CivicMemory

Timeline / Data.gov — Environment Datasets

changed Source changed

A new raw object was archived. Both versions are preserved. 5661 line(s) added, 7694 line(s) removed.

Evidence

SourceData.gov — Environment Datasets
AgencyData.gov
URLhttps://api.gsa.gov/technology/datagov/v4/search?q=environment&sort=last_harvested_date&per_page=100&api_key=${DATAGOV_API_KEY}
Observed by Civic Memory, directly, on 2026-10-09T00:26:45+00:00
Content typeapplication/json
Current object 9dc82d040b39f415c3e37f59e81f2f8fc947c25b8c19cf05351c11d332bf8c1b download raw metadata
Previous object f14a03dff2899cd9cc5bc1347abc496d85af561c67203ad6097a8a614d21ab4e download raw metadata

What changed derived

This diff is not evidence. It was produced by civic-memory.diff_engine 1.1.0 at 2026-10-09T00:26:45+00:00 by normalizing the two archived objects above. The objects are authoritative; this reading of them can be regenerated or deleted without loss. 5661 line(s) added, 7694 line(s) removed.

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+ "description": "<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>",
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+ "title": "Genome analysis of the ubiquitous boxwood pathogen Pseudonectria foliicola: A small fungal genome with an increased cohort of genes associated with loss of virulence"
+ },
+ "description": "<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>). 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- "PA",
- "PR",
- "Pennsylvania",
- "Puerto Rico",
- "RI",
- "Rhode Island",
- "SC",
- "SD",
- "South Carolina",
- "South Dakota",
- "TN",
- "TX",
- "Tennessee",
- "Texas",
- "US",
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- "UT",
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- "Utah",
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- "VT",
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- "Virgin Islands of the U.S.",
- "Virginia",
- "WA",
- "WI",
- "WV",
- "WY",
- "Washington",
- "West Virginia",
- "Wisconsin",
- "Wyoming",
- "aquaculture",
- "aquaculture water use",
- "commercial",
- "commercial water use",
- "consumptive use",
- "domestic",
- "domestic water use",
- "environment",
- "industrial",
- "industrial water use",
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- "irrigation",
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- "reclaimed wastewater",
- "self-supplied water use",
- "thermoelectric power generation",
- "thermoelectric power generation water use",
- "water resources",
- "water use"
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- "slug": "water-use-data-for-various-spatial-scales-in-the-united-states-1985-2015",
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- "theme": [
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- "title": "Water use data for various spatial scales in the United States, 1985-2015",
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- "description": "&lt;p&gt;This data release contains estimated water-use data for 2015 aggregated to\nthe county and principal aquifer levels in the United States, and HUC8 levels\nfor select states. The included datasets are:&lt;/p&gt;\n&lt;p&gt;\"&lt;a href = \"https://pubs.usgs.gov/publication/cir1441\"&gt;Estimated Use\nof Water in the United States in 2015&lt;/a&gt;\" (USGS Circular 1441, Dieter and\nothers, 2018). County data for all of the United States.&lt;/p&gt;\n&lt;p&gt;\"&lt;a href = \"https://doi.org/10.5066/F7TB15V5\"&gt;Estimated Use of Water in the\nUnited States County-Level Data for 2015 (ver. 2.0, June 2018)&lt;/a&gt;\" (USGS Data Release, Dieter and\nothers, 2018). County data for all of the United States. These county-level data are based on\nDieter and others, 2018b, but include revisions to estimates\nmade after original publication.&lt;/p&gt;\n&lt;p&gt;\"&lt;a href = \"https://doi.org/10.3133/cir1464\"&gt;Estimated Groundwater Withdrawals from Principal Aquifers\nin the United States, 2015&lt;/a&gt;\" (USGS circular 1464, Lovelace and others, 2020). Contains published\ncounty-aquifer data for all the United States with supporting data available in the companion\n&lt;a href = \"https://doi.org/10.5066/P9EI0KMR\"&gt;data release&lt;/a&gt;. Revised county-aquifer data included\nin this data release are based on Lovelace and others, 2020a and 2020b.&lt;/p&gt;\n&lt;p&gt;Revised HUC8 data were entered as optional in AWUDS, but were published as parts\nof local studies (Painter, 2019; Sargent et al., 2020; Ivahnenko and Galanter,\n2021; Gonthier and Painter, 2020).&lt;/p&gt;\n&lt;p&gt;The estimates are shown for the following water use categories: public\nsupply, domestic, commercial, irrigation, thermoelectric power, industrial,\nmining, livestock, and aquaculture. Each estimate dataset includes an\nassociated methods table that describes the method used for each estimate\nby water use category. Please visit the metadata.xml for more\ninformation.&lt;/p&gt;\n&lt;p&gt;Note on the irrigation attributes: This dataset includes multiple irrigation attributes: irrigation\nundifferentiated (IR), crop irrigation (IC), golf course irrigation (IG) and total irrigation (IT). Datasets\nprior to 2000 only include IR. Other irrigation attributes are availabl