Dataset Open Access

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

De Vega, JJ


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    <subfield code="a">Supplementary dataset to "Draft genome assembly of the biofuel grass crop Miscanthus sacchariflorus"</subfield>
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    <subfield code="a">&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;
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