Comparative transcriptome analysis reveals differentially expressed genes associated with the development of Jerusalem artichoke tuber (Helianthus tuberosus L.)

Jerusalem artichoke (Helianthus tuberosus L.), a rapidly developing industrial crop in China, has been widely used as a raw material to produce biofuels, functional feed and food in recent years. The tuber is the main organ of Jerusalem artichoke used for processing, for its high concentration of the fructan inulin. Here, tubers of culitivar Qingyu no. 1 at four different stages of development were selected for transcriptome analysis, with three biological replicates at each stage, to identify the genes differentially expressed during tuber development. A total of 76,515 unigenes were obtained, with 43,459 (56.79 %) of the unigenes being annotated by BLAST searcher based on the database NCBI non-redundant (Nr), the Swiss-Prot, the Cluster of Orthologous Groups (COGs) and the Kyoto Encyclopedia of Genes and Genomes (KEGG). A venn diagram of analysis of differentially expressed genes (DEGs) showed that 586 unigenes were identified in all pairwise comparisons. KEGG enrichment analysis indicated that the expression of genes involved in fatty acid metabolism, biosynthesis of unsaturated fatty acids, starch and sucrose metabolism, and plant hormone signal transduction were closely associated with the development of Jerusalem artichoke tubers. Transcription factors (TF) analysis showed that ethylene-response factor (ERF) and heat shock factor (HSF) gene families were predominant among the TF DEGs. These results provide us with a foundation for further analysis of the development of the Jerusalem artichoke tuber.