Comparative transcriptome analysis of two Cercospora sojina strains reveals differences in virulence under nitrogen starvation stress

Abstract

Background: Cercospora sojina is a fungal pathogen that causes frogeye leaf spot in soybean-producing regions, leading to severe yield losses worldwide. It exhibits variations in virulence due to race differentiation between strains. However, the candidate virulence-related genes are unknown because the infection process is slow, making it difficult to collect transcriptome samples. Results: In this study, virulence-related differentially expressed genes (DEGs) were obtained from the highly virulent Race 15 strain and mildly virulent Race1 strain under nitrogen starvation stress, which mimics the physiology of the pathogen during infection. Weighted gene co-expression network analysis (WGCNA) was then used to find coexpressed gene modules and assess the relationship between gene networks and phenotypes. Upon comparison of the transcriptomic differences in virulence between the strains, a total of 378 and 124 DEGs were upregulated, while 294 and 220 were downregulated in Race 1 and Race 15, respectively. Annotation of these DEGs revealed that many were associated with virulence differences, including scytalone dehydratase, 1,3,8-trihydroxynaphthalene reductase, and β-1,3-glucanase. In addition, two modules highly correlated with the highly virulent strain Race 15 and 36 virulence-related DEGs were found to contain mostly β-1,4-glucanase, β-1,4-xylanas, and cellobiose dehydrogenase.Conclusions: These important nitrogen starvation-responsive DEGs are frequently involved in the synthesis of melanin, polyphosphate storage in the vacuole, lignocellulose degradation, and cellulose degradation during fungal development and differentiation. Transcriptome analysis indicated unique gene expression patterns, providing further insight into pathogenesis.

Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean

“…C. sojina races used in previous sequencing studies are unique to the US, and we used the latest variant race of China. Different countries adopt their own local differential soybean cultivars to identify C. sojina races by phenotype, making the races unable to be unified [ 6 ]. Genetic studies of many plant-pathogen interactions indicate that plants often contain single locus that confers resistance to specific races of a pathogen containing a complementary avirulence gene [ 41 ].…”

“…However, the disadvantage of this strategy is that the resistance of cultivars may be rapidly lost. The main reason for this is that resistance mechanisms can be overcome by the emergence of new C. sojina pathotypes [ 6 ]. Therefore, high-density markers and methods to counter new pathotype races are key to disease resistance breeding.…”

Morphological Physiological and Transcriptional Response to Low Nitrogen Stress in Populus Deltoides Marsh. Clones With Contrasting Nitrogen Use Efficiency

“…In multi-sample ( ≥ 15) RNA-seq data analysis, combined with the phenotypic or physiological characteristics data, weighted gene co-expression network analysis (WGCNA) could realize the high clustering of a large number of DEGs, and select the gene modules that are closely related to specific traits, from which the hub genes can be screened quickly and effectively by constructing expression regulation networks according to the connectivity of genes and the weight of gene correlation in the special module. WGCNA has been widely used for key gene mining in response to biotic and abiotic stresses [26,[30][31].…”