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10 results for “Macrophomina”
The first annotated genome assembly of Macrophomina tecta associated with charcoal rot of sorghum
<p>Raw reads of Macrophomina tecta were obtained from Nanopore, Illumina, and NextSeq (RNA). Files with information about the genome annotation, functional prediction, repeats, effectors and orthologous genes are included. </p>
Alphafold2 and AlphaFold-Multimer Predicted Interactions of Soybean Proteins with Macrophomina phaseolina Effectors reveals putative protease inhibitors and SUSS effectors.
<p> </p> <ul> <li> <p><strong>Kunitz Monomer Prediction</strong>:</p> <ul> <li><strong>Data</strong>: Analysis of soybean Kunitz proteins.</li> <li><strong>Details</strong>: Detected on the apoplast at 3 days post-infection with <em>Macrophomina phaseolina</em>.</li> <li><strong>File</strong>: <code>KUNITZ_monomers_outputdir.zip</code></li> </ul> </li> <li> <p><strong>Uncharacterized M. phaseolina Protein Monomer Prediction</strong>:</p> <ul> <li><strong>Data</strong>: Predictions for uncharacterized proteins.</li> <li><strong>Details</strong>: Detected on the apoplast at 3 days post-infection.</li> <li><strong>File</strong>: <code>uncharacterised_proteins_SUSS_effectoroutputdir.zip</code></li> </ul> </li> </ul> <ul> <li> <p><strong>Positive Validation Set</strong>:</p> <ul> <li><strong>Data</strong>: Experimental verification of protein-inhibitor pairs.</li> <li><strong>Details</strong>: Pairs include experimentally verified interactions, specifically proteins and inhibitors, but lack resolved crystal structures.</li> <li><strong>File</strong>: <code>existing_non_existinpairs_Validation_outputdir.zip</code></li> </ul> </li> </ul> <ul> <li> <p><strong>Soybean Serine Protease-Kunitz Interaction</strong>:</p> <ul> <li><strong>Data</strong>: Interactions between soybean serine proteases and Kunitz proteins.</li> <li><strong>Details</strong>: Analyzed in the apoplastic space at 3 days post-infection.</li> <li><strong>File</strong>: <code>glycine max_Serine protease_Vs_Gmaxkunitz_outputdir.zip</code></li> </ul> </li> </ul> <ul> <li> <p><strong>Cysteine Protease without Pro-domain-MoErs-like effector Interaction</strong>:</p> <ul> <li><strong>Data</strong>: Interactions involving cysteine proteases.</li> <li><strong>Details</strong>: Rice RD21 and soybean cysteine proteases with pro-domains removed interacting with <em>MoErs1</em> and <em>MoErs1</em>-like M.phaseolina effectors.</li> <li><strong>File</strong>: <code>AF2-Multimer_RD21&GmaxCproteases_MoERS1_screening_outputdir.zip</code></li> </ul> </li> </ul> <ul> <li> <p><strong>Fungal Serine Protease-Kunitz Interaction</strong>:</p> <ul> <li><strong>Data</strong>: Interactions between <em>Macrophomina phaseolina</em> serine proteases and soybean Kunitz proteins.</li> <li><strong>Details</strong>: Evaluated in the apoplastic space at 3 days post-infection.</li> <li><strong>File</strong>: <code>fungalSerineprotease_Vs_Gmax_kunitzoutputdir.zip</code></li> </ul> </li> <li> <p><strong>Negative Validation Set</strong>:</p> <ul> <li><strong>Data</strong>: Known non-interacting pairs.</li> <li><strong>Details</strong>: Non-interacting pairs of serine proteases-chitinases that are not resolved as crystal structures</li> <li><strong>File</strong>: <code>Gmax_Serineprotease_Vs_Gmaxchitinases_Validation_outputdir.zip</code></li> </ul> </li> </ul>
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
<p><u>Background</u>: <i>Macrophomina phaseolina</i> is a fungal plant pathogen with a broad host range, but one genotype was shown to exhibit host preference/specificity on strawberry. This pathogen lacked a high-quality genome assembly and annotation, and little was known about genomic differences among isolates from different hosts.