README.txt

Title: Supplementary Materials for “Molecular Phylogenetic Analysis of Woody Plants in India and Sri Lanka”
Author: Harsimran Kaur
Affiliation: MSc Biology, Dayanandan Lab, Concordia University
Email: amritpadam2811@gmail.com
ORCID: https://orcid.org/0000-0002-0791-437X
Date: June 2025

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Overview:
This supplementary archive supports the Master's thesis by Harsimran Kaur and includes datasets, phylogenetic trees, alignments, and R scripts used in constructing and visualizing phylogenies of woody plants in India and Sri Lanka.

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Contents:

1. /01_Combined trees/
   - rbcL_matK_alignment.fasta — aligned and trimmed sequences for reference
   - rbcL_matK_tree.tre - rbcL + matK tree - pens with Figtree, Geneious and iToL
   - rbcL_matK_trnH_alignment.fasta — aligned and trimmed sequences used for phylogeny (concatenated matrix of psbA_trnH)
   - rbcL_matK_trnH.tre - rbcL + matK + psbA-trnH tree - opens with Figtree, Geneious and iToL 
   - rbcL_matK_trnH_ITS_alignment.fasta — aligned and trimmed sequences used for phylogeny of cpDNA and rDNA combined
   - rbcL_matK_trnH_ITS.tre - rbcL + matK + psbA-trnH + ITStree - opens with Figtree, Geneious and iToL
   - rbcL_matK_trnH.pdf - rectangular phylogenetic tree coloured for each order for rbcL + matK + psbA-trnH
   - rbcL_matK_trnH_ITS.pdf - rectangular phylogenetic tree coloured for each order for rbcL + matK + psbA-trnH + ITS

3. /02_Alignments for Order Wise Trees/
   * Arranged in each folder of genes

4. /03_Order Wise Trees and Tanglegrams/
   * Arranged in each folder of Orders
   - order_name.tre - cpDNA tree
   - order_name_its2.tre - rDNA tree
   - order_name_comparison.pdf - pdf of tanglegram
   - order_name_comparison.jpg - jpg of tanglegram


5. /054Scripts/
   - Scripts.Rmd — including R script to fetch and clean sequences from GenBank and to generate tanglegrams from cpDNA and rDNA trees - opens in RStudio
   - Scripts.nd.html - html version of scripts - opens in web browsers

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Software & Tools Used:
- Geneious Prime (platform for sequence sampling and concatenation)
- CIPRES (cloud based platform used for phylogenetic reconstruction)
- MAFFT (multiple sequence alignment)
- jModeTest (nucleotide model testing)
- MrBayes (phylogenetic reconstruction)
- FigTree, iToL, cophylo (tree visualization)

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How to Use:
- Open .tre files using FigTree or R (ape package) for visualization.
- Run R scripts after installing dependencies listed in the script headers.
- Use the reference files for each to run the codes successfully.
- Refer to the thesis (Appendix section) for interpretation of each dataset/tree.
- MrBayes and jModelTest result files can be provided upon request.

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Citation:
If you use this dataset or scripts for any future research, please cite:

Kaur, H. (2025). Molecular Phylogenetic Analysis of Woody Plants in India and Sri Lanka. MSc Thesis, Concordia University.

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Thank you!
If you have questions, feel free to reach out: amritpadam2811@gmail.com