show Abstracthide AbstractRhizomes are underground stems that send out both roots and shoots, and serve various purposes including vegetative propagation, invasion of new territory, and bioactive compound synthesis and storage. One such rhizomatous plant is sacred lotus (Nelumbo nucifera), which is prized in Asian medicines as well as Asian cooking, thus being widely cultivated. RNA-seq and total transcriptome analysis of rhizomes and other lotus tissues were applied to identify genes involved in rhizome growth, development and metabolism. Root, petiole, rhizome, and leaf tissues were used for single-read (SR) RNA-seq analysis to construct 20 lotus Illumina sequencing libraries. Two total transcriptome paired-end (PE) read libraries from rhizome apical tip and elongation zone tissues were also generated in order to survey gene expression profiles.