Dataset Open Access

Supplementary dataset to "Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus"

De Vega, JJ


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/all.satsuma.blocks_Msac_v2-vs-Msin.gz"
      }, 
      "checksum": "md5:b493a76ed8924b4a082980c3911532ae", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "all.satsuma.blocks_Msac_v2-vs-Msin.gz", 
      "type": "gz", 
      "size": 78059898
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v2.fasta.gz"
      }, 
      "checksum": "md5:e456585fa4e4237be9bdd6da207e2388", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v2.fasta.gz", 
      "type": "gz", 
      "size": 491778438
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v2.func_annot.tsv"
      }, 
      "checksum": "md5:38c3e140e85770fad9c3568da4d1c648", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v2.func_annot.tsv", 
      "type": "tsv", 
      "size": 15916033
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v2.gff3.gz"
      }, 
      "checksum": "md5:df9e133a543e50996e7bbbf9b2233478", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v2.gff3.gz", 
      "type": "gz", 
      "size": 13020101
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v2.masked.fasta.gz"
      }, 
      "checksum": "md5:feb3f65b33c3ac8f1ebcebd9bbd72530", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v2.masked.fasta.gz", 
      "type": "gz", 
      "size": 252671952
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v2.orthology_Msin.tsv"
      }, 
      "checksum": "md5:ba7464cf36bef8f2bd9354c753f770d2", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v2.orthology_Msin.tsv", 
      "type": "tsv", 
      "size": 2463510
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v2.repeats_annotation.gff3.gz"
      }, 
      "checksum": "md5:67ee8454829335c92b894c228f1f5c01", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v2.repeats_annotation.gff3.gz", 
      "type": "gz", 
      "size": 58502872
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v3.agp"
      }, 
      "checksum": "md5:785ed643fe645f250895d98e3cce0668", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v3.agp", 
      "type": "agp", 
      "size": 3628287
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v3.fasta.gz"
      }, 
      "checksum": "md5:f3378c92b42155ebd2d43adaa6be1e2d", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v3.fasta.gz", 
      "type": "gz", 
      "size": 407787383
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v3.gff3.gz"
      }, 
      "checksum": "md5:e47be8ab3527580e8cdc241b6f75902b", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v3.gff3.gz", 
      "type": "gz", 
      "size": 7931915
    }, 
    {
      "links": {
        "self": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773/Msac_v3-vs-Msin.tsv"
      }, 
      "checksum": "md5:5c821a80a2093ee10acab2be1a8d7241", 
      "bucket": "ec36f28d-6a30-4769-90b3-1d0414c3a773", 
      "key": "Msac_v3-vs-Msin.tsv", 
      "type": "tsv", 
      "size": 1535721
    }
  ], 
  "owners": [
    12550
  ], 
  "doi": "10.5281/zenodo.4270235", 
  "stats": {
    "version_unique_downloads": 22.0, 
    "unique_views": 66.0, 
    "views": 69.0, 
    "version_views": 69.0, 
    "unique_downloads": 22.0, 
    "version_unique_views": 66.0, 
    "volume": 7597622752.0, 
    "version_downloads": 46.0, 
    "downloads": 46.0, 
    "version_volume": 7597622752.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.4270235", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.4270234", 
    "bucket": "https://zenodo.org/api/files/ec36f28d-6a30-4769-90b3-1d0414c3a773", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.4270234.svg", 
    "html": "https://zenodo.org/record/4270235", 
    "latest_html": "https://zenodo.org/record/4270235", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.4270235.svg", 
    "latest": "https://zenodo.org/api/records/4270235"
  }, 
  "conceptdoi": "10.5281/zenodo.4270234", 
  "created": "2020-11-12T17:48:42.678424+00:00", 
  "updated": "2020-11-13T00:27:04.155117+00:00", 
  "conceptrecid": "4270234", 
  "revision": 2, 
  "id": 4270235, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.4270235", 
