Comparative genomics of plant pathogenic Diaporthe species and transcriptomics of Diaporthe caulivora during host infection reveal insights into pathogenic strategies of the genus

Abstract

Background Diaporthe caulivora is a fungal pathogen causing stem canker in soybean worldwide. The generation of genomic and transcriptomic information of this ascomycete, together with a comparative genomic approach with other pathogens of this genus, will contribute to get insights into the molecular basis of pathogenicity strategies used by D. caulivora and other Diaporthe species. Results In the present work, the nuclear genome of D. caulivora isolate (D57) was resolved, and a comprehensive annotation based on gene expression and genomic analysis is provided. Diaporthe caulivora D57 has an estimated size of 57,86 Mb and contains 18,385 predicted protein-coding genes, from which 1501 encode predicted secreted proteins. A large array of D. caulivora genes encoding secreted pathogenicity-related proteins was identified, including carbohydrate-active enzymes (CAZymes), necrosis-inducing proteins, oxidoreductases, proteases and effector candidates. Comparative genomics with other plant pathogenic Diaporthe species revealed a core secretome present in all Diaporthe species as well as Diaporthe-specific and D. caulivora-specific secreted proteins. Transcriptional profiling during early soybean infection stages showed differential expression of 2659 D. caulivora genes. Expression patterns of upregulated genes and gene ontology enrichment analysis revealed that host infection strategies depends on plant cell wall degradation and modification, detoxification of compounds, transporter activities and toxin production. Increased expression of effectors candidates suggests that D. caulivora pathogenicity also rely on plant defense evasion. A high proportion of the upregulated genes correspond to the core secretome and are represented in the pathogen-host interaction (PHI) database, which is consistent with their potential roles in pathogenic strategies of the genus Diaporthe. Conclusions Our findings give novel and relevant insights into the molecular traits involved in pathogenicity of D. caulivora towards soybean plants. Some of these traits are in common with other Diaporthe pathogens with different host specificity, while others are species-specific. Our analyses also highlight the importance to have a deeper understanding of pathogenicity functions among Diaporthe pathogens and their interference with plant defense activation.

Genome Analyses of Two Blueberry Pathogens: Diaportheamygdali CAA958 and Diaporthe eres CBS 160.32

“…The proportion of CAZymes in the D. amygdali secretome (29.1%) is consistent with previous reports in other Diaporthe species, such as D. capsici and D. citri (30.7%), D. caulivora (30.6%), and D. longicolla (31.4%), emphasizing the importance of CAZymes in Diaporthe pathogenicity [ 16 ]. Nevertheless, the proportion of CAZymes in the secretome of D. eres CBS 160.32 was estimated at 5.4%, which is low when compared with the abovementioned species (average = 30.5%).…”

“…These genomes, whose annotations are publicly available, were used to perform a comparison of GC content, genome size, BUSCO completeness, predicted proteins, and abundance of CAZymes and BGCs. These taxa include mainly pathogens of citrus [ 17 ], grapevine [ 22 ], soybean [ 16 , 21 ], sunflower [ 20 ], sweet potato [ 23 ], and walnut [ 24 ].…”

“…Nevertheless, recent studies using genomic and transcriptomic approaches have been carried out to understand how species of Diaporthe infect their hosts. For instance, Mena et al [ 16 ] revealed insights into the molecular traits involved in the pathogenicity of D. caulivora on soybean plants. Gai et al [ 17 ] demonstrated that the genomic analyses of Diaporthe species that are responsible for melanose on citrus ( D. citri , D. citriasiana , and D. citrichinensis ) helped unveil the molecular mechanism of fungicide resistance, pathogen–host interaction, and population genome-related research of this relevant plant pathogen.…”

“…Additionally, a comparative analysis was performed to gain knowledge on the strategies of Diaporthe species to successfully enter and colonize their plant host. For this, we analyzed the genomes of nine important plant pathogens, namely D. ampelina DA912, D. batatas CRI 302-4, D. capsici GY-Z16, D. caulivora D57, D. citri ZJUD2, D. citriasiana ZJUD30, D. citrichinensis ZJUD34, D. helianthi DHEL01, and D. longicolla MSPL 10–6, whose annotations are available and/or published on public databases [ 16 , 17 , 20 , 21 , 22 , 23 , 24 ].…”

New real‐time PCR assay for detecting the blueberry and cranberry twig blight pathogen

“…As TEF1 is a single copy gene (Hasegawa et al, 2010), this was an expected result, comparable to the sensitivity reported for other TEF1 based real‐time PCR assays, e.g., of Fusarium oxysporum and Monilinia kusanoi assays (Dharmaraj et al, 2021; Haegi et al, 2013). While there are no genome data available for D. vaccinii , using the average known genome size of other Diaporthe species (.06 pg) (Mena et al, 2022), it is estimated that the real‐time PCR assay could detect approximately less than 20 haploid hyphal cells.…”