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ARS Home » Pacific West Area » Albany, California » Western Regional Research Center » Crop Improvement and Genetics Research » Research » Publications at this Location » Publication #306458

Research Project: Small Grains Database and Bioinformatics Resources

Location: Crop Improvement and Genetics Research

Title: De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum

Author
item FOX, SAMUEL - Oregon State University
item GENIZA, MATTHEW - Oregon State University
item HANUMAPPA, MAMATHA - Oregon State University
item NAIHANI, SUSHAMA - Oregon State University
item SULLIVAN, CHRIS - Oregon State University
item PREECE, JUSTIN - Oregon State University
item TIWARI, VIJAY - Oregon State University
item ELSER, JUSTIN - Oregon State University
item LEONARD, JEFFREY - Oregon State University
item SAGE, ABIGAIL - Oregon State University
item GRESHAM, CATHY - Mississippi State University
item KERHORNOU, ARNAUD - European Bioinformatics Institute
item BOLSER, DAN - European Bioinformatics Institute
item MCCARTHY, FIONA - University Of Arizona
item KERSEY, PAUL - European Bioinformatics Institute
item Lazo, Gerard
item JAISWAL, PANKAJ - Oregon State University

Submitted to: PLoS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/12/2014
Publication Date: 5/12/2014
Citation: Fox, S.E., Geniza, M., Hanumappa, M., Naihani, S., Sullivan, C., Preece, J., Tiwari, V.K., Elser, J., Leonard, J.M., Sage, A., Gresham, C., Kerhornou, A., Bolser, D., Mccarthy, F., Kersey, P., Lazo, G.R., Jaiswal, P. 2014. De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS One. 9:E96855.

Interpretive Summary: RNA isolated from two distinct Triticum monococcum sub species having different trait characteristics relating to light response were isolated and sequenced using modern high-throughput sequencing methodologies. The sequences represented the transcriptomes of the germplasm and helped to resolve distinct genes which were up-regulated and down-regulated under different light conditions. The sequences were annotated and matched to model reference genome sequences to assist characterizing the gene networks. A system was developed to potentially follow the gene network in other grass species using developed reference sequences; this represents an improved method for developing genome annotations.

Technical Abstract: Triticum monococcum (2n), a close ancestor of the A-genome progenitor of cultivated hexaploid wheat, was used as a model to study components regulating photomorphogenesis in diploid wheat. Constructed were 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. 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. 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.