| Title | PAGD: the Persea americana Genome Database and a Docker-based transcriptome analysis workflow |
| Author | Ma, Siyi |
| Publication | BMC GENOMICS |
| Year | 2026 |
| Volume | 27 |
| Issue | 1 |
| Corresponding Author | Zhang, CJ;Yang, YQ |
| Abstract | 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; ), 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. |
