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PhytoPipe: a phytosanitary pipeline for plant pathogen detection and diagnosis using RNA-seq data
Xiaojun Hu1, Oscar P Hurtado-Gonzales2, Bishwo N Adhikari2
1United States Department of Agriculture (USDA), Animal and Plant Health Inspection Service (APHIS), Plant Protection and Quarantine (PPQ), Plant Germplasm Quarantine Program (PGQP), Beltsville, MD, USA. xiaojun.hu@usda.gov.
PhytoPipe is a new bioinformatics tool for analyzing high-throughput sequencing (HTS) data to detect a wide range of plant pathogens, including viruses, bacteria, fungi, and oomycetes. This user-friendly pipeline generates comprehensive reports, aiding in plant disease diagnostics and agricultural biosecurity.
Area of Science:
- Plant Pathology
- Bioinformatics
- Genomics
Background:
- Protecting agricultural systems from exotic plant pathogens is crucial for global trade.
- High-throughput sequencing (HTS) is vital for pathogen discovery but data analysis remains a challenge.
- Existing bioinformatics tools primarily focus on viruses and viroids, lacking comprehensive pathogen detection.
Purpose of the Study:
- To develop an integrated bioinformatics pipeline for detecting a broad spectrum of plant pathogens in HTS data.
- To provide a user-friendly tool for plant pathology diagnosticians.
- To generate comprehensive phytosanitary reports from HTS RNA-seq data.
Main Methods:
- Developed PhytoPipe, an open-source bioinformatics pipeline using Snakemake, Python 3, and bash scripts.
- Integrated quality control, read classification, assembly-based annotation, and reference-based mapping.
- Ensured compatibility with Linux environments and provided a Docker image for easy installation.
Main Results:
- PhytoPipe successfully detects viruses, viroids, bacteria (including phytoplasmas), fungi, and oomycetes from HTS RNA-seq data.
- The pipeline generates comprehensive reports for easy interpretation of phytosanitary status.
- PhytoPipe is user-friendly and provides integrated analysis and visualization.
Conclusions:
- PhytoPipe offers an integrative solution for analyzing HTS data to detect diverse plant pathogens.
- The tool is easily installable on Linux/Mac systems and accessible via Docker.
- PhytoPipe is freely available on GitHub and Docker Hub, supporting routine pathogen detection.
