First assembly of the gene-space of the Lolium multiflorum genome and comparison to other Poaceae genomes

The genome of a diploid, heterozygous <em>L. multiflorum</em> genotype was sequenced using the Illumina HiSeq2000 platform, resulting in approximately 69 Gb of raw data. These data were assembled into 130k scaffolds greater than 2kb in size and with a total assembly size of 574 Mb. We annotated 61k gene models with 81k splice variants to these scaffolds. Assessment of genome completeness using BUSCO analysis showed that 80.5% of BUSCOs were complete, indicating that the assembly provides a good representation of the gene content. A mining for simple sequence repeats (SSR) was performed between <em>L. multiflorum</em> and <em>L.</em> <em>perenne</em> and revealed 29,840 SSR loci for <em>L. multiflorum</em> and 46,780 for <em>L. perenne</em>, of which 4,601 were shared. The proteome of<em> Lolium</em> ssp. was compared with other Poaceae proteomes and the protein clusters including the SAUR-like auxin-responsive protein family, glutathione S-transferases, BTB-POZ and the photosystem II light harvesting complex gene B1B2 were found to be enriched. The number of protein clusters between <em>L. multiflorum</em> and <em>L. perenne</em> was compared and 86 were more abundant in <em>L. multiflorum</em> than in <em>L. perenne</em> and 293 reciprocally. High numbers of disease resistance genes and proteins involved in metal transport were found.