A Draft Sequence Assembly of the Perennial Ryegrass (Lolium perenne) Genome

Perennial ryegrass (Lolium perenne L.) is an outbreeding diploid species and one of the principal forage crops used in temperate agriculture. A sequenced genome will both enhance efforts to understand the genetic control of important traits, and accelerate the application of molecular breeding strategies to forage grasses. Sequencing efforts have focused on the inbred genotype p226/135/16 that has an estimated genome size of 2,068 Mbp (Kmer spectrum analysis). Using Illumina GAIIx, and Illumina HiSeq 2000, we have sequenced a range of libraries for de novo assembly, including paired-end libraries with insert sizes of ~140 bp and ~550 bp. We have also sequenced jumping libraries with insert sizes up to 30 Kbp, to aid scaffolding of contigs. A ten time’s coverage of the genome in PacBio RS II sequence data was generated, and used to address gaps in the scaffolds. These data have been used to generate a draft assembly of the perennial ryegrass genome that has been annotated with the aid of multiple RNA-Seq data sets. The current assembly has a total scaffold length of 1,111 Mbp present in 48,267 scaffolds, a contig N50 of 8.3 Kbp, and a scaffold N50 of 70 Kbp. Using the PacBio reads, 74,682 out of 76,244 total gaps were addressed, from which 27,889 were completely filled. The total gap length was reduced from 441 Mbp to 292 Mbp. Anchoring of genotype data to the scaffolds has enabled us to determine that the average extent of linkage disequilibrium within the genome is extremely low.