is consistent with that of TaCAMTA4. Since calmodulin-binding transcription activators are Ca2+ sensors and catalases catalyze the decomposition of H2O2, we hypothesize that Ca2+ regulates the plant immune networks that are controlled by H2O2 and implicate a potential mechanism for Pt to suppress resistance by inducing the expression of the TaCAMTA4-TaCAT1 module, which consequently enhances H2O2 scavenging and attenuates H2O2-dependent resistance.

Genomic analysis of Nypa fruticans elucidates its intertidal adaptations and early palm evolution

Nypa fruticans (Wurmb), a mangrove palm species with origins dating back to the Late Cretaceous period, is a unique species for investigating long-term adaptation strategies to intertidal environments and the early evolution of palms. Here, we present a chromosome-level genome sequence and assembly for N. fruticans. We integrated the genomes of N. fruticans and other palm family members for a comparative genomic analysis, which confirmed that the common ancestor of all palms experienced a whole-genome duplication event around 89 million years ago, shaping the distinctive characteristics observed in this clade. We also inferred a low mutation rate for the N. fruticans genome, which underwent strong purifying selection and evolved slowly, thus contributing to its stability over a long evolutionary period. Moreover, ancient duplicates were preferentially retained, with critical genes having experienced positive selection, enhancing waterlogging tolerance in N. fruticans. Furthermore, we discovered that the pseudogenization of Early Methionine-labelled 1 (EM1) and EM6 in N. fruticans underly its crypto-vivipary characteristics, reflecting its intertidal adaptation. Our study provides valuable genomic insights into the evolutionary history, genome stability, and adaptive evolution of the mangrove palm. Our results also shed light on the long-term adaptation of this species and contribute to our understanding of the evolutionary dynamics in the palm family.

Overexpression of Nta-miR6155 confers resistance to Phytophthora nicotianae and regulates growth in tobacco (Nicotiana tabacum L.)

Tobacco black shank induced by Phytophthora nicotianae causes significant yield losses in tobacco plants. MicroRNAs (miRNAs) play a pivotal role in plant biotic stress responses and have great potential in tobacco breeding for disease resistance. However, the roles of miRNAs in tobacco plants in response to P. nicotianae infection has not been well characterized. In this study, we found that Nta-miR6155, a miRNA specific to Solanaceae crops, was significantly induced in P. nicotianae infected tobacco. Some of predicted target genes of Nta-miR6155 were also observed to be involved in disease resistance. To further investigate the function of miR6155 in tobacco during P. nicotianae infection, Nta-miR6155 overexpression plants (miR6155-OE) were generated in the Honghua Dajinyuan tobacco variety (HD, the main cultivated tobacco variety in China). We found that the Nta-miR6155 overexpression enhanced the resistance in tobacco towards P. nicotianae infections. The level of reactive oxygen species (ROS) was significantly lower and antioxidant enzyme activities were significantly higher in miR6155-OE plants than those in control HD plants during P. nicotianae infection. In addition, we found that the accumulation of salicylic acid and the expression of salicylic acid biosynthesis and signal transduction-related genes is significantly higher in miR6155-OE plants in comparison to the control HD plants. Furthermore, we found that Nta-miR6155 cleaved target genes NtCIPK18 to modulate resistance towards P. nicotianae in tobacco plants. Additionally, phenotypic analysis of miR6155-OE plants showed that Nta-miR6155 could inhibit the growth of tobacco by suppressing nitrogen uptake and photosynthesis. In conclusion, our findings indicated that miR6155 plays a crucial role in the regulation of growth and resistance against P. nicotianae infections in tobacco plants.