Genome-assisted phylogenetic analysis of Indian medicinal plants using chloroplast markers (rbcL, matK, trnL-F)

Project Abstract

Genome-assisted phylogenetic analysis was conducted to resolve evolutionary relationships among diverse Indian medicinal plants using three chloroplast markers (rbcL, matK, trnL-F). The study integrates multilocus chloroplast genomes to overcome limitations of single-marker barcoding by providing complementary phylogenetic signals with higher resolution at species and genus levels. A comprehensive collection of 180 accessions representing 120 described medicinal taxa across families such as Fabaceae, Asteraceae, Lamiaceae, Rubiaceae, and Apocynaceae was assembled from national herbaria and in situ collections. DNA was extracted using a high-salt CTAB protocol optimized for plant tissues rich in secondary metabolites. Target regions rbcL, matK, and the trnL-F spacer were amplified via PCR with primers validated for broad taxonomic transferability. Amplicons were sequenced using Sanger methodology, and raw reads were quality-trimmed before assembly. Sequences were aligned with MAFFT, and incongruence among partitions was assessed using locus-specific phylogenies and partitioned by gene. Maximum likelihood and Bayesian inference methods were employed to reconstruct robust phylogenies, with model selection guided by AICc and Bayes factors. Node support was evaluated through bootstrap resampling and posterior probabilities. To contextualize molecular data, morphological and phytochemical characters previously linked to medicinal efficacy were collated and mapped onto the molecular phylogeny using trait-phylogeny association tests. The resulting phylogenetic framework revealed several well-supported clades corresponding to major ethnobotanical groupings, while clarifying species delimitations where morphological convergence obscured diagnostic features. Notably, rbcL contributed to deep-branching resolution at the family level, matK enhanced resolution at generic and species levels, and the trnL-F spacer provided informative variation for resolving recent divergences within rapidly radiating lineages. Congruence tests indicated substantial agreement among loci, yet targeted conflict in a subset of taxa suggested historical introgression or lineage sorting events. The integration of molecular phylogeny with traditional medicinal knowledge enabled the identification of several polyphyletic taxa currently used interchangeably in traditional medicine, prompting taxonomic reevaluation and standardization of plant materials for pharmacognostic studies. Phytochemical mapping demonstrated clade-specific enrichment of bioactive compounds such as alkaloids, flavonoids, and terpenoids, highlighting evolutionary trajectories that may influence medicinal properties. The study also identifies cryptic species complexes within widely distributed taxa, underscoring the necessity for region-specific conservation strategies and quality control in pharmacopoeial standards. Data generated provide a comprehensive, publicly accessible phylogenetic resource to assist botanists, pharmacists, and policymakers in accurate species identification, safety assessment, and the sustainable utilization of India's rich medicinal flora. The findings lay a foundation for future genome-scale analyses and comparative genomics to further elucidate the evolution of secondary metabolite pathways in medicinal plants.

Project Overview

What This Project Is About

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A plain-language overview of the topic and what the project investigates.

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The Problem It Addresses

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What problem or gap this project tackles and why it matters to the field or society.

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Objectives of the Project

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1. Identify relationships among Indian medicinal plants using chloroplast DNA markers.
2. Explain how markers differentiate closely related species and varieties.
3. Build a simple tree (phylogeny) showing evolutionary connections.
4. Assess which markers work best for Indian flora in this context.
5. Discuss implications for taxonomy, conservation, and traditional knowledge.

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What You Will Do Step by Step

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1. Review basic literature on chloroplast markers and phylogenetics.
2. Collect plant samples or obtain existing sequence data for rbcL, matK, and trnL-F.
3. Extract DNA or download public sequences and format data for analysis.
4. Align sequences to compare similarities and differences.
5. Construct a simple phylogenetic tree using standard methods.
6. Evaluate the usefulness of each marker and interpret results.
7. Prepare a report highlighting methods, findings, and limitations.

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Expected Outcome

Expected outcome is a clear, student-friendly report showing how chloroplast markers reveal relationships among Indian medicinal plants, with Recommendations for future work and potential applications in taxonomy and conservation.