A transcriptome resource of ginger under Pythium stress

Explore infection-responsive genes in Zingiber officinale

Interactive tools to search transcripts, browse Gene Ontology, and view KEGG pathways derived from ginger challenged with Pythium myriotylum (P0822).

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Infected ginger plant
Infection culture

Statistics

Key summaries from differential expression and enrichment analyses.

Volcano plot of differentially expressed genes
Volcano plot showing distribution of differentially expressed genes where, Green = Absolute log2 fold change above 1, Blue = Significant with an FDR less than 0.05, Red = Significant with an FDR less than 0.05 and absolute log2 fold change greater than 1.

GO BP terms
Plot showing enriched Gene Ontology terms for BP
GO CC terms
Plot showing enriched Gene Ontology terms for CC

GO MF terms
Plot showing enriched Gene Ontology terms for MF
KEGG pathways
Plot showing enriched KEGG pathways

About This Project

Ginger (Zingiber officinale) is one of the widely cultivated spice crops, yet highly susceptible to soft rot caused by Pythium spp., leading to substantial yield losses worldwide. The GiPyDB consolidates transcriptome data from ginger inoculated with Pythium myriotylum isolate P0822, enabling exploration of infection responsive transcriptional changes.

  • Interactively explore differentially expressed genes (DEGs).
  • Browse functional annotations via GO (BP, CC, MF).
  • Inspect pathway enrichment using KEGG.

Ginger plants were inoculated with P. myriotylum (P0822); RNA was extracted and paired‑end sequenced.

Reads were assessed with FastQC and trimmed with Fastp to retain high‑quality data.

Clean reads were aligned to the Zingiber officinale reference genome using HISAT2.

Comparisons between infected and control samples used edgeR; DEGs were defined at FDR < 0.05 and |log2FC| > 1.

Gene Ontology (GO) and KEGG pathway enrichment analysis using the DAVID annotation.

Team

Dr. praveena
Dr. Praveena R
Senior Scientist Division of Crop Protection ICAR‑IISR,Kozhikode
Dr. Biju CN
Dr. Biju CN
Principal Scientist Division of Crop Protection ICAR‑IISR,Kozhikode
Dr. Sona Charles
Dr. Sona Charles
Scientist Division of Crop Improvement and biotechnology ICAR‑IISR,Kozhikode
Dr. Divya P S
Dr. Divya P S
Senior Scientist Division of Crop Improvement and biotechnology ICAR‑IISR,Kozhikode
Dr. T.E. Sheeja
Dr. T.E. Sheeja
Principal Scientist and Head Division of Crop Improvement and Biotechnology
Project Support Team
RESHMA K S
Young Professional II
MUHAMMED FAYAD A
Young Professional II
SHAHANA ARIF
Project Associate I
ARUN SASEENDRAN NP
IT Technician (Software)
Contact
Project Summary

This database centralizes infection‑responsive transcripts in ginger to support research in plant–pathogen interactions and molecular breeding for disease resistance.

  • Search and annotate DEGs
  • GO and KEGG enrichment views
  • Download‑ready tables from search pages
Funding Support

The work was supported by the ICAR project, ICAR-CIB IV: Enabling Climate Resilience and ensuring food and Nutritional security through Genome Editing in Horticultural Crops [Sub project: - Application of genome editing to develop trait-specific varieties in ginger]