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

De Vega, JJ


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  <identifier identifierType="DOI">10.5281/zenodo.4270235</identifier>
  <creators>
    <creator>
      <creatorName>De Vega, JJ</creatorName>
      <givenName>JJ</givenName>
      <familyName>De Vega</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-2847-5158</nameIdentifier>
      <affiliation>Earlham Institute</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Supplementary dataset to "Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus"</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2020</publicationYear>
  <subjects>
    <subject>Genome assembly</subject>
    <subject>Miscanthus</subject>
    <subject>biofuel</subject>
    <subject>C4 photosynthesis</subject>
    <subject>gene annotation</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2020-11-12</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/4270235</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsVersionOf">10.5281/zenodo.4270234</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="https://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;em&gt;Miscanthus sacchariflorus&lt;/em&gt; (Maxim.) Hack. is a C4 perennial rhizomatous biofuel grass crop. &lt;em&gt;M. sacchariflorus&lt;/em&gt; 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 &lt;em&gt;M.&amp;nbsp;&amp;times;&amp;nbsp;giganteus&lt;/em&gt;. We generated a 2.54 Gbps whole-genome assembly of the diploid &lt;em&gt;M. sacchariflorus&lt;/em&gt; &amp;ldquo;Robustus 297&amp;rdquo; genotype, which represented ~59% of the expected genome size. We later anchored this assembly in the chromosomal-scale &lt;em&gt;M. sinensis&lt;/em&gt; 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 &lt;em&gt;M. sacchariflorus&lt;/em&gt; genes based on homology, core markers and RNA-seq alignments stats. Raw data and further metadata are available under Bioproject PRJNA435476.&lt;/p&gt;

&lt;ul&gt;
	&lt;li&gt;Msac_v2.fasta: Unanchored whole-genome assembly (WGA) of M. sacchariflorus in FASTA format.&lt;/li&gt;
	&lt;li&gt;Msac_v3.fasta: The previous WGA re-scaffolded with the M. sinensis public reference.&lt;/li&gt;
	&lt;li&gt;Msac_v3.agp: Chromosomal position in the M. sinensis reference of the previous scaffolds in Msac_v3.fasta&lt;/li&gt;
	&lt;li&gt;Msac_v2.gff3: Gene annotation of the unanchored WGA in GFF3 format, which contains 86,767 coding genes&lt;/li&gt;
	&lt;li&gt;Msac_v3.gff3: Gene annotation of the anchored WGA in GFF3 format, which contains 69,049 coding genes&lt;/li&gt;
	&lt;li&gt;Msac_v2.func_annot.tsv: Text table containing the functional annotation of the 86,767 coding genes in Msac_v2.gff3&lt;/li&gt;
	&lt;li&gt;Msac_v2.repeats_annotation.gff3: Repeats annotation (Repeatmasker) of the unanchored reference.&lt;/li&gt;
	&lt;li&gt;Msac_v2.masked.fasta.gz: Repeats-masked version (Repeatmasker) of Msac_v2.fasta&lt;/li&gt;
	&lt;li&gt;all.satsuma.blocks_Msac_v2-vs-Msin.gz: Every alignment from scaffolds in Msac_v3.fasta into M. sinensis reference&lt;/li&gt;
	&lt;li&gt;Msac_v2.orthology_Msin.tsv: Ortologous between Msac_v2 and M. sinensis&lt;/li&gt;
	&lt;li&gt;Msac_v3-vs-Msin.tsv: Ortologous between Msac_v3 and M. sinensis&lt;/li&gt;
&lt;/ul&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>Research Councils UK</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000690</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/RCUK/BBSRC/BBS%2FE%2FT%2F000PR9818/">BBS/E/T/000PR9818</awardNumber>
      <awardTitle>Signatures of Domestication and Adaptation</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>Research Councils UK</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000690</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/RCUK/BBSRC/BBS%2FE%2FW%2F10963A01A/">BBS/E/W/10963A01A</awardNumber>
      <awardTitle>Genetic resources for the dissection of bioenergy traits</awardTitle>
    </fundingReference>
  </fundingReferences>
</resource>
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