TY - JOUR
KW - RNA-Seq
KW - de novo transcriptome assembly
KW - photomorphogenesis
KW - wheat A genome
KW - Triticum monococcum
AU - Samuel Fox
AU - Matthew Geniza
AU - Mamatha Hanumappa
AU - Sushma Naithani
AU - Christopher Sullivan
AU - Justin Preece
AU - VIjay Tiwari
AU - Justin Elser
AU - Jeffrey Leonard
AU - Abigail Sage
AU - Cathy Gresham
AU - Arnaud Kerhornou
AU - Dan Bolser
AU - Fiona McCarthy
AU - Paul Kersey
AU - Gerard Lazo
AU - Pankaj Jaiswal
AB - 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.
BT - PLoS ONE
DA - 05/2014
DO - 10.1371/journal.pone.0096855
IS - 5
N2 - 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.
PY - 2014
T2 - PLoS ONE
TI - De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum.
UR - http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0096855
VL - 9
ER -