Comparative transcriptome analysis of Alpinia oxyphylla Miq. reveals tissue-specific expression of flavonoid biosynthesis genes

Abstract

Background Alpinia 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. Results In 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. Conclusion The 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.

Challenges of International Trade and Government Governance from the Perspective of Economic Globalization

“…Restricted by scientific research and the author's research ability, this method still has many shortcomings, and the next step needs to increase exploration from the following aspects. (1) ere are many reasons related to foreign trade. In this paper, only eight indexes with strong correlation were selected, and the next one is to extract more indexes related to import and export transactions.…”

“…In 2002, China actually used 52.7 billion US dollars of foreign investment, an increase of 12.5%, becoming the country that used the most foreign direct investment in that year. In 2003, while maintaining a large scale of foreign investment, the quality and level were further improved [1].…”

Transcriptional regulation mechanism of flavonoids biosynthesis gene during fruit development in astragalus membranaceus

“…The gene expression characteristic of space and time at the transcriptional level regulates plant phenotype, substance content and stress response. Twenty-seven flavonoid-related genes are screened in the fruit, root, and leaf tissues of Alpinia oxyphylla , of which seven genes are highly expressed in fruits and six genes are highly expressed in roots ( Yuan et al, 2021 ). The five CHS genes are identified in three different tissues of Dendrobium officinale based on the gene expression and flavonoid content ( Yuan et al, 2020 ).…”

Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis

“…Moreover, the biosynthesis of catechin and gallic acid of our concern is a complex process involving the shikimate pathway, phenylpropanoid biosynthetic pathway, and flavonoid biosynthetic pathway [ 9 ]. Secondary metabolites are usually differentially distributed in diverse tissues of higher plants, which are associated with the tissue-specific expression of biosynthetic enzyme genes and transcript factors (TFs) related to the corresponding biosynthetic pathways [ 10 , 11 , 12 ]. Therefore, elaborating the expression differences of key enzyme genes in different tissues would deepen our understanding of the molecular mechanisms underlying the tissue specificity of the active compounds [ 5 , 13 , 14 ].…”

“…Currently, RNA sequencing (RNA-seq) is broadly used as an important approach for gene expression level analyses and molecular marker development [ 7 , 12 , 13 , 15 ]. Many studies have utilized transcriptomic analyses to identify critical candidate genes and tissue-specific differentially expressed genes (DEGs) for the biosynthesis of terpenoid, stilbene, saponin, lignin, anthraquinone, and flavonoid [ 11 , 16 , 17 ].…”