    "description": "<p><em>Miscanthus sacchariflorus</em> (Maxim.) Hack. is a C4 perennial rhizomatous biofuel grass crop. <em>M. sacchariflorus</em> is among the most widely distributed species within the genus, particularly at cold northern latitudes, and one of the progenitor species of the main biomass commercial crop <em>M.&nbsp;&times;&nbsp;giganteus</em>. We generated a 2.54 Gbps whole-genome assembly of the diploid <em>M. sacchariflorus</em> &ldquo;Robustus 297&rdquo; genotype, which represented ~59% of the expected genome size. We later anchored this assembly in the chromosomal-scale <em>M. sinensis</em> genome to improve its contiguity. We annotated 86,767 and 69,049 protein-coding genes in the unanchored and anchored, respectively. We estimated our assemblies include ~85% of the <em>M. sacchariflorus</em> genes based on homology, core markers and RNA-seq alignments stats. Raw data and further metadata are available under Bioproject PRJNA435476.</p>\n\n<ul>\n\t<li>Msac_v2.fasta: Unanchored whole-genome assembly (WGA) of M. sacchariflorus in FASTA format.</li>\n\t<li>Msac_v3.fasta: The previous WGA re-scaffolded with the M. sinensis public reference.</li>\n\t<li>Msac_v3.agp: Chromosomal position in the M. sinensis reference of the previous scaffolds in Msac_v3.fasta</li>\n\t<li>Msac_v2.gff3: Gene annotation of the unanchored WGA in GFF3 format, which contains 86,767 coding genes</li>\n\t<li>Msac_v3.gff3: Gene annotation of the anchored WGA in GFF3 format, which contains 69,049 coding genes</li>\n\t<li>Msac_v2.func_annot.tsv: Text table containing the functional annotation of the 86,767 coding genes in Msac_v2.gff3</li>\n\t<li>Msac_v2.repeats_annotation.gff3: Repeats annotation (Repeatmasker) of the unanchored reference.</li>\n\t<li>Msac_v2.masked.fasta.gz: Repeats-masked version (Repeatmasker) of Msac_v2.fasta</li>\n\t<li>all.satsuma.blocks_Msac_v2-vs-Msin.gz: Every alignment from scaffolds in Msac_v3.fasta into M. sinensis reference</li>\n\t<li>Msac_v2.orthology_Msin.tsv: Ortologous between Msac_v2 and M. sinensis</li>\n\t<li>Msac_v3-vs-Msin.tsv: Ortologous between Msac_v3 and M. sinensis</li>\n</ul>", 
    "license": {
      "id": "CC-BY-4.0"
    }, 
    "title": "Supplementary dataset to \"Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus\"", 
    "relations": {
      "version": [
        {
          "count": 1, 
          "index": 0, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "4270234"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "4270235"
          }
        }
      ]
    }, 
    "grants": [
      {
        "code": "BBS/E/T/000PR9818", 
        "links": {
          "self": "https://zenodo.org/api/grants/10.13039/501100000690::BBS/E/T/000PR9818"
        }, 
        "title": "Signatures of Domestication and Adaptation", 
        "acronym": "", 
        "program": "BBSRC", 
        "funder": {
          "doi": "10.13039/501100000690", 
          "acronyms": [], 
          "name": "Research Councils UK", 
          "links": {
            "self": "https://zenodo.org/api/funders/10.13039/501100000690"
          }
        }
      }, 
      {
        "code": "BBS/E/W/10963A01A", 
        "links": {
          "self": "https://zenodo.org/api/grants/10.13039/501100000690::BBS/E/W/10963A01A"
        }, 
        "title": "Genetic resources for the dissection of bioenergy traits", 
        "acronym": "", 
        "program": "BBSRC", 
        "funder": {
          "doi": "10.13039/501100000690", 
          "acronyms": [], 
          "name": "Research Councils UK", 
          "links": {
            "self": "https://zenodo.org/api/funders/10.13039/501100000690"
          }
        }
      }
    ], 
    "keywords": [
      "Genome assembly", 
      "Miscanthus", 
      "biofuel", 
      "C4 photosynthesis", 
      "gene annotation"
    ], 
    "publication_date": "2020-11-12", 
    "creators": [
      {
        "orcid": "0000-0003-2847-5158", 
        "affiliation": "Earlham Institute", 
        "name": "De Vega, JJ"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "dataset", 
      "title": "Dataset"
    }, 
    "related_identifiers": [
      {
        "scheme": "bioproject", 
        "identifier": "PRJNA435476", 
        "relation": "isDerivedFrom", 
        "resource_type": "dataset"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.4270234", 
        "relation": "isVersionOf"
      }
    ]
  }
}
69
46
views
downloads
All versions This version
Views 6969
Downloads 4646
Data volume 7.6 GB7.6 GB
Unique views 6666
Unique downloads 2222

Share

Cite as