Transcriptome landscapes of multiple tissues highlight the genes involved in the flavor metabolic pathway in Chinese chive (Allium tuberosum)

The unique flavor of Allium tuberosum is primarily associated with the hydrolysis of a series of organosulfur compounds, S-alk(en)yl cysteine sulphoxides (CSOs), upon tissue bruising or maceration. To obtain the tissue-specific transcriptomes, 18 RNA-Seq libraries representing leaf, root, stem, mature flower, inflorescence, and seed tissues of A. tuberosum were sequenced, finally yielding 133.7 Gb clean reads. The de novo assembled transcriptomes enabled the identification of 223,529 unigenes, which were functionally annotated and analyzed for the gene ontology and metabolic pathways. Furthermore, to reveal the flavor metabolic pathways, a total of 205 unigenes involved in the sulfur assimilation and CSO biosynthesis were identified, and their expression profiles were analyzed by RNA-Seq and qRT-PCR. Collectively, this study provides a valuable resource for in-depth molecular and functional researches especially on flavor formation, as well as for the development of molecular markers, and other genetic studies in A. tuberosum. •Assembled the reference transcriptomes representing leaf, root, rhizome, mature flower, Inflorescence, and seed tissues in A. tuberosum.•Identified and analyzed an array of genes involved in the molecular metabolic pathway for the flavor formation in Chinese chive.•The flower contains more S-alk(en)yl cysteine sulphoxides (CSOs) than any other tissues in A. tuberosum.