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Abstract
Lotus root is a popular wetland vegetable which produces edible rhizome. At the molecular level, the regulation of rhizome formation is very complex, which has not been sufficiently addressed in research. In this study, to identify differentially expressed genes (DEGs) in lotus root, four libraries (L1 library: stolon stage, L2 library: initial swelling stage, L3 library: middle swelling stage, L4: later swelling stage) were constructed from the rhizome development stages. High-throughput tag-sequencing technique was used which is based on Solexa Genome Analyzer Platform. Approximately 5.0 million tags were sequenced, and 4542104, 4474755, 4777919, and 4750348 clean tags including 151282, 137476, 215872, and 166005 distinct tags were obtained after removal of low quality tags from each library respectively. More than 43% distinct tags were unambiguous tags mapping to the reference genes, and 40% were unambiguous tag-mapped genes. From L1, L2, L3, and L4, total 20471, 18785, 23448, and 21778 genes were annotated, after mapping their functions in existing databases. Profiling of gene expression in L1/L2, L2/L3, and L3/L4 libraries were different among most of the selected 20 DEGs. Most of the DEGs in L1/L2 libraries were relevant to fiber development and stress response, while in L2/L3 and L3/L4 libraries, major of the DEGs were involved in metabolism of energy and storage. All up-regulated transcriptional factors in four libraries and 14 important rhizome formation-related genes in four libraries were also identified. In addition, the expression of 9 genes from identified DEGs was performed by qRT-PCR method. In a summary, this study provides a comprehensive understanding of gene expression during the rhizome formation in lotus root.
Highlights
Lotus root (Nelumbo nucifera Gaertn), which originated from India and China, is an aquatic herb vegetable and a member of the family Nelumbonaceae [1]
The rhizome of lotus root is formed underground, and it grows in size after sprouting in the shallow water, such as the pools, water gardens, tanks or tubs of the greenhouse, which indicates that the plant has developed mechanisms of surviving in the submerged environment
2.1 Transcriptome of Rhizome Four stages of rhizome development: stolon stage, initial swelling, middle swelling and later swelling stages were selected to construct libraries using the Illumina sequencing platform to investigate the genes involved in rhizome formation
Summary
Lotus root (Nelumbo nucifera Gaertn), which originated from India and China, is an aquatic herb vegetable and a member of the family Nelumbonaceae [1]. It is one of the oldest dicot plants in the world with many features of monocot plants, and has been widely cultivated in China, Japan, and other Southeast Asian counties for multiple purposes [2]. Similar with other wetland vegetable (corm, tuber, and bulbs), rhizome is a kind of underground stems, and work as storage organs. These are storage units for food that provide the plants with the energy for growth, blooming, and completing their lifecycle
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