Summary statistics of functional annotation for unigenes.

<p>Summary statistics of functional annotation for unigenes.</p

The expression differences of structural genes in the phenylalanine pathway.

<p>Arrow shows the metabolic stream, abbreviation left or upward arrows represent the genes catalyzing the progress, the light abbreviation means these genes were found in assembly unigenes, the number represent the in crease time of the expression in purple pericarp against white pericarp.</p

Distribution of lengths of the assembled unigenes in wheat pericarps.

<p>Distribution of lengths of the assembled unigenes in wheat pericarps.</p

The length of unigenes in Gy115 and reference genes relative to flavonoids biosynthesis.

<p>The length of unigenes in Gy115 and reference genes relative to flavonoids biosynthesis.</p

Gene Ontology (GO) classifications of differentially expressed unigenes.

<p>Unigenes were assigned to three categories: cellular components, molecular functions and biological process.</p

Summary of transcriptome sequencing data in the GY115 and Opata.

<p>Summary of transcriptome sequencing data in the GY115 and Opata.</p

Transcriptome Analysis of Purple Pericarps in Common Wheat (<i>Triticum aestivum</i> L.)

<div><p>Wheat (<i>Triticum aestivum</i> L.) cultivars possessing purple grain arethought to be more nutritious because of high anthocyanin contents in the pericarp. Comparative transcriptome analysis of purple (cv Gy115) and white pericarps was carried out using next-generation sequencing technology. There were 23,642 unigenes significantly differentially expressed in the purple and white pericarps, including 9945 up-regulated and 13,697 down-regulated. The differentially expressed unigenes were mainly involved in encoding components of metabolic pathways, The flavonoid biosynthesis pathway was the most represented in metabolic pathways. In the transcriptome of purple pericarp in Gy115, most structural and regulatory genes biosynthesizing anthocyanin were identified, and had higher expression levels than in white pericarp. The largestunigene of anthocyanin biosynthesis in Gy115 was longer than the reference genes, which implies that high-throughput sequencing could isolate the genes of anthocyanin biosynthesis in tissues or organs with high anthocyanin content. Based on present and previous results, three unigenes of <i>MYB</i> gene on chromosome 7BL and three unigenes of <i>MYC</i> on chromosome 2AL were predicted as candidate genes for the purple grain trait. This article was the first to provide a systematic overview comparing the transcriptomes of purple and white pericarps in common wheat, which should be very valuable for identifying the key genes for the purple pericarp trait.</p></div

Differentially expressed genes between opata and Gy115.

<p>The genes were classified into three classes. Red genes are up-regulated if gene expression of right sample is larger than left sample. Green genes are down-regulated that gene expression of left sample is larger if right sample. Blue genes are not differentially expressed. The horizontal coordinates is the expression level of right and the vertical coordinates is the expression level of left sample.</p

The expression differences of structural genes and transcription factors related to the anthocyanin biosynthesis pathway in blue and white aleurones.

<p>Arrows show the metabolic stream, and the abbreviations represent the genes catalyzing the progress. The first number in the parentheses represent the number of assembled unigenes, the second number represents the number of up-regulated unigenes in blue aleurone compared with white aleurone, and the third number represents the unigenes with homologous genes residing on Chromosome 4 of <i>Triticum aestivum</i>.</p

Wheat coleoptiles two days after bombardment with different plasmids.

<p>ZmC1, ZmR and ThMYC4E represent the constructs pBract214:ZmC1, pBract214:ZmR and pBract214:ThMYC4E, respectively.</p