Distribution of total clean tags and distinct clean tags count from the four libraries.

<p>Distribution of total clean tags and distinct clean tags count from the four libraries.</p

Categorization and abundance of tags.

<p>About 5.0 million tags were sequenced, and clean tags and distinct tags were obtained after removal of low quality tags from each library. Some distinct tags were unambiguous tags after mapping to the reference genes, and some were unambiguous tag-mapped genes.</p

DEGs across all libraries.

<p>All the genes mapped to the reference sequence and genome sequences were examined for their expression differences across different libraries. Numbers of differentially expressed genes represent transcripts, using threshold values FDR≤0.001 and |log2 Ratio|≥1 for controlling false discovery rates. L1, L2, L3, and L4 represent the samples which were collected at stolon stage, initial swelling stage, middle swelling stage, and later swelling stage of rhizome, respectively.</p

Validation of tag-mapped genes from three stages of lotus root with quantitative RT–PCR.

<p>Validation of tag-mapped genes from three stages of lotus root with quantitative RT–PCR.</p

Expression abundance of up-regulated transcriptional factors during rhizome formation.

<p>Expression abundance of up-regulated transcriptional factors during rhizome formation.</p

Detailed information about primers used for qRT-PCR variation.

<p>All primers used for qPCR were designed according to CDS obtained in this study in lotus root.</p

Analysis of tag mapped genes among four libraries.

<p>Analysis of tag mapped genes among four libraries.</p

Expressed abundance of some rhizome formation-related genes identified previously.

<p>TMP, transcripts per million clean tags.</p

20 most differentially expressed annotated genes in L1/L2, L2/L3, and L3/L4 libraries based on expressed tag frequency.

<p>20 most differentially expressed annotated genes in L1/L2, L2/L3, and L3/L4 libraries based on expressed tag frequency.</p

Identification of Differentially Expressed Genes Relevant to Corm Formation in <em>Sagittaria trifolia</em>

<div><p><em>Sagittaria trifolia</em> is a good model of wetland plants to elucidate the formation of corm. However, few studies have been conducted to uncover the complexity of gene expression involved in corm formation. In this study, high-throughput tag-sequencing based on Solexa Genome Analyzer Platform was applied to monitor the changes in gene expression with three libraries of differentially expressed genes (DEGs) (C1 library: stolon stage, C2 library: initial swelling stage and C3 library: swelling stage) during corm formation in <em>Sagittaria trifolia</em>. Approximately 6.0 million tags were sequenced, and 5854021, 5983454, and 5761079 clean tags including 138319, 116804, and 101739 distinct tags were obtained after removal of low quality tags from each library, respectively. About 46% distinct tags were unambiguous tags mapping to the reference genes, and 33% were unambiguous tag-mapped genes. Totally, 20575, 19807, and 18438 were annotated in C1, C2, and C3 libraries, respectively, after mapping their functions in existing databases. In addition, we found that profiling of gene expression in C1/C2 and C2/C3 libraries were different among most of the selected 20 DEGs. Most DEGs in C1/C2 libraries were relevant to hormone synthesis and response; energy metabolism and stress response, while most of the genes in C2/C3 libraries were involved in carbohydrate metabolism. All up-regulated transcriptional factors and 16 important genes relevant to corm formation in three libraries were also identified. To further analyze the expression of 9 genes, from the results of tag-sequencing, qRT-PCR was applied. In summary, this study provides a comprehensive understanding of gene expression, during the formation of corm in <em>Sagittaria trifolia</em>.</p> </div