Lolium perenne Assembly and Gene Annotation

About Lolium perenne

Alone or in mixture with legumes, Lolium and Festuca spp. are the main crops used as a feed source for livestock. Perennial ryegrass (Lolium perenne L.) is the most cultivated grass species in Western European grasslands. It is a diploid (2n = 2x = 14) species with a haploid genome size of about 2.6 Gb.

Assembly

Oxford Nanopore Technologies’ sequencing protocol was optimized, obtaining sequencing reads with an N50 of 62. The assembly of such reads produced a highly complete (2.3 of 2.7 Gb), correct (QV 45), and contiguous (contig N50 and N90 11.74 and 3.34 Mb, respectively) genome assembly.

Annotation

Protein-coding genes were annotated by combining ab initio and homology-based evidence. The latter set was constituted of proteomes of annotations of closely related species (Brachypodium, barley, bread wheat [Triticum aestivum L.], perennial and Italian ryegrass) and transcripts reconstructed from publicly available RNA-Seq data from NCBI SRA. Gene predictions with homology to transposable elements were removed prior to renaming the models. 38,868 protein coding genes were identified.

• Ultralong Oxford Nanopore Reads Enable the Development of a Reference-Grade Perennial Ryegrass Genome Assembly.
  Frei D, Veekman E, Grogg D, Stoffel-Studer I, Morishima A, Shimizu-Inatsugi R, Yates S, Shimizu KK, Frey JE, Studer B, Copetti D.. Genome Biol Evol 13 (8)

Picture credit: Wikipedia