De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum

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dc.contributor.author Fox, Samuel E.
dc.contributor.author Geniza, Matthew
dc.contributor.author Hanumappa, Mamatha
dc.contributor.author Naithani, Sushma
dc.contributor.author Sullivan, Chris
dc.contributor.author Preece, Justin
dc.contributor.author Tiwari, Vijay K.
dc.contributor.author Elser, Justin
dc.contributor.author Leonard, Jeffrey M.
dc.contributor.author Sage, Abigail
dc.contributor.author Gresham, Cathy
dc.contributor.author Kerhornou, Arnaud
dc.contributor.author Bolser, Dan
dc.contributor.author McCarthy, Fiona
dc.contributor.author Kersey, Paul
dc.contributor.author Lazo, Gerard R.
dc.contributor.author Jaiswal, Pankaj
dc.date.accessioned 2014-07-23T20:58:18Z
dc.date.available 2014-07-23T20:58:18Z
dc.date.issued 2014-07-23
dc.identifier.uri http://hdl.handle.net/2097/18133
dc.description.abstract Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes of two Triticum monococcum subspecies, the wild winter wheat T. monococcum ssp. aegilopoides (accession G3116) and the domesticated spring wheat T. monococcum ssp. monococcum (accession DV92) by generating de novo assemblies of RNA-Seq data derived from both etiolated and green seedlings. Principal Findings: The de novo transcriptome assemblies of DV92 and G3116 represent 120,911 and 117,969 transcripts, respectively. We successfully mapped ~90% of these transcripts from each accession to barley and ~95% of the transcripts to T. urartu genomes. However, only ~77% transcripts mapped to the annotated barley genes and ~85% transcripts mapped to the annotated T. urartu genes. Differential gene expression analyses revealed 22% more light up-regulated and 35% more light down-regulated transcripts in the G3116 transcriptome compared to DV92. The DV92 and G3116 mRNA sequence reads aligned against the reference barley genome led to the identification of ~500,000 single nucleotide polymorphism (SNP) and ~22,000 simple sequence repeat (SSR) sites. Conclusions: De novo transcriptome assemblies of two accessions of the diploid wheat T. monococcum provide new empirical transcriptome references for improving Triticeae genome annotations, and insights into transcriptional programming during photomorphogenesis. The SNP and SSR sites identified in our analysis provide additional resources for the development of molecular markers. en_US
dc.language.iso en_US en_US
dc.relation.uri http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096855 en_US
dc.subject Triticum monococcum (2n) en_US
dc.subject Wheat en_US
dc.subject Diploid wheat en_US
dc.subject De novo transcriptome assemblies en_US
dc.title De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum en_US
dc.type Article (publisher version) en_US
dc.date.published 2014 en_US
dc.citation.doi doi:10.1371/journal.pone.0096855 en_US
dc.citation.issue 5 en_US
dc.citation.jtitle PLoS ONE en_US
dc.citation.spage e96855 en_US
dc.citation.volume 9 en_US
dc.contributor.authoreid vijtiwari en_US


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