Application of digital gene expression tag profiling on differential gene expression of two developmental stages in bulbs of Lycoris sprengeri

Gene expression-profiling data are necessary to understand more clearly the differential gene expression that occurs in biological developmental process. This study is aimed to compare the differential gene expression between bulb and bulblet of Lycoris sprengeri, as to reveal the biological and molecular mechanisms in bulb development. Method: Two Digital Gene Expression tag profiling (DGE) libraries of different developmental stages of Lycoris sprengeri were built according to Illumina sequencing and compared using bioinformatics methods. The altered expression levels of these genes, as well as the enrichment of gene ontology terms and pathways in the KEGG database were then analyzed in detail. Result: A total number of 3,476,452 and 3,597,890 of raw tags were generated for the mature and juvenile DGE libraries, and 4,389 significantly differentially expressed genes were obtained. 45,181 (13.95%) and 41,093 (32.25%) distinct tags for the mature and juvenile bulbs were mapped to a unique sequence in the reference database, respectively. For the DGE data quality check, the lowly-expressed tags (the copy number < 10) comprised most of the distinct clean tags, and the number of detected genes kept stable when the tag number larger than 2 million. Most genes expressed in fewer than 10 copies (log 10 < 1). The metabolic process, the catalytic activity, cell and cell part were the most significantly enriched GO term in the three categories, consisting of 74, 67.7, and 98.6% of their differentially expressed gene groups, respectively. Conclusion: DGE is proved to be effective method for differentially expressed gene analysis on bulb development of Lycoris sprengeri.