Plant-mSyn

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Overview

Plant-mSyn is a web application for comparative genomics and microsynteny analysis across plant genomes. Visualize gene conservation, synteny relationships, and discover functionally related gene clusters across species. The application comprises a pre-computed database of over 400 plant genomes with 26,000+ pairwise synteny comparisons, enabling instant access to comparative analyses.

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Application Modules

Select a module below to get started with your analysis.

Atlas-Microsynteny

Generate microsynteny plots for specific genes of interest across plant species. Input custom gene lists, assign colors, compare across genomes, and export in PNG/SVG/CSV formats.

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Pangenome-Microsynteny

Plot microsynteny for your custom genes across 4 plant pangenomes. Select a query pangenome, choose comparisons, and visualize syntenic relationships.

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Custom-Microsynteny

Upload your own genome (GFF3 + protein sequences) and automatically identify syntenic blocks against database genomes using MCscan.

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Batch-Microsynteny

Upload up to 30 genomes with a central genome for reference-based comparisons, or up to 5 genomes for all-vs-all pairwise synteny analysis. Ideal for comparative genomics across related species or varieties.

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Cluster Discovery

Search for syntenic blocks with specific functional annotations. Upload custom annotations, define search criteria, and discover conserved gene clusters or metabolic pathways.

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If you found our work useful, please cite:

Plant-mSyn: [Our work - citation pending]
JCVI: Tang, Haibao, et al. "JCVI: A versatile toolkit for comparative genomics analysis." Imeta 3.4 (2024): e211.
MCscan: Tang, Haibao, et al. "Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps." Genome research 18.12 (2008): 1944-1954.
LAST: Kiełbasa SM, et al. (2011) Adaptive seeds tame genomic sequence comparison. Genome Research 21:487-493.

Atlas-Microsynteny

Generate microsynteny plots for your custom gene list across multiple plant species. Select your query genome, specify genes of interest, choose comparison genomes, and visualize syntenic relationships with customizable parameters including flanking gene windows and color schemes. Instantly access our pre-computed database of over 200 plant genomes with 20,000+ pairwise synteny comparisons.

Select Query Genome

Query Genome

Input Genes

Enter gene IDs from the query genome. Choose annotation source for color legend.

Select Comparison Genomes

Check genomes to include in the plot.

Filter by Family

Add More Genomes

🔍

Advanced Search (recommended to use before plotting)

Choose Layout

Select how genomes are arranged in rows. Query genome should be alone in its own row.

Select comparison genomes first

Generate Plot

⏳ Ready to generate

Results

📷 PNG 🎨 SVG 📊 CSV

🔧 Plot Tweaking Options

Fine-tune your plot by adjusting window sizes, gene counts, genome labels, and gene highlighting. Changes take effect when you regenerate the plot.

📏 Window Size Controls

(Filter performed by window padding AND max flanking genes)

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

Select which query genes should display their name as a label on the plot.

🎨 Connection Coloring

Keep coloring for low-confidence matches

By default, only high-confidence syntenic matches that pass the strict C-score cutoff (approximately equivalent to a reciprocal best hit) are drawn with colors. Enable this option to also color connections for lower-confidence matches.

Pangenome-Microsynteny

Plot microsynteny for your custom genes across 4 plant pangenomes. Select a query pangenome, choose comparisons, and visualize syntenic relationships, backed by 5,000+ precomputed pairwise synteny comparisons.

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Select Pangenome

Pangenome

Select Query Genome

Query Genome

Input Genes

Enter gene IDs from the query genome. Choose annotation source for color legend.

Select Comparison Genomes

Check genomes to include in the plot (from selected pangenome).

🔍

Advanced Search (recommended to use before plotting)

Choose Layout

Select how genomes are arranged in rows. Query genome should be alone in its own row.

Select comparison genomes first

Generate Plot

⏳ Ready to generate

Results

📷 PNG 🎨 SVG 📊 CSV

🔧 Plot Tweaking Options

Fine-tune your plot by adjusting window sizes, gene counts, genome labels, and gene highlighting. Changes take effect when you regenerate the plot.

📏 Window Size Controls

(Filter performed by window padding AND max flanking genes)

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

Select which query genes should display their name as a label on the plot.