</p> <p><u>Results</u>: We used PacBio sequencing and Hi-C scaffolding to provide nearly complete genome assemblies for <i>M. phaseolina </i>isolates representing the strawberry-specific genotype and another genotype recovered from alfalfa. The strawberry isolate had 59 contigs/scaffolds with an N50 of 4.3 Mb. The isolate from alfalfa had an N50 of 5.0 Mb and 14 nuclear contigs with half including telomeres. Both genomes were annotated with MAKER using transcript evidence generated in this study with over 13,000 protein-coding genes predicted. Unique groups of genes for each isolate were identified when compared to closely related fungal species. Structural comparisons between the isolates reveal large-scale rearrangements including chromosomal inversions and translocations. To include isolates representing a range of pathogen genotypes, an additional 30 isolates were sequenced with Illumina, assembled, and compared to the strawberry genotype assembly. Within the limits of comparing Illumina and PacBio assemblies, no conserved structural rearrangements were identified among the isolates from the strawberry genotype compared to those from other hosts, but some candidate genes were identified that were largely present in isolates of the strawberry genotype and absent in other genotypes.</p> <p><u>Conclusions</u>: High-quality reference genomes of <i>M. phaseolina </i>have allowed for the identification of structural changes associated with a genotype that has a host preference toward strawberry and will enable future comparative genomics studies. Having more complete assemblies allows for structural rearrangements to be more fully assessed and ensures a greater representation of all the genes. Work with Illumina data from additional isolates suggests that some genes are predominately present in isolates of the strawberry genotype, but additional work is needed to confirm the role of these genes in pathogenesis. Additional work is also needed to complete the scaffolding of smaller contigs identified in the strawberry genotype assembly and to determine if unique genes in the strawberry genotype play a role in pathogenicity.</p>
Draft genome assembly of Macrophomina pseudophaseolina strain WAC 2767, and ex-epitype strain of M. phaseolina.
<p>This genome assembly is published in "Draft genome assemblies of <em>Fusarium marasasianum</em>, <em>Huntiella abstrusa</em>, two <em>Immersiporthe knoxdaviesiana</em> isolates, <em>Macrophomina pseudophaseolina</em>, <em>Macrophomina phaseolina</em>, <em>Naganishia randhawae</em>, and <em>Pseudocercospora cruenta</em>, Wingfield, B.D., De Vos, L., Wilson, A.M. <em>et al.</em> IMA Genome - F16. <em>IMA Fungus</em> <strong>13, </strong>3 (2022)". 10.1186/s43008-022-00089-z</p> <p> </p> <p> </p>
Assembly, annotation, and comparison of Macrophomina phaseolina isolates from strawberry and other hosts
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Figure 2 from: Zhao L, Cai J, He W, Zhang Y (2019) Macrophomina vaccinii sp. nov. causing blueberry stem blight in China. MycoKeys 55: 1-14. https://doi.org/10.3897/mycokeys.55.35015
Figure 2 Macrophominavaccinii (from ex-type: CGMCC 3.19503). a Pycnidia forming on pine needle bSclerotia on the synthetic nutrient-poor agar c Conidiogenous cells d Microconidia e–f Conidia with apical appendages (arrows). Scale bars: 1 mm (a); 10 µm (b–f).
Figure 3 from: Zhao L, Cai J, He W, Zhang Y (2019) Macrophomina vaccinii sp. nov. causing blueberry stem blight in China. MycoKeys 55: 1-14. https://doi.org/10.3897/mycokeys.55.35015
Figure 3 Macrophominavaccinii causes stem blight of blueberry. a Death of the blueberry (Vaccinium spp.) plants in the field b Symptoms of stem blight of blueberry in the field c Symptoms of Macrophominavaccinii after three days inoculation d Symptoms of Macrophominavaccinii after one-week inoculation e Symptoms of Macrophominavaccinii after three weeks inoculation f Symptoms of blueberry twig of Macrophominavaccinii after three weeks inoculation.
Figure 1 from: Zhao L, Cai J, He W, Zhang Y (2019) Macrophomina vaccinii sp. nov. causing blueberry stem blight in China. MycoKeys 55: 1-14. https://doi.org/10.3897/mycokeys.55.35015
Figure 1 Maximum parsimony tree generated from sequence analysis of the concatenated ITS, tef1-α, TUB and ACT dataset. Designated out group taxa is B.dothidea. Maximum parsimony (MP) and maximum likelihood (ML) bootstrap support greater than or equal to 60% are shown above the nodes (* = value less than 60%). The positions of the Macrophominavaccinii isolates are indicated in bold and red text.
Genome-wide profiling of Arabidopsis thaliana Col-0 and ein2/jar1 host responses to Macrophomina phaseolina infection
GEO Series GSE127574. Arabidopsis thaliana. 16 samples. Type: Expression profiling by high throughput sequencing.
Transcriptional changes in mycorrhizal and non-mycorrhizal soybean roots in presence of the fungal pathogen Macrophomina phaseolina
GEO Series GSE87740. Glycine max. 4 samples. Type: Expression profiling by array.
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