Perennial Ryegrass Genome Draft Assembly and Anchoring by GBS

We describe a genotyping by sequencing (GBS) study in perennial ryegrass, Lolium perenne, and its usage in anchoring scaffolds from a de novo assembled genome of the same.

A draft de novo genome assembly for L. perenne was generated using Illumina sequencing of paired-end (PE), mate-pair (MP) and long jumping distance (LJD) libraries. Using this, some 207-fold raw coverage was achieved, reduced to around 105-fold by subsequent quality control. The draft assembly contains 424,750 scaffolds, reflecting 1.11Gbp of the 2.5Gbp genome, with scaffold N50 of 25,213 bp and contig N50 of 3,790 bp.

Gene regions were identified using a combination of ab initio gene prediction, in-house RNA-Seq, comparison with publicly available Lolium transcriptome sequences, and homology with related species. Comparing gene-containing scaffolds identified by these methods resulted in a core set of 12,245 scaffolds that were found to be common to all four sets, equivalent to around 482 Mbp in length.

In conjunction with de novo genome assembly, a high-density SNP-based genetic linkage map, with 3,092 SNPs and 7,260 presence/absence variants (PAVs), was developed from an F2 Biomass mapping population of L. perenne. This map was used to anchor 4,767 genomic scaffolds with a total size of approximately 200Mbp, or 18% of the assembled genome size.