De Novo Transcriptome Assembly of Calotropis procera for Insights into the Natural Rubber Biosynthesis Pathway

Document Type : Original Article

Authors

Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Tehran, Iran

Abstract

Calotropis procera has been widely researched as a medicinal plant mainly due to its medicinal properties, including the presence of cardiac glycosides; However, less attention has been paid to its study as a source for natural rubber production. The biosynthesis of natural rubber occurs through the mevalonate (MVA) pathway in the cytoplasm and the methylerythritol phosphate (MEP) pathway in the plastids, with acetyl-CoA being converted to isopentenyl pyrophosphate (IPP), the building block of natural rubber. Given the lack of detailed information on the natural rubber biosynthesis pathway in this plant and the absence of an annotated genome sequence, research based on de novo transcriptome assembly is particularly crucial. In this study, the Trinity and rnaSPAdes tools were employed to assemble the de novo transcriptome of C. procera from the data set available in the SRA database. Following a comprehensive evaluation of the assembly’s quality, the transcriptome was annotated using the Hayai-Annotation Plants tool. Subsequently, pathways associated with natural rubber biosynthesis were reconstructed and mapped using the GhostKOALA and KEGG Mapper tools, with pathway visualizations created through the Color tool. According to the results, unigenes received putative annotations in three domains: biological processes, cellular components and molecular functions. Additionally, during the KEGG pathway reconstruction, 19 ortholog genes involved in the terpenoid backbone biosynthetic pathway were identified, including 7 ortholog genes related to the MVA pathway, 8 orthologs related to the MEP pathway, and 4 ortholog genes associated with the biosynthesis of C10-C20 isoprenoids. This study enhances our understanding of the natural rubber biosynthesis pathways in C. procera, providing a foundation for future research aimed at exploring its biotechnological applications.

Graphical Abstract

De Novo Transcriptome Assembly of Calotropis procera for Insights into the Natural Rubber Biosynthesis Pathway

Highlights

  • Natural rubber biosynthesis occurs via the mevalonate (MVA) pathway in the cytoplasm and the methylerythritol phosphate (MEP) pathway in plastids.
  • De novo transcriptome assembly of Calotropis procera was performed using Trinity and rnaSPAdes tools with data retrieved from the SRA database.
  • Functional annotation was conducted using the Hayai-Annotation Plants tool, while pathway mapping for rubber biosynthesis was carried out with GhostKOALA and KEGG Mapper.
  • A total of 19 orthologous genes involved in the terpenoid backbone pathway were identified, including 7 related to the MVA pathway, 8 to the MEP pathway, and 4 involved in the biosynthesis of C10–C20 isoprenoids.
  • This study provides a comprehensive set of candidate genes for future functional validation and efforts to optimize rubber production.

 

Keywords

Main Subjects

References

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Agrotechniques in Industrial Crops
Volume 6, Issue 2
Agrotechniques in Industrial Crops (Agrotech Ind Crops) (Online ISSN: 2783-2945)
July 2026
Pages 169-179

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