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 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.

Figure 1. Mappings DV92 and G3116 transcripts to the sequenced Hordeum vulgare (barley) genome v1.0 (source: Gramene/Ensembl Plants).

(A) A hive plot shows comparison between Triticum monococcum accessions G3116 and DV92 vs. the barley genome. (B) A density plot view of the Ensembl Plants genome browser showing barley chromosome-1H karyotype view (track-1) with annotated barley genes (track-2; maroon) and the mapped G3116 transcripts (track-3; blue) and DV92 transcripts (track-4; red).

Figure 2. Analyses of the differentially expressed transcripts.

A scatter plot of light up- regulated (red colored) and down-regulated (green colored) transcripts from G3116 (A) and DV92 (B) accessions of T. monococcum. Each spot represents a single transcript. (C) The table lists counts of differentially expressed transcripts from the DV92 and G3116 accessions shown in the adjacent scatter plots and their barley homologs. The four-way Venn diagram shows the distribution of barley homolog counts with reference to the mapped light up-regulated (red shaded boxes) and light down-regulated (green shaded boxes) transcripts. (D) Barley homologs from various unique sets identified in the Venn diagram (C) and their selected molecular function enrichment.

Figure 3. Genetic marker discovery.

Polymorphic sites identified in the transcriptome of DV92 (blue) and G3116 (red). (A) Number of SSR identified in the transcriptomes. (B) Number of SNPs identified in the two genotypes by aligning against the sequenced barley reference genome. 9,808 out of 340,250 common SNP sites have polymorphism between DV92 and G3116. (C) Mapping of common, variable 9,808 SNP and 148 SSR sites identified in the DV92 and G3116 transcriptomes on the karyotype view of the reference barley genome hosted by the Ensembl Plants. The SNP sites are shown as red colored density plot and SSR sites are depicted as black triangles along the length of the respective barley chromosomes.