Abstract
Berberis koreana is a medicinal plant containing berberine, which is a bioactive compound of the benzylisoquinoline alkaloid (BIA) class. BIA is widely used in the food and drug industry for its health benefits. To investigate the berberine biosynthesis pathway, gene expression analysis was performed in leaves, flowers, and fruits at different stages of growth. This was followed by full-length cDNA sequencing analysis using the PacBio sequencer platform to determine the number of isoforms of those expressed genes. We identified 23,246 full-length unigenes, among which 8479 had more than one isoform. The number of isoforms ranged between two to thirty-one among all genes. Complete isoform analysis was carried out on the unigenes encoding BIA synthesis. Thirteen of the sixteen genes encoding enzymes for berberine synthesis were present in more than one copy. This demonstrates that gene duplication and translation into isoforms may contribute to the functional specificity of the duplicated genes and isoforms in plant alkaloid synthesis. Our study also demonstrated the streamlining of berberine biosynthesis via the absence of genes for enzymes of other BIAs, but the presence of all the genes for berberine biosynthesize in B. koreana. In addition to genes encoding enzymes for the berberine biosynthesis pathway, the genes encoding enzymes for other BIAs were not present in our dataset except for those encoding corytuberine synthase (CTS) and berbamunine synthase (BS). Therefore, this explains how B. koreana produces berberine by blocking the pathways leading to other BIAs, effectively only allowing the pathway to lead to berberine synthesis.
Highlights
The genus Berberis (Berberidaceae), known as barberry, is a large genus containing approximately 500 species that are distributed throughout temperate and subtropical regions of the world [1,2]
Our analysis proved that this pipeline could be applied to characterize full-length transcriptomes in any other species lacking a reference genome
86.16% (20,029) and 69.9% (16,179) of the 23,246 identified unigenes matched with the nucleotide sequences (Nt) and non-redundant protein sequences (Nr) databases, which are lower than the percentages of matches for ginseng (95.8%) [20]
Summary
The genus Berberis (Berberidaceae), known as barberry, is a large genus containing approximately 500 species that are distributed throughout temperate and subtropical regions of the world [1,2]. Many Berberis species are known to have diverse phytochemicals, such as various alkaloids, terpenoids, flavonoids, sterols, anthocyanins, lignans, lipids, and carotenoids, so they have been used in traditional medicine in various parts of the world since ancient times [1]. BIAs include a diverse class of nitrogen-containing plant secondary metabolites, with approximately 2500 molecules, such as morphine, codeine, sanguinarine, and Papaverine [4,5]. BIAs are present in only restricted plant families, including Berberidaceae, Papaveraceae, and Ranunculaceae in Ranunculales; Fabaceae in Fabales; and Magnoliaceae in Magnoliales [6,7]
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