{"@type": "dcat:Dataset", "accessLevel": "public", "bureauCode": ["005:18"], "contactPoint": {"fn": "Cantu, Dario", "hasEmail": "mailto:dacantu@ucdavis.edu"}, "description": "<p>The ascomycete <em>Neofusicoccum parvum</em>, one of the causal agents of Botryosphaeria dieback, is a destructive wood\u2010infecting fungus and a serious threat to grape production worldwide. The capability to colonize woody tissue, combined with the secretion of phytotoxic compounds, is thought to underlie its pathogenicity and virulence. Here, we describe the repertoire of virulence factors and their transcriptional dynamics as the fungus feeds on different substrates and colonizes the woody stem. We assembled and annotated a highly contiguous genome using single\u2010molecule real\u2010time DNA sequencing. Transcriptome profiling by RNA sequencing determined the genome\u2010wide patterns of expression of virulence factors both <em>in vitro</em> (potato dextrose agar or medium amended with grape wood as substrate) and <em>in planta</em>. Pairwise statistical testing of differential expression, followed by co\u2010expression network analysis, revealed that physically clustered genes coding for putative virulence functions were induced depending on the substrate or stage of plant infection. Co\u2010expressed gene clusters were significantly enriched not only in genes associated with secondary metabolism, but also in those associated with cell wall degradation, suggesting that dynamic co\u2010regulation of transcriptional networks contributes to multiple aspects of <em>N. parvum</em> virulence. In most of the co\u2010expressed clusters, all genes shared at least a common motif in their promoter region, indicative of co\u2010regulation by the same transcription factor. Co\u2010expression analysis also identified chromatin regulators with correlated expression with inducible clusters of virulence factors, suggesting a complex, multi\u2010layered regulation of the virulence repertoire of <em>N. parvum</em>. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Link to Supporting Information.</p> <p>File Name: Web Page, url: <a href=\"https://bsppjournals.onlinelibrary.wiley.com/doi/10.1111/mpp.12491#support-information-section\">https://bsppjournals.onlinelibrary.wiley.com/doi/10.1111/mpp.12491#support-information-section</a> </p><p>Link to Supporting Information at <em>Molecular Plant Pathology</em>. Files are:</p>\n<p>Appendix S1 Supplementary tables and figures - Download</p>\n<ol>\n<li>Table S1: Statistics and SRA accession numbers of PacBio and Illumina genome sequences of N. parvum UCD646So.</li>\n<li>Table S2: Comparison of repeat content between assemblies generated with PacBio (N. parvum isolate UCD646So) and Illumina reads (N. parvum isolate UCR-NP2; Blanco-Ulate et al., 2013).</li>\n<li>Table S3: Comparison of the predicted proteomes in N. parvum isolate UCD646So and N. parvum isolate UCR-NP2 (Blanco-Ulate et al., 2013).</li>\n<li>Table S4: Gene space completeness estimations using CEGMA (Parra et al., 2009) and BUSCO (Sim\u00e3o et al., 2015).</li>\n<li>Table S5: N. parvum CAZymes families involved in plant cell wall degradation.</li>\n<li>Table S6: Summary of the major putative virulence categories of differentially expressed genes.</li>\n<li>Table S7: Summary of RNA-seq data and mapping metrics.</li>\n<li>Fig. S1: (A) Contig length distribution (log10 scale) over the N. parvum genome in the assemblies generated using PacBio reads and Illumina reads. (B) Dot plot showing the nucmer alignments between the contigs of the N. parvum UCD646So and N. parvum UCR-NP2 genomes.</li>\n<li>Fig. S2: Graphical representation of telomere sequences found at the ends of the N. parvum contigs. Figure was prepared using WebLogo (Crooks et al., 2004).</li>\n<li>Fig. S3: Number of reads mapped onto N. parvum UCD646So transcriptome per sample in the in planta (A) and in vitro (B) experiments.</li>\n<li>Fig. S4: Hierarchical clustering analysis of the 78 DE genes during N. parvum infections of grapevine woody stems, using Pearson\u2019s correlation distance (MeV; Saeed et al., 2003).</li>\n<li>Fig. S5: Identification of putatively constitutively expressed genes during N. parvum stem infections using Pearson correlation (R) coefficient and coefficient of variation (CV) cutoffs.</li>\n<li>Fig. S6: Estimation of most appropriate number of clusters for k-means clustering. Line plot shows \u201cFigure of merit value (FOM; y-axis) values\u201d in function of the number of clusters. (1-20 clusters, 100 iterations) (MeV v.4.9; Saeed et al., 2003).</li>\n</ol>\n<p>Appendix S2 Genome assemblies and protein\u2010coding gene coordinates - Download</p>\n<p>Appendix S3 Functional annotations - Download Excel (.xlsx) file.</p>\n<p>Appendix S4 Normalized RNA\u2010sequencing counts - Download\nNormalized RNA\u2010sequencing counts in the in vitro (A) and in planta (B) experiments, list of genes up\u2010regulated in the presence of wood (C) and exclusively expressed in planta (D), and groups of co\u2010expressed genes during Neofusicoccum parvum colonization obtained by both K\u2010means and hierarchical clustering analysis (E). Gene co\u2010expression modules obtained from Weighted Gene Co\u2010expression Network Analysis (WGCNA) and the corresponding degree of connectivity in the unweighted network (F), genomic clusters identified among the gene co\u2010expression modules (G), network properties of the gene co\u2010expression modules (H) and transcription factor\u2010coding genes and PHD finger domain\u2010containing protein genes identified among the most highly connected genes (5%) (I).</p>\n<p>Appendix S5 Shared motifs showing similarity to yeast motifs - Download\nShared motifs showing similarity to yeast motifs (MacIsaac_v1 database) and Saccharomyces cerevisiae motifs and motif\u2010associated proteins (ScAPs) (SCPD database) (E\u2009<\u20091 and motif length\u2009\u2264\u20099) (A) and Neofusicoccum parvum protein homologues of ScAPs (B).</p>\n<p></p></li></ul><p></p>", "distribution": [{"@type": "dcat:Distribution", "downloadURL": "https://bsppjournals.onlinelibrary.wiley.com/doi/10.1111/mpp.12491#support-information-section", "mediaType": "text/html", "title": "https://bsppjournals.onlinelibrary.wiley.com/doi/10.1111/mpp.12491#support-information-section"}], "identifier": "10.1111/mpp.12491", "keyword": ["ARS", "Botryosphaeria dieback", "CAZymes", "Condition\u2010dependent co\u2010regulation", "RNA-Seq", "SMRT sequencing", "cell wall degradation", "data.gov"], "license": "https://creativecommons.org/licenses/by/4.0/", "modified": "2024-02-13", "programCode": ["005:040"], "publisher": {"@type": "org:Organization", "name": "Agricultural Research Service"}, "title": "Data from: Condition\u2010dependent co\u2010regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum"}