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13 results for “Phaseolinae”
The Natural History Museum's collection of Dalbergia, Pterocarpus and the Phaseolinae subtribe
<p>In 2018 the Natural History Museum (NHMUK, herbarium code: BM) undertook a pilot digitisation project together with the Royal Botanic Gardens Kew (project Lead) and the Royal Botanic Garden Edinburgh to collectively digitise non-type herbarium material of the subtribe <em>Phaseolinae</em> and the genera <em>Dalbergia </em>L.f. and <em>Pterocarpus</em> Jacq. (rosewoods and padauk), all from the economically important family of legumes (<em>Leguminosae</em> or <em>Fabaceae</em>). </p> <p>These taxonomic groups were chosen for two case studies using the herbarium collections to support the aims of the UK’s Department for Environment Food & Rural Affairs (DEFRA)-allocated, Official Development Assistance (ODA) funding: study 1 - to support the development of dry beans as a sustainable and resilient crop; study 2 - to aid conservation and sustainable use of rosewoods and padauk.</p> <p>We present the images and metadata for 11,222 NHMUK specimens. This includes label transcription and georeferencing, along with summary data on geographic, taxonomic, collector and temporal coverage. We also provide timings and the methodology for our transcription and georeferencing protocols. Approximately 35% of specimens digitised were collected in ODA-listed countries, in tropical Africa, but also in south east Asia and South America.</p>
The Natural History Museum's collection of Dalbergia, Pterocarpus and the Phaseolinae subtribe
<p>In 2018 the Natural History Museum (NHMUK, herbarium code: BM) undertook a pilot digitisation project together with the Royal Botanic Gardens Kew (project Lead) and the Royal Botanic Garden Edinburgh to collectively digitise non-type herbarium material of the subtribe <em>Phaseolinae</em> and the genera <em>Dalbergia </em>L.f. and <em>Pterocarpus</em> Jacq. (rosewoods and padauk), all from the economically important family of legumes (<em>Leguminosae</em> or <em>Fabaceae</em>). </p> <p>These taxonomic groups were chosen for two case studies using the herbarium collections to support the aims of the UK’s Department for Environment Food & Rural Affairs (DEFRA)-allocated, Official Development Assistance (ODA) funding: study 1 - to support the development of dry beans as a sustainable and resilient crop; study 2 - to aid conservation and sustainable use of rosewoods and padauk.</p> <p>We present the images and metadata for 11,222 NHMUK specimens. This includes label transcription and georeferencing, along with summary data on geographic, taxonomic, collector and temporal coverage. We also provide timings and the methodology for our transcription and georeferencing protocols. Approximately 35% of specimens digitised were collected in ODA-listed countries, in tropical Africa, but also in south east Asia and South America.</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>
Annotated genome of M. phaseolina MP2_2471002
<p>Annotated genome of <em>Macrophomina phaseolina </em>MP2_2471002</p>
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
Open the record for dataset details and reuse information.
Systematics of Vigna subgenus Lasiospron (Benth.) Maréchal et al. (Leguminosae: Papilionoideae: Phaseolinae)
<p><span>A taxonomic treatment is herein provided for the six primarily Neotropical species of <i>Vigna</i> subg. <i>Lasiospron</i>. This subgenus is distinguished, in part, by its close relationship with Old World <i>Vigna</i> species, but rather than having an Old World <i>Vigna</i> floral asymmetry where distal floral parts can have a right-hand curvature (from a face-view perspective), distal parts of subg. <i>Lasiospron</i> flowers, like those of American Phaseolinae, curve to the left. Our proposed taxonomy reflects published phylogenetic analyses that resolve the subg. <i>Lasiospron</i> species in a subclade of the primarily Old World clade of species of <i>Vigna</i> sensu stricto. <i>Vigna</i> subg. <i>Lasiospron</i> is therefore distinctive in having a primarily neotropical distribution. Three of the six subg. <i>Lasiospron</i> species have an amphi-Atlantic distribution, which we suggest was achieved naturally be the ability of these species to disperse and colonize coastal habitats. Nomenclatural and taxonomic synonyms are reported, along with species descriptions and the biogeographical, genetic, and morphological evidence that argues for each of the six <i>Lasiospron</i> species fitting a unified species concept.</span></p>
High-throughput phenotyping of drought response in Phaseolinae
<p><span>Using a high-throughput phenotypic imaging system, we evaluated the drought tolerance of 151 bean accessions (Phaseolinae; Fabaceae) by quantifying five different traits simultaneously: biomass, water use efficiency, relative water content, chlorophyll content, and root/shoot ratio. </span>The base data for calculating the drought response indicators and the accessions used in the study are listed in these datasets</p>
Systematics of Vigna subgenus Lasiospron (Benth.) Maréchal et al. (Leguminosae: Papilionoideae: Phaseolinae)
Open the record for dataset details and reuse information.
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.
Repeat Annotation of M. phaseolina MP2_2471002
<p>Repeat annotation and regions generated using RepeatModeler and RepeatMasker</p>
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Allen Brain Atlas
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