The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics

dc.contributor.author Pfeifer, Matthias
dc.contributor.author Martis, Mihaela
dc.contributor.author Lubberstedt, Thomas
dc.contributor.author Asp, Torben
dc.contributor.author Mayer, Klaus
dc.contributor.author Lubberstedt, Thomas
dc.contributor.author Byrne, Stephen
dc.contributor.author Frei, Ursula
dc.contributor.author Studer, Bruno
dc.contributor.department Agronomy
dc.date 2018-04-02T16:09:49.000
dc.date.accessioned 2020-06-29T23:05:25Z
dc.date.available 2020-06-29T23:05:25Z
dc.date.copyright Tue Jan 01 00:00:00 UTC 2013
dc.date.issued 2013-02-01
dc.description.abstract <p>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 are yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne L.) genome on the basis of conserved synteny to barley (Hordeum vulgare L.) and the model grass genome Brachypodium (Brachypodium distachyon L.), as well as rice (Oryza sativa L.) and sorghum [Sorghum bicolor (L.) Moench]. 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 macro-collinearity, and was then utilised to anchor a collection of perennial ryegrass genes in silico to their predicted genome position. 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 genomewide 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.</p>
dc.description.comments <p>This is a manuscript of an article published as Pfeifer, Matthias, Mihaela Martis, Torben Asp, Klaus FX Mayer, Thomas Lübberstedt, Stephen Byrne, Ursula Frei, and Bruno Studer. "The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics." <em>Plant physiology</em> 161, no. 2 (2013): 571-582. doi: <a href="http://dx.doi.org/10.1104/pp.112.207282" target="_blank">10.1104/pp.112.207282</a>. Copyright American Society of Plant Biologists. Posted with permission.</p>
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dc.identifier archive/lib.dr.iastate.edu/agron_pubs/459/
dc.identifier.articleid 1508
dc.identifier.contextkey 11886690
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath agron_pubs/459
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/4819
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/agron_pubs/459/2013_Lubberstedt_PerennialRyegrassManuscript.pdf|||Sat Jan 15 00:21:49 UTC 2022
dc.source.uri 10.1104/pp.112.207282
dc.subject.disciplines Agronomy and Crop Sciences
dc.subject.disciplines Computational Biology
dc.subject.disciplines Genetics and Genomics
dc.subject.disciplines Plant Breeding and Genetics
dc.title The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 4e4330cd-db15-4ac5-8924-41119139cf32
relation.isOrgUnitOfPublication fdd5c06c-bdbe-469c-a38e-51e664fece7a
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