Genome expression profile analysis of two types of new roots in apple rootstock via Solexa sequencing

Currently, the molecular regulation mechanisms involved in the early development of new roots are poorly known in apple. To gain insight into the transcriptome dynamics that are associated with its development, genome-wide gene expression profiling was conducted by Solexa sequencing. More than five million tags were generated from two type new roots, long root and short root, including 5,913,044 and 6,236,711 clean tags in the two libraries, respectively. Of these, 44,513 (26.61%) and 43,117 (20.02%) tags were matched to the reference genes. The most differentially expressed tags with FDR ≤ 0.001 and | log2Ratio | ≥ 1 were analyzed further, representing 815 up-regulated and 831 down-regulated genes, except for unknown transcripts. These genes participated in biosynthesis of secondary metabolites, plant-pathogen interaction, plant hormone signal transduction, phenylpropanoid biosynthesis, ribosomes and flavonoid biosynthesis. Most genes were identified in the cell part function (82.7%), catalytic activity (71.1%), ion binding (59.2%) and membrane transcription (24.5%), etc. Next, the expression patterns of 20 genes were assessed by quantitative real-time PCR, and the results obtained showed general agreement with the Solexa analysis. Moreover, a visual database was constructed in order to browse and query the results, and the website is http://www.applegene.org/deg/. In conclusion, we first reveal the complex changes in the transcriptome during the early development of apple new root and provide a comprehensive set of data that are essential for understanding its molecular regulation.