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

De Vega, JJ


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{
  "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": "https://creativecommons.org/licenses/by/4.0/legalcode", 
  "creator": [
    {
      "affiliation": "Earlham Institute", 
      "@id": "https://orcid.org/0000-0003-2847-5158", 
      "@type": "Person", 
      "name": "De Vega, JJ"
    }
  ], 
  "url": "https://zenodo.org/record/4270235", 
  "datePublished": "2020-11-12", 
  "keywords": [
    "Genome assembly", 
    "Miscanthus", 
    "biofuel", 
    "C4 photosynthesis", 
    "gene annotation"
  ], 
  "@context": "https://schema.org/", 
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  "identifier": "https://doi.org/10.5281/zenodo.4270235", 
  "@id": "https://doi.org/10.5281/zenodo.4270235", 
  "@type": "Dataset", 
  "name": "Supplementary dataset to \"Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus\""
}
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