PGDD Wiki

Documentation and user guides for Plant Genome Duplication Database

What is PGDD?

The Plant Genome Duplication Database (PGDD) is a resource for comparative plant genomics, providing tools for synteny analysis, gene duplication classification, and cross-species gene family exploration. It hosts curated plant genomes with pre-computed synteny blocks and supports user-uploaded custom genomes for on-the-fly analysis.

MCScanX Pipeline

The MCScanX pipeline accepts protein FASTA and GFF files for 2+ genomes and runs:

All-vs-all protein similarity search (MMseqs2, Diamond, RAPSearch2, or BLASTP)
Synteny block detection (MCScanX or JCVI MCScan)
Optional Ka/Ks calculation
Interactive visualization via SynVisio, Multi-Synteny, and Chromosome Browser

Search Tool Options:

Tool	Speed	Sensitivity	Best for
MMseqs2	Superfast	High	Large datasets (>10 genomes)
Diamond	Fast	High	Standard analyses
RAPSearch2	Fast	Medium	Quick screening
BLASTP	Slow	Highest	Small datasets, reference

MCScanX GFF Format

The GFF file must be 4-column tab-separated with chromosome, gene ID, start, and end positions. Chromosome and gene ID must be prefixed with the species abbreviation:

At_Chr1\tAt_AT1G01010\t3631\t5899
At_Chr1\tAt_AT1G01020\t6788\t9130
Vv_chr1\tVv_VIT_01s0011g00010\t1000\t3000

The species abbreviation prefix is required. Use the same abbreviation consistently across all files for a genome.

REST API

PGDD provides a REST API for programmatic access. See the API documentation page for endpoints and examples.

PGDD Documentation (Read the Docs)

This section mirrors the Read the Docs structure and covers each page, feature, and tool with a short description and screenshot placeholder.

Site Pages (Top Navigation)

Home

Landing page with entry points to tools, featured genomes, and recent updates.

Browse Genomes

Searchable list of genomes with metadata, versions, and links to tool workflows.

Locus Search

Search gene or locus identifiers and jump to detailed synteny context.

Dot Plot

Pairwise synteny dotplot visualization with filters for block size and quality.

Riparian Plot

Enhanced dotplot view optimized for dense block visualization and interactive zoom.

3-Way Synteny

Three-genome synteny comparison for quick validation across species.

Multi-Synteny

Multi-genome synteny display for conserved block inspection.

Synteny Network

Network-based view of synteny relationships with filtering and exploration.

SynVisio

Block viewer for MCScanX/JCVI outputs with interactive inspection.

MCScanX Tutorial

Walkthrough and guidance for MCScanX workflows and file preparation.

MCScanX Web

Web interface for MCScanX outputs, filters, and block navigation.

Upload & Analyse

Pipeline entry point for user-uploaded genomes and on-the-fly synteny analysis.

Downloads

Dataset downloads, export bundles, and user-selected carts.

Taxonomy

Taxonomy viewer for species organization and browsing by clade.

PhyloWGD

Phylogenetic and WGD-focused summaries for genome evolution context.

Local Synteny

Neighborhood-focused synteny view around a seed locus or gene.

BLAST-IT

Sequence similarity search against PGDD genomes with direct links to hits.

Release Notes

Chronological updates for features, datasets, and fixes.

Core Features

Locus Search

Locate genes/loci by identifier and navigate to synteny context pages.

Block & Synteny Search

Search synteny blocks by genome pair, size, and quality metrics.

Family Synteny

Compare conserved neighborhoods across multiple genomes for a gene family.

Ks/KaKs Filtering

Filter blocks and gene pairs by evolutionary distance and quality metrics.

Genome Management

Maintain genome metadata, abbreviations, and version consistency.

Analytics & Metrics

Monitor usage, performance, and processing pipelines.

Tools

Dotplot

Pairwise synteny dotplot with block filtering and export.

Multi-synteny

Compare synteny across multiple genomes in a unified display.

Multi-block

Consolidated view for multiple block sets and comparisons.

Riparian Dotplot

Enhanced dotplot mode optimized for dense synteny views.

Local Synteny

Zoomed-in micro-synteny comparison around an anchor locus.

Circos

Circular genome plots for whole-genome synteny context.

MCScanX Webapp

Browse MCScanX-derived blocks and metadata with filters.

MCScanX Visualizer

Graphical visualization of MCScanX alignments and blocks.

Three-way Synteny Viewer

Tri-genome synteny visualization for comparative inspection.

Ka/Ks Browser

Explore Ka/Ks values and filter gene pairs by evolutionary rates.

Ka/Ks Calculator

Calculate Ka, Ks, and Ka/Ks for selected gene pairs.

Synteny Network

Network view for synteny relationships across genomes.

Genome Detail

Genome metadata summary with links to tools and downloads.

BLAST-It

Sequence similarity search and hit exploration.

SynVisio

Block viewer for synteny alignments and neighborhood inspection.

Upload & Analyse (Pipeline)

End-to-end pipeline for user genomes and MCScanX processing.

Data, Admin, and API

Data & Schema

Core schema, block tables, and genome/species metadata sources.

Admin

User management, permissions, and deployment notes.

API

Programmatic access to PGDD endpoints and examples.