De novo Genome Sequencing and Gene Prediction in Lolium perenne, Perennial Ryegrass

E. M. B. Mollison, S. Barth, D. Milbourne, L. Milne, C. Halpin, M. McCabe, C. Creevey, D. F. Marshall

Research output: Chapter in Book/Report/Conference proceedingChapter


A 1.11Gbp de novo assembly of the Lolium perenne genome was generated, containing 424,745 scaffolds and with N50 of 25,193. Gene prediction on genomic, mitochondrial and chloroplast scaffolds was carried out using both ab initio and RNA-Seq based methods. Ab initio gene prediction, carried out using wheat-based gene models, identified a total of 188,822 potential gene models from genomic scaffolds and 109 from mitochondrial. Mapping of reads from a broad-based RNA-Seq study identified 67,706 potential genes from genomic scaffolds, 90 from mitochondrial and 18 from chloroplast. Comparison of ab initio predicted genes with RNA-Seq genes identified 44,252 predicted gene models from genomic scaffolds and three from mitochondrial that overlapped with RNA-Seq derived transcripts by more than 20 % of their length.
Original languageEnglish
Title of host publicationBreeding in a World of Scarcity
Subtitle of host publicationProceedings of the 2015 Meeting of the Section “Forage Crops and Amenity Grasses” of Eucarpia
EditorsIsabel Roldán-Ruiz , Joost Baert, Dirk Reheul
PublisherSpringer Nature
ISBN (Electronic)978-3-319-28932-8
ISBN (Print)978-3-319-28930-4, 3319289306
Publication statusPublished - 14 Jun 2016


  • perennial ryegrass
  • genome sequencing
  • RNA-Seq
  • transcriptome
  • gene predicition


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