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Title: Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolism gene clusters in the grapevine Esca pathogen Phaeoacremonium minimum

Author
item MASSENNET, MELANIE - University Of California
item MORALES-CRUZ, ABRAHAM - University Of California
item MINIO, ANDREA - University Of California
item FIGEROA-BALDERAS, ROSA - University Of California
item LAWRENCE, DANIEL - University Of California
item TRAVADON, RENAUD - University Of California
item ROLSHAUSEN, PHILIPPE - University Of California
item Baumgartner, Kendra
item CANTU, DARIO - University Of California

Submitted to: Frontiers in Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2018
Publication Date: 8/13/2018
Citation: Massennet, M., Morales-Cruz, A., Minio, A., Figeroa-Balderas, R., Lawrence, D.P., Travadon, R., Rolshausen, P.E., Baumgartner, K., Cantu, D. 2018. Whole-genome resequencing and pan-transcriptome reconstruction highlight the impact of genomic structural variation on secondary metabolism gene clusters in the grapevine Esca pathogen Phaeoacremonium minimum. Frontiers in Microbiology. 9:1784. https://doi.org/10.1101/252221.
DOI: https://doi.org/10.1101/252221

Interpretive Summary: The fungal grapevine pathogen Phaeoacremonium minimum causes Esca, a widespread and damaging so-called ‘trunk disease’. Isolates (aka strains) vary in aggressiveness and we examined the fungal genome to identify gene families involved with aggressiveness, to see if aggressive isolates differ in these gene families from weak isolates. The gene families we examined potentially have a role in aggressiveness because they are associated with secondary metabolism, cellular transport, and cell wall decomposition, all of which have been characterized in this fungus and others to have a role in the disease cycle. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.

Technical Abstract: The Ascomycete fungus Phaeoacremonium minimum is one of the primary causal agents of Esca, a widespread and damaging grapevine trunk disease. Variation in virulence among Pm. minimum isolates has been reported, but the underlying genetic basis of the phenotypic variability remains unknown. The goal of this study was to characterize intraspecific genetic diversity and explore its potential impact on virulence functions associated with secondary metabolism, cellular transport, and cell wall decomposition. We generated a chromosome-scale genome assembly, using single molecule real-time sequencing, and resequenced the genomes and transcriptomes of multiple isolates to identify sequence and structural polymorphisms. Numerous insertion and deletion events were found for a total of about 1 Mbp in each isolate. Structural variation in this extremely gene dense genome frequently caused presence/absence polymorphisms of multiple adjacent genes, mostly belonging to biosynthetic clusters associated with secondary metabolism. Because of the observed intraspecific diversity in gene content due to structural variation we concluded that a transcriptome reference developed from a single isolate is insufficient to represent the virulence factor repertoire of the species. We therefore compiled a pan-transcriptome reference of Pm. minimum comprising a non-redundant set of 15,245 protein-coding sequences. Using naturally infected field samples expressing Esca symptoms, we demonstrated that mapping of meta-transcriptomics data on a multi-species reference that included the Pm. minimum pan-transcriptome allows the profiling of an expanded set of virulence factors, including variable genes associated with secondary metabolism and cellular transport.