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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.

bmc genomics

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