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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
Conference paper

Abstract

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.

Keywords

Perennial ryegrass Genome sequencing RNA-Seq Transcriptome Gene prediction 

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  • E. M. B. Mollison
    • 1
  • S. Barth
    • 2
  • D. Milbourne
    • 2
  • L. Milne
    • 1
  • C. Halpin
    • 3
  • M. McCabe
    • 4
  • C. Creevey
    • 4
  • D. F. Marshall
    • 1
  1. 1.ICS GroupJames Hutton InstituteDundeeUK
  2. 2.CELUP Crop Science DepartmentTeagasc, CELUP Oak Park Research CentreCarlowIreland
  3. 3.Division of Plant SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
  4. 4.Teagasc Animal and Bioscience Research DepartmentAnimal & Grassland Research and Innovation Centre, Teagasc, GrangeDunsany Co. MeathIreland

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