🎨 Connection Coloring

Keep coloring for low-confidence matches

Custom-Microsynteny

Upload and process your own genome data (GFF3 and PEP files) for microsynteny analysis. The system will automatically extract gene coordinates, create BED files, and run MCscan to identify syntenic blocks against available comparison genomes in the database. You can then visualize these synteny relationships using your uploaded genome as the query.

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Run New / Upload MCscan

📋 File Format Requirements

GFF3 Annotation File (.gff3)

Standard GFF3 format with gene features
Must contain ID= or gene_id= attributes

Protein FASTA File (.pep, .fa, .fasta)

Protein sequences for all genes
Header format: >TranscriptID or >GeneID.X

📁 Storage: Files are retained for 2 weeks, then automatically deleted.

Run Name * Required. Name for your analysis run.

Genome Display Name * Required. Genome name shown in plot.

Visibility *

🌐 Public 🔒 Private

Public runs appear in "Available Custom Genomes". Private runs are only accessible via the Run Key.

GFF3 Annotation File

Protein FASTA File

📋 File Format Requirements

BED File

6-column BED format
Columns: chrom chromStart chromEnd name score strand
Score should be set to 0

Protein Sequences (FASTA format)

Standard FASTA format
Gene names NOT ending in .N are main isoforms
Names like GeneA.1 indicate isoform 1

⚠️ Requirements: Minimum 4 genes required. We recommend ~40 surrounding genes for meaningful synteny analysis.

📁 Storage: Files are retained for 2 weeks, then automatically deleted.

Run Name * Required. Name for your analysis run.

Genome Display Name * Required. Genome name shown in plot.

Visibility *

🌐 Public 🔒 Private

Public runs appear in "Available Custom Genomes". Private runs are only accessible via the Run Key.

BED File Content * Paste your BED file content. 6-column format: chrom, chromStart, chromEnd, name, score (0), strand (+/-). Header rows are automatically detected and skipped.

Protein Sequences (FASTA format) * Paste your protein sequences in FASTA format. Each sequence must correspond to a gene in your BED file.

🔑 Load by Run Key

Enter a run key to load your custom genome for plotting:

Run Key

📁 Available Custom Genomes

No custom genomes available

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Plot Microsynteny

Input Genes

Enter gene IDs from your custom genome.

Select Comparison Genomes

Check genomes to include in the plot (only genomes analyzed in your MCscan run are available).

🔍

Advanced Search (recommended before plotting)

Search for syntenic hits before plotting to verify which genomes have ortholog matches.

Minimum Query Genes with Matches At least this many query genes must have ortholog matches

Required Genes (optional)

Selected genes MUST have at least one match

Search selected genomes Search all available genomes

Choose Layout

Select how genomes are arranged in rows. Your custom genome should be alone in its own row.

Select comparison genomes first

Generate Plot

⏳ Ready to generate

Results

📷 PNG 🎨 SVG 📊 CSV

🔧 Plot Tweaking Options

Fine-tune your plot by adjusting window sizes, gene counts, genome labels, and gene highlighting. Changes take effect when you regenerate the plot.

📏 Window Size Controls

(Filter performed by window padding AND max flanking genes)

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

Select which query genes should display their name as a label on the plot.

🎨 Connection Coloring

Keep coloring for low-confidence matches

Batch-Microsynteny

Upload up to 30 genomes (each with GFF3 and PEP files) with a central genome for reference-based comparisons, or up to 5 custom genomes for comprehensive pairwise synteny comparisons. The system processes all uploaded genomes and identifies syntenic blocks between each pair. This is ideal for comparative genomics studies across closely related species or varieties.

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Setup Multi-Genome Comparison

📤 Central Genome Comparison

Upload up to 30 genomes. The first genome is the central reference—all other genomes will be compared against it. You can also include up to 3 database genomes for additional comparisons.

⏱️ Processing Time: Initiation takes 5 minutes. Each comparison takes ~2 minutes. With 5 genomes, expect ~15 minutes.

📁 Storage: Files are retained for 2 weeks, then automatically deleted.

Project Settings

Project Name * Name for your synteny project.

Visibility *

🌐 Public 🔒 Private

Public runs appear in "Available Custom Genomes" list.

📁 Custom Genomes (2-30)

🌿 Include Database Genomes (Optional, max 3)

Select up to 3 database genomes to include in comparisons against your central genome.

▶ ⚙️ Advanced MCscan Options (optional)

⏳ Add at least 2 genomes to begin (Genome 1 is the central genome)

📋 Multi-Genome Comparison

Upload 2-5 custom genomes to compare pairwise synteny between them. You can also include up to 3 database genomes for additional comparisons.

