Phylogenetic tree and map of plant viruses

Help and Getting Started
1

Subject: Request for Assistance in Building Phylogenetic Tree and Map for Plant Virus Sequences

Dear Nextstrain Team,

I hope this message finds you well.

My name is Amir, and I am currently working on a research project involving the genomic analysis of plant viruses, specifically Chilli Leaf Curl Disease (ChiLCD). I have compiled a dataset of complete genome FASTA sequences from different geographic regions and I’m interested in visualizing the viral evolution using a time-scaled phylogenetic tree alongside a geospatial map, similar to the powerful frameworks that Nextstrain provides.

I would be grateful if you could guide me on how to:

  • Prepare my data (FASTA sequences and metadata) in the correct format for Nextstrain
  • Customize the pipeline for plant viruses (as most examples are for human/animal pathogens)
  • Build and visualize the phylogenetic tree and associated map

Your support or pointing me toward the right documentation/resources or any plant-virus specific examples would be incredibly helpful.

Looking forward to your guidance.

Warm regards,
Muhammad Amir
amirbzu2023@gmail.com

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Dear Muhammad,

Thank you for introducing your use case. I’m no expert in the field, but my understanding is that as long as there is enough evolution over time and not too much recombination, it should be possible to build a time-scaled phylogenetic tree no matter the host (human/animal/plant).

I would begin by going through the tutorial series on Nextstrain documentation
up through Creating a phylogenetic workflow to familiarize with the typical workflow steps. From there, it should be a matter of changing the input data and adjusting settings within each step. To prepare your data, you can refer to How do I prepare metadata? — Augur 31.3.0 documentation.

Through a quick Google search, I found these Nextstrain datasets for plant viruses. Hopefully they are helpful:

– Victor