Abstract
BackgroundAlpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. Flavonoids are one of the main chemical compounds in A. oxyphylla; however, the genetic and molecular mechanisms of flavonoid biosynthesis are not well understood. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant.ResultsIn all, 8.85, 10.10, 8.68, 6.89, and 8.51 Gb clean data were obtained for early-, middle-, and late-stage fruits, leaves, and roots, respectively. Furthermore, 50,401 unigenes were grouped into functional categories based on four databases, namely Nr (47,745 unigenes), Uniprot (49,685 unigenes), KOG (20,153 unigenes), and KEGG (27,285 unigenes). A total of 3110 differentially expressed genes (DEGs) and five distinct clusters with similar expression patterns were obtained, in which 27 unigenes encoded 13 key enzymes associated with flavonoid biosynthesis. In particular, 9 DEGs were significantly up-regulated in fruits, whereas expression of 11 DEGs were highly up-regulated in roots, compared with those in leaves.ConclusionThe DEGs and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla. These results provide insights into the molecular mechanism of flavonoid biosynthesis in A. oxyphylla and application of genetically engineered varieties of A. oxyphylla.
Highlights
Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine
The differentially expressed genes (DEGs) and metabolic pathway related to flavonoids biosynthesis were identified in root, leaf, and different stages of fruits from A. oxyphylla
A total of 50,401 unigenes were grouped into the databases, nonredundant protein (Nr) (47,745 unigenes), Universal Protein (Uniport) (49,685 unigenes), EuKaryotic Orthologous Groups (KOG) (20,153 unigenes), and Kyoto Encyclopedia of Genes and Genomes (KEGG) (27,285 unigenes), respectively, while an additional 89,725 unigenes were not found in these databases
Summary
Alpinia oxyphylla Miq. is an important edible and medicinal herb, and its dried fruits are widely used in traditional herbal medicine. We performed transcriptome analysis in the fruit, root, and leaf tissues of A. oxyphylla to delineate tissue-specific gene expression and metabolic pathways in this medicinal plant. Alpinia oxyphylla Miq., a member of the Zingiberaceae family, is an important plant species for traditional Chinese medicine, which originates in the Hainan Province and is widely cultivated in southern China [1]. The transcriptome is a complete set of RNA transcripts in a cell at a specific developmental stage, and provides information on gene expression and regulation related to a variety of cellular processes including secondary metabolite biosynthesis [19, 20]. It is important to explore the whole genome transcriptome of A. oxyphylla to identify candidate genes contributing to metabolic processes and regulatory mechanisms
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