A Novel De Novo Assembly Approach for Transcriptome Profiling and Marker Identification in Grewia Asiatica (Phalsa), a Medicinal Plant, Across Leaf And Root Tissues

Introduction: This study aims to conduct a comprehensive transcriptome analysis of Grewia asiatica (Phalsa) to identify molecular markers and differential gene expression in leaf and root tissues. G. asiatica is recognized for its medicinal properties, attributed to its rich phytochemical profile, including antioxidant, anti-inflammatory, antimicrobial, and hypoglycemic effects. However, genetic insights into the molecular basis of these bioactive properties remain limited. Methodology: High-throughput Illumina sequencing was performed, generating 32.97 million clean reads from roots and 33.96 million from leaves. A 98.75% complete de novo assembly yielded 41,678 unigenes. SNP and SSR markers were identified, and transcription factors across 100 families were characterized. Differential gene expression analysis was conducted, followed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Key differentially expressed genes (DEGs) were validated through qRT-PCR. Results: A total of 316,613 SNPs were identified in roots and 247,967 SNPs in leaves. SSR analysis revealed 21,634 markers, with mononucleotide repeats being predominant. A total of 5,781 transcription factors (TFs) were characterized, including members of the C2H2, MYB-HB-like, and bHLH families. Differential expression analysis identified 4,643 DEGs, with flavonoid biosynthesis genes upregulated in leaves and lignin-associated genes upregulated in roots. Discussion: GO and KEGG analyses highlighted significant enrichment of metabolic and biosynthetic pathways. The medicinal benefits of G. asiatica are linked to its antioxidant properties, which combat oxidative stress; anti-inflammatory effects, which may aid in arthritis relief; antimicrobial activity against pathogens; hypoglycemic effects for blood sugar regulation; and iron content, which is beneficial for anemia treatment. Conclusion: This study provides valuable SNP and SSR markers and offers insights into the genetic mechanisms underlying the medicinal properties of G. asiatica. These findings support future molecular breeding programs and pharmacological research on this underutilized medicinal plant.