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

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 FindingsThe 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.

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

“…Similarly, 120,911 and 117,969 transcripts were identified in DV92 and G3116 (Triticum monococcum) using a de novo transcriptomic approach (Fox et al, 2014). We observed response to heat stress, protein folding, and oxidation reduction process with higher number of upregulated genes.…”

“…Plant omics and new biotechnologies such as massively parallel sequencing and microarray analysis were preferred tools to identify and characterize the differentially expressed genes (DEGs) under HS in different modal species (Gong et al 2014;Qian et al 2014;Rabara et al 2014), but NextGeneration Sequencing (NGS) is now the most preferred technique used for transcriptome study. The transcriptome data generated through NGS provide very useful information on the regulatory pathway networks operating in plants under different conditions (Rensink and Buell, 2005).…”

De Novo Assembly and Analysis of the Testes Transcriptome from the Menhaden, Bervoortia tyrannus

“…Velvet and Oases, common assembly programs in de novo transcriptomic studies using Illumina reads, were employed to assemble the processed reads [7,10,14,21,22,34,35,42,43]. It should be noted that the quality of the de novo transcriptome assembly is reliant on the user-defined k-mer value characterized as the length parameter defining the sequence overlap between two reads forming a contiguous sequence (referred as a contig) [44,45].…”

“…(Table 1). Velvet and Oases, common assembly programs successfully used in previous Illumina based de novo transcriptome studies, were employed to perform the assembly [7,10,14,21,22,34,35]. The paired-end sequence reads were assembled into 254,446 contigs with an N50 length of 1,324 bp and average contig length of 831.68 bp ( Table 2).…”

De novo assembly and characterization of leaf transcriptome for the development of EST-SSR markers of the non-model species Indigofera szechuensis

“…In addition, by making use of RNA-sequencing a large number of micro-satellite markers have been identified in plants, e.g. Triticum monococcum (Fox et al, 2014), Salvia Splendens (Ge et al, 2014), and chickpea (Cicer arietinum and Cicer reticulatum) (Verma et al, 2015) with the rapid development of nextgeneration sequencing (NGS).…”