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.本研究针对二倍体杂合型多花黑麦草（*L. multiflorum*）基因型的基因组，采用Illumina HiSeq2000测序平台开展测序，最终获得约69 Gb的原始测序数据。研究人员将上述原始数据组装为130,000个长度大于2 kb的支架序列，总组装长度达574 Mb。我们为这些支架序列注释得到61,000个基因模型，对应81,000个剪接变体。采用BUSCO（Benchmarking Universal Single-Copy Orthologs）分析对基因组组装的完整性进行评估，结果显示80.5%的BUSCO为完整型，表明该组装结果可较好地覆盖该物种的基因组成。本研究还开展了多花黑麦草（*L. multiflorum*）与多年生黑麦草（*L. perenne*）间的简单序列重复（simple sequence repeats，SSR）挖掘工作，分别获得29,840个SSR位点与46,780个SSR位点，其中4,601个位点为二者共有。将黑麦草属（*Lolium*）亚种的蛋白质组与其他禾本科（Poaceae）物种的蛋白质组进行比较分析，发现SAUR类生长素响应蛋白家族、谷胱甘肽S-转移酶、BTB-POZ结构域蛋白以及光系统II捕光复合物基因B1B2所在的蛋白簇呈现显著富集趋势。对比多花黑麦草与多年生黑麦草的蛋白簇数量差异，发现有86个蛋白簇在多花黑麦草中丰度更高，另有293个蛋白簇在多年生黑麦草中丰度更高。本研究同时鉴定得到大量抗病基因以及参与金属转运过程的功能蛋白。