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Updated: Aug 7, 2025
A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants
Published on: January 21, 2020
Full-length transcriptome combined with RNA sequence analysis of Fraxinus chinensis
1Co-construction Collaborative Innovation Center for Chineses Medicine Resources Industrialization by Shaanxi and Education Ministry, Shaanxi University of Chinese Medicine, Xianyang, China.
Background:
The dry root or stem bark of Fraxinus chinensis is a famous herb Qin Pi which is known for its anti-inflammatory, analgesic, anti-tumor, liver protective and diuretic pharmacological effects, the fundamental chemical components are coumarin, phenylethanol glycosides and flavonoids. However, it is difficult to clarify the secondary metabolite synthesis pathway and key genes involved in the pathway because of lack genome information of Fraxinus chinensis.
Objective:
To generate a complete transcriptome of Fraxinus chinensis and to clarify the differentially expressed genes (DEGs) in leaves and stem barks.
Methods:
In this study, full-length transcriptome analysis and RNA-Seq were combined to characterize Fraxinus chinensis transcriptome.
Results:
A total of 69,145 transcripts were acquired and regarded as reference transcriptome, 67,441 transcripts (97.47%) were annotated to NCBI non-redundant protein (Nr), SwissProt, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and eukaryotic orthologous groups (KOG) databases. A total of 18,917 isoforms were annotated to KEGG database and classified to 138 biological pathways. In total, 10,822 simple sequence repeat (SSRs) and 11,319 resistance (R) gene were classified to 18 types, and 3947 transcription factors (TFs) were identified in full-length transcriptome analysis. Additionally, 15,095 DEGs were detected by RNA-seq in leaves and barks, including 4696 significantly up-regulated and 10,399 significantly down-regulated genes. And 254 transcripts were annotated into phenylpropane metabolism pathway containing 86 DEGs and ten of these enzyme genes were verified by qRT-PCR.
Conclusion:
It laid the foundation for further exploration of the biosynthetic pathway of phenylpropanoids and related key enzyme genes.
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