Article
 

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

Público Deposited
Ainda não disponível

Baixe o arquivo

https://ir.library.oregonstate.edu/concern/articles/zs25xb08c

Descriptions

Attribute NameValues
Creator
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.
License
Resource Type
DOI
Date Available
Date Issued
Citation
  • Fox SE, Geniza M, Hanumappa M, Naithani S, Sullivan C, et al. (2014) De Novo Transcriptome Assembly and Analyses of Gene Expression during Photomorphogenesis in Diploid Wheat Triticum monococcum. PLoS ONE 9(5): e96855. doi:10.1371/journal.pone.0096855
Journal Title
Journal Volume
  • 9
Journal Issue/Number
  • 5
Declaração de direitos
Publisher
Peer Reviewed
Language
Replaces

Relações

Parents:

This work has no parents.

Itens

Miniatura Título Data de carga Acesso Ações
file details GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome.pdf 07/26/2017 Público
file details GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome_SupportingInformation.zip 07/26/2017 Público