Research Article: Comparative analysis of the root and leaf transcriptomes in Chelidonium majus L.

Date Published: April 15, 2019

Publisher: Public Library of Science

Author(s): Helen Pourmazaheri, Aboozar Soorni, Bahram Baghban Kohnerouz, Nafiseh Khosravi Dehaghi, Enayatollah Kalantar, Mansoor Omidi, Mohammad Reza Naghavi, Tapan Kumar Mondal.


Chelidonium majus is a traditional medicinal plant, which commonly known as a rich resource for the major benzylisoquinoline alkaloids (BIAs), including morphine, sanguinarine, and berberine. To understand the biosynthesis of C. majus BIAs, we performed de novo transcriptome sequencing of its leaf and root tissues using Illumina technology. Following comprehensive evaluation of de novo transcriptome assemblies produced with five programs including Trinity, Bridger, BinPacker, IDBA-tran, and Velvet/Oases using a series of k-mer sizes (from 25 to 91), BinPacker was found to produce the best assembly using a k-mer of 25. This study reports the results of differential gene expression (DGE), functional annotation, gene ontology (GO) analysis, classification of transcription factor (TF)s, and SSR and miRNA discovery. Our DGE analysis identified 6,028 transcripts that were up-regulated in the leaf, and 4,722 transcripts that were up-regulated in the root. Further investigations showed that most of the genes involved in the BIA biosynthetic pathway are significantly expressed in the root compared to the leaf. GO analysis showed that the predominant GO domain is “cellular component”, while TF analysis found bHLH to be the most highly represented TF family. Our study further identified 10 SSRs, out of a total of 39,841, that showed linkage to five unigenes encoding enzymes in the BIA pathway, and 10 conserved miRNAs that were previously not detected in this plant. The comprehensive transcriptome information presented herein provides a foundation for further explorations on study of the molecular mechanisms of BIA synthesis in C. majus.

Partial Text

Chelidonium majus L. is an herbaceous medicinal plant belonging to the botanical family Papaveraceae. C. majus is widely distributed in Europe and Western Asia and also as an introduced species in Northern America. The species is commonly known as celandine, greater celandine, celandine poppy, elon-wort, felon-wort, rock poppy, swallow-wort, and tetter-wort. C. majus is highly toxic due to the presence of various secondary metabolites in the roots and stems, but is used in both traditional and modern medicines [1].

In the current study, we generated and characterized a fully annotated and deep-sequencing transcriptome assembly for leaves and root tissues of C. majus. This represents an important initial resource that will enable further studies on the molecular mechanisms of bioactive alkaloids biosynthesis, as well as for studies of the molecular genetics and functional genomics of this important medicinal plant. Based on transcriptome assembly metrics, BinPacker was found to be the best among all the assemblers used in this study. Generally, our analysis revealed that most of the genes involved in the sanguinarine, berberine, and morphine pathways are broadly expressed in root. We observed that relatively few of these genes are up-regulated in leaves. Our results also showed that the most frequent transcription factor families represented here are involved in regulating secondary metabolism pathways, especially those for alkaloid biosynthesis. Development of a large number of EST-SSR markers and the design of high-quality PCR primers for potential EST-SSR loci amplification in the C. majus transcriptome will be useful for evaluating genetic diversity and also in marker-assisted breeding in C. majus. Furthermore, our computational methods enabled the identification of a set of potential miRNAs which were previously unknown for this plant.




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