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PAGD: the Persea americana Genome Database and a Docker-based transcriptome analysis workflow
Siyi Ma1,2, Huadong Feng2, Danni Yang3
1Institute of International Rivers and Eco-security, Yunnan University, Kunming, Yunnan, 650091, China.
BMC Genomics
|June 2, 2026
Summary
The Persea americana Genome Database (PAGD) integrates avocado genome assemblies and transcriptomic data. This platform offers pre-computed analyses and reproducible workflows for enhanced avocado research.
Area of Science:
- Genomics
- Bioinformatics
- Plant Science
Background:
- Avocado (Persea americana) is a significant global fruit crop.
- Existing genomic resources are fragmented and lack integrated multi-omics analyses.
- A need exists for a unified platform for avocado genomic data.
Purpose of the Study:
- To develop an integrated platform for avocado genomic and transcriptomic data.
- To provide pre-computed multi-omics analyses and reproducible workflows.
- To facilitate functional genomics, breeding, and comparative studies in avocado.
Main Methods:
- Consolidated two high-quality avocado genome assemblies (Hass and West Indian).
- Integrated RNA-seq datasets from 13 NCBI BioProjects with uniform reprocessing and metadata.
- Developed Docker-encapsulated Snakemake workflows for transcriptome analysis.
Main Results:
- Launched the Persea americana Genome Database (PAGD) with integrated multi-omics data.
- PAGD includes gene family classification, collinearity, gene density, and expression profiles.
- Provided tools like BLAST, JBrowse, interactive heatmaps, and data download.
Conclusions:
- PAGD enhances avocado genomic resources through data integration and reproducible workflows.
- The platform lowers the technical barrier for RNA-seq analysis.
- PAGD supports diverse applications in plant science, breeding, and comparative genomics.
