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Updated: Jun 3, 2026
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
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.
Background:
Avocado (Persea americana) is an economically important fruit with growing global production. While multiple genome assemblies and transcriptomic datasets are publicly available-including the dedicated platform AvoBase-these resources remain fragmented and lack integration with pre‑computed multi‑omics analyses and reproducible workflows.
Results:
We present the Persea americana Genome Database (PAGD; http://bioinfor.kib.ac.cn/ ), an integrated platform consolidating two high‑quality genome assemblies (Hass chromosome‑level and West Indian telomere‑to‑telomere). It also hosts RNA‑seq datasets from 13 NCBI BioProjects, each linked to detailed biosample metadata, all uniformly re‑processed. Pre‑computed results include gene family classification (68 TPS genes), collinearity, gene density, and expression profiles. PAGD offers BLAST, JBrowse, interactive heatmaps, and data download. Additionally, we developed three Docker‑encapsulated Snakemake workflows for reference‑based and reference‑free transcriptome analysis, eliminating manual software configuration.
Conclusion:
PAGD advances existing avocado genomic resources by integrating multi‑omics data with pre‑computed analyses and a reproducible transcriptome workflow. The encapsulated workflows lower the technical barrier for RNA‑seq analysis, are adaptable to other plant species, and support functional genomics, breeding, and comparative studies.
