Assembly and Annotation of a Physical Map-Based Draft Genome of the Forage Grass Lolium perenne

Perennial ryegrass (Lolium perenne L.) is a diploid grass species that belongs to the Pooeae sub-family together with oats, wheat, barley and the grass model Brachypodium distachyon. Perennial ryegrass is a forage grass that is widely cultivated in temperate regions and it plays an important role in grassland-based agriculture and amenity industries and activities. Perennial ryegrass has a genome size of 2.5Gb, and a BAC-based HICF physical map (c. 4000 ctgs) was constructed, using LTC software, from the homozygous genotype P226/135/16. The c. 40k BAC clones spanning the minimum tiling path were then individually sequenced and the sequence was assembled, guided both by the physical map and the raw mate-pair short-length reads from the published draft de novo genome assemblies (also based on genotype p226/135/16; Byrne S. et al., Plant J, 2015, 84:816; Velmurugan et al., Ann Bot, 2016, 118:71). This generated a draft genome consisting of c. 50k scaffolds accounting from 2.14 Gb, or the 85.6 % of the genome. Subsequently, the draft genome was annotated using a combination of de novo and transcript- and protein-guided (Poaceae and other) gene predictions, resulting in 19713 structurally annotated genes. The resulting draft genome will make an important contribution to the development of genetic and genomic tools for perennial ryegrass breeding.