Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola: A small fungal genome with an increased cohort of genes associated with loss of virulence

<p>Boxwood plants are affected by many different diseases caused by fungi.  Some boxwood diseases are deadly and quickly kill the infected plants, but with others, the plant can survive and even thrive when infected.  The fungus that causes volutella blight is the most common of these weak boxwood pathogens.  Even the healthiest boxwood plants are infected  by the volutella fungus, and often there are no signs that the plants are hurt by the infection. In order to understand why the volutella blight fungus is such a weak pathogen and to understand the genetic mechanisms it uses to interact with boxwood, the complete genome of the volutella fungus was sequenced and characterized.  These datasets are generated from the genome sequence of <em>Pseudonectria foliicola</em>, strain  ATCC13545, the fungus responsible for volutella disease of boxwood.  Datasets include the nuclear genome and mitochondrial genome assemblies (sequenced using Illumina technology), the predicted gene model dataset generated using MAKER, the multiple sequence alignment of single-copy orthologs used for phylogenetic analysis, CMAP files generated from SimpleSynteny analysis of mitogenomes, and high quality photographic images. </p><div><br>Resources in this dataset:</div><br><ul><li><p>Resource Title: Ab initio gene prediction for the draft genome assembly of Pseudonectria foliicola ATCC 13545.</p> <p>File Name: Pfoliicola<em>makerRun.all</em>.maker<em>.proteins.txt</em></p><p><em>Resource Description: Ab initio gene prediction for the draft genome assembly of Pseudonectria foliicola ATCC 13545 was performed using the MAKER2 v.2.31.6 annotation pipeline. Gene training was performed according to the program documentation using SNAP and AUGUSTUS v.3.2.1 (Stanke et al. 2004) using Fusarium graminearum as a model organism.</em></p></li><em><br></em><li><em><p>Resource Title: SimpleSynteny CMAP file of Pseudonectria foliicola mitogenome.</p> </em><p><em>File Name: 1VB.cmap</em>.txt</p></li><br><li><p>Resource Title: SimpleSynteny CMAP file of Dactylonectria macrodidyma mitogenome.</p> <p>File Name: 2DM.cmap<em>.txt</em></p></li><em><br></em><li><em><p>Resource Title: SimpleSynteny CMAP file of Fusarium graminearum mitogenome.</p> </em><p><em>File Name: 3FG.cmap</em>.txt</p></li><br><li><p>Resource Title: Genome assembly of Pseudonectria foliicola ATCC 13545 .</p> <p>File Name: Volutella foliicola_ATCC13545_genome assembly.txt</p><p>Resource Description: The genome of <em>Pseudonectria foliicola</em> ATCC 13545 was sequenced on an Illumina MiSeq from gDNA used to construct a TruSeq Nano DNA LT Library.  The library was sequenced on an Illumina MiSeq in two independent runs using paired-end 300-cycle reagent cartridge v.3 (Illumina, Inc.). Reads were processed and assembled using CLC Genomics Workbench version 7.5.1 (CLC Bio, Boston, MA, USA). Illumina adapters were trimmed and low quality reads (Phred score <0.05) were removed. Summary statistics for the draft genome were generated using CLC Genomics Workbench, PRINSEQ v.0.20.4 and QUAST.  Completeness of the <em>P. foliicola</em> draft genome assembly was evaluated using BUSCO v.1.1b1 </p></li><br><li><p>Resource Title: Photograph of Pseudonectria foliicola growing from boxwood leaf.</p> <p>File Name: Pseudonectria_foliicola_leaf1.jpg</p></li><br><li><p>Resource Title: Photograph of Pseudonectria foliicola growing from boxwood leaf.</p> <p>File Name: Pseudonectria_foliicola_leaf2.jpg</p></li><br><li><p>Resource Title: Multiple sequence alignment of single-copy orthologs.</p> <p>File Name: All_OrthMCL2316_PHYLIP_alignment.txt</p><p>Resource Description: Fourteen publicly available fungal genomes were used to examine the phylogenetic placement of <em>Pseudonectria foliicola</em> through the analysis of single copy orthologous genes. For this analysis, the predicted proteomes of <em>Aspergillus nidulans</em> FGSC A4 (ASM114v1), <em>Botrytis cinerea</em> BcDW1 (Assembly GCA000349525), <em>Fusarium graminearum</em> PH-1 (GCA000240135), <em>Macrophomina phaseolina</em> MS6 (GCA000302655), <em>Magnaporthe oryzeae</em> 70-15 (MG8), <em>Neurospora crassa</em> (GCA000786625), <em>Penicillium oxalicum</em> 114-2 (GCA000346795), <em>Pyrenophora tritici-repentis</em> (GCA000149985), <em>Sclerotinia sclerotiorum</em> 1980 UF-70 (ASM1469v1), <em>Trichoderma reesei</em> RUT C-30 (GCA000513815), <em>Ustilago maydis</em> 521 (UM1), <em>Verticillium dahliae</em> JR2 (GCA000400815) and <em>Yarrowia lipolytica</em> CLIB122 (GCA000002525) were downloaded from the EnsemblFungi database (<a href="https://fungi.ensembl.org/index.html">https://fungi.ensembl.org/index.html</a>). The genome of the <em>Dactylonectria macrodidyma</em> JAC15-245 (NCBI GenBank accession JYGD00000000 was downloaded and used to generate gene models using the program MAKER.  The program OrthoMCL identified 16,356 gene clusters, from which 1,884 orthologous genes were shared across all 15 fungal species. From these shared gene clusters, 1,511 orthologous genes were found as single copy genes and used for the phylogenetic analysis. All proteomes were searched against each other using BLASTp and clustered in orthologous gene sets using OrthoMCL v1.4 in the iPLANT Discovery Environment. Single copy genes found in all 15 fungal proteomes were extracted from the orthologous dataset and amino acid alignments were performed using MUSCLE v3.8.31. Gblocks v.0.91b  was used to remove ambiguously aligned regions using less stringent settings.  The final aligned dataset after removal of ambiguously aligned regions consists of 388.7 Mb.  The alignment is provided in PHYLIP format.</p></li></ul><p></p>

Tags: ars, ascomycota, boxwood, data-gov, fungi, genome-assembly, mitochondrial-dna, nectriaceae, np303, ornamental-plant, pathogen, plant-pathogens
Organization: Department of Agriculture