02867nas a2200373   4500000000100000008004100001260001200042653001200054653003500066653002300101653001900124653002400143100001500167700001900182700002200201700002000223700002500243700001800268700001700286700001700303700002000320700001700340700001800357700002100375700001500396700001900411700001600430700001600446700001900462245013100481856007900612490000600691520179600697       2014                            d  c05/201410aRNA-Seq10ade novo transcriptome assembly10aphotomorphogenesis10awheat A genome10aTriticum monococcum1 aSamuel Fox1 aMatthew Geniza1 aMamatha Hanumappa1 aSushma Naithani1 aChristopher Sullivan1 aJustin Preece1 aVIjay Tiwari1 aJustin Elser1 aJeffrey Leonard1 aAbigail Sage1 aCathy Gresham1 aArnaud Kerhornou1 aDan Bolser1 aFiona McCarthy1 aPaul Kersey1 aGerard Lazo1 aPankaj Jaiswal00aDe Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum.  uhttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.00968550 v93 aBackground

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.