title: The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.
abstract: Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.
authors.affiliation: Institute of Bioinformatics and Systems Biology, Helmholtz Center Munich, German Research Center for Environmental Health, 85764 Neuherberg, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Pfeifer
authors.forename: Mihaela
authors.initials: M
authors.lastname: Martis
authors.forename: Torben
authors.initials: T
authors.lastname: Asp
authors.forename: Klaus F X
authors.initials: KF
authors.lastname: Mayer
authors.forename: Thomas
authors.initials: T
authors.lastname: Lübberstedt
authors.forename: Stephen
authors.initials: S
authors.lastname: Byrne
authors.forename: Ursula
authors.initials: U
authors.lastname: Frei
authors.forename: Bruno
authors.initials: B
authors.lastname: Studer
mesh_terms: D058431:Brachypodium / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics; D019295:Computational Biology / Q000379:methods*; D018745:Genome, Plant / Q000235:genetics*; D023281:Genomics / Q000379:methods; D008129:Lolium / Q000235:genetics*; D012275:Oryza / Q000235:genetics; D006109:Poaceae / Q000145:classification / Q000235:genetics; D015203:Reproducibility of Results; D045868:Sorghum / Q000235:genetics; D026801:Synteny; D059467:Transcriptome / Q000235:genetics