Identification of RT-qPCR reference genes suitable for gene function studies in the pitaya canker disease pathogen Neoscytalidium dimidiatum

Host-pathogen interaction between pitaya and Neoscytalidium dimidiatum reveals the mechanisms of immune response associated with defense regulators and metabolic pathways

BACKGROUND

Understanding how plants and pathogens regulate each other's gene expression during their interactions is key to revealing the mechanisms of disease resistance and controlling the development of pathogens. Despite extensive studies on the molecular and genetic basis of plant immunity against pathogens, the influence of pitaya immunity on N. dimidiatum metabolism to restrict pathogen growth is poorly understood, and how N. dimidiatum breaks through pitaya defenses. In this study, we used the RNA-seq method to assess the expression profiles of pitaya and N. dimidiatum at 4 time periods after interactions to capture the early effects of N. dimidiatum on pitaya processes.

RESULTS

The study defined the establishment of an effective method for analyzing transcriptome interactions between pitaya and N. dimidiatum and to obtain global expression profiles. We identified gene expression clusters in both the host pitaya and the pathogen N. dimidiatum. The analysis showed that numerous differentially expressed genes (DEGs) involved in the recognition and defense of pitaya against N. dimidiatum, as well as N. dimidiatum's evasion of recognition and inhibition of pitaya. The major functional groups identified by GO and KEGG enrichment were responsible for plant and pathogen recognition, phytohormone signaling (such as salicylic acid, abscisic acid). Furthermore, the gene expression of 13 candidate genes involved in phytopathogen recognition, phytohormone receptors, and the plant resistance gene (PG), as well as 7 effector genes of N. dimidiatum, including glycoside hydrolases, pectinase, and putative genes, were validated by qPCR. By focusing on gene expression changes during interactions between pitaya and N. dimidiatum, we were able to observe the infection of N. dimidiatum and its effects on the expression of various defense components and host immune receptors.

CONCLUSION

Our data show that various regulators of the immune response are modified during interactions between pitaya and N. dimidiatum. Furthermore, the activation and repression of these genes are temporally coordinated. These findings provide a framework for better understanding the pathogenicity of N. dimidiatum and its role as an opportunistic pathogen. This offers the potential for a more effective defense against N. dimidiatum.

Plant-Associated Neoscytalidium dimidiatum-Taxonomy, Host Range, Epidemiology, Virulence, and Management Strategies: A Comprehensive Review

Neoscytalidium dimidiatum, a plant- and human-associated fungus, has emerged as a substantial global ecological and agricultural threat aggravated by global warming. It inflicts various diseases, including canker, blight, dieback, leaf spot, root rot, and fruit rot, across a wide spectrum of fruit trees, field crops, shrubs, and arboreal species, with a host range spanning 46 plant families, 84 genera, and 126 species, primarily affecting eudicot angiosperms. Six genera are asymptomatic hosts. Neoscytalidium dimidiatum exhibits worldwide distribution, with the highest prevalence observed in Asia and North America, notably in Iran, Turkey, and California. Rising disease prevalence and severity, aggravated by climate change, particularly impact tropical arid places across 37 countries spanning all 7 continents. This comprehensive review encapsulates recent advancements in the understanding of N. dimidiatum, encompassing alterations in its taxonomic classification, host range, symptoms, geographic distribution, epidemiology, virulence, and strategies for effective management. This study also concentrates on comprehending the taxonomic relationships and intraspecific variations within N. dimidiatum, with a particular emphasis on N. oculus and N. hylocereum, proposing to consider these two species as synonymous with N. dimidiatum. Furthermore, this review identifies prospective research directions aimed at augmenting our fundamental understanding of host-N. dimidiatum interaction.

Screening of reference genes for microRNA analysis in the study of solider caste differentiation of Formosan subterranean termite Coptotermes formosanus Shiraki

The soldier caste differentiation is a complex process that is governed by the transcriptional regulation and post-transcriptional regulation. microRNAs (miRNAs) are noncoding RNAs that control a wide range of activities. However, their roles in solider caste differentiation are barely studied. RT-qPCR is a powerful tool to study the function of genes. A reference gene is required for normalization for the the relative quantification method. However, no reference gene is available for miRNA quantification in the study of solider caste differentiation of Coptotermes formosanus Shiraki. In this research, in order to screen the suitable reference genes for the study of the roles of miRNAs in solider caste differentiation, the expression levels of 8 candidate miRNA genes were quantified in the head and thorax + abdomen during soldier differentiation. The qPCR data were analyzed using geNorm, NormFinder, BestKeeper, ΔCt method and RefFinder. The normalization effect of the reference genes was evaluated using the let-7-3p. Our study showed that novel-m0649-3p was the most stable reference gene, while U6 was the least stable reference gene. Our study has selected the most stable reference gene, and has paved the way for functional analysis of miRNAs in solider caste differentiation.