⏱️ Processing Time: Initiation takes 5 minutes. Each genome pair takes ~2 minutes. With 3 genomes + 3 database genomes (15 pairs), expect ~35 minutes.

📁 Storage: Files are retained for 2 weeks, then automatically deleted.

Project Settings

Project Name * Name for your synteny project.

Visibility *

🌐 Public 🔒 Private

Public runs appear in "Available Custom Genomes" list.

📁 Custom Genomes (2-5)

🌿 Include Database Genomes (Optional, max 3)

Select up to 3 database genomes to include in comparisons with your custom genomes.

▶ ⚙️ Advanced MCscan Options (optional)

⏳ Add at least 2 genomes to begin

🔑 Load by Run Key

Enter a run key to load your multi-genome synteny project:

Run Key

📁 Available Batch-Microsynteny Projects

No batch microsynteny projects available

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Plot Microsynteny

Select Query Genome

Choose which genome to use as the query (your genes of interest).

Input Genes

Enter gene IDs from your selected query genome.

Select Comparison Genomes

Check genomes to include in the plot (only genomes with completed comparisons are available).

🔍

Advanced Search (recommended before plotting)

Search for syntenic hits before plotting to verify which genomes have ortholog matches.

Minimum Query Genes with Matches At least this many query genes must have ortholog matches

Required Genes (optional)

Selected genes MUST have at least one match

Search selected genomes Search all available genomes

Choose Layout

Select how genomes are arranged in rows. Query genome should be alone in its own row.

Select comparison genomes first

Generate Plot

⏳ Ready to generate

Results

📷 PNG 🎨 SVG 📊 CSV

🔧 Plot Tweaking Options

Fine-tune your plot by adjusting window sizes, gene counts, genome labels, and gene highlighting. Changes take effect when you regenerate the plot.

📏 Window Size Controls

(Filter performed by window padding AND max flanking genes)

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

Select which query genes should display their name as a label on the plot.

🎨 Connection Coloring

Keep coloring for low-confidence matches

Cluster Discovery

Search for syntenic blocks containing genes with specific functional annotations across plant genomes. Upload custom annotations or use database genomes to identify conserved gene clusters matching required and optional search terms. Results show complete syntenic blocks with gene annotations and confidence scores for each match.

Select Query Genome

Select Comparison Genomes

Check genomes to search for syntenic blocks.

Match Mode

ALL genomes — Results must be found in every selected genome (more stringent)

ANY genome — Results found in at least one selected genome (more inclusive)

Filter by Family

Add More Genomes

Custom Annotations

Optional for database genomes: Upload custom annotations to override the built-in database annotations. Your uploaded annotations will be used instead of the default ones for the search.
Required for custom genomes: If you're using a custom genome (uploaded via the Custom Genome page), you must provide annotations here since there are no built-in annotations for custom genomes.

📋 Expected Format

Two columns: gene ID and description. First row can be a header (will be auto-detected).

Example:

gene	description
GeneA	Terpene Synthase
GeneB	Cytochrome P450
GeneC	Kinase domain

Upload Annotation File (TSV or CSV)

Search Criteria

Search using extracted keywords from annotations. Add terms, then categorize them as "Must Match" (required) or "Optional".

Search Annotation Terms

Available Terms

Select a query genome to load annotation terms

Click a term to add it to your search criteria

Selected Search Terms

Required Groups (set "At least X" per group, all groups must pass)

Group 1 (any one matches)

Click a term → select "Group 1"

Optional — shown if found, not required for results

Click term → "Add as Optional"

Run Discovery Search

⏳ Ready to search

About Plant-mSyn

🧬 Overview

🌿 Available Database Genomes

All database genomes have pre-computed pairwise synteny blocks for rapid analysis.

📥 Genome Assembly Sources

Download the complete list of genome assembly versions and accession numbers used in this database.

📄 Download Genome Assembly Sources

🔑 Key Features

Multiple Export Formats: PNG, SVG (editable), CSV (alignment data)
Project Management: Save and reload analyses using unique run keys (public or private)
Customizable Visualization: Control layout, colors, gene windows, and genome ordering
Upload Support: GFF3/GFF (annotations), PEP/FA/FASTA/FAA (sequences), CSV (functional annotations)
Rate Limiting: 5 uploads per hour, max 1 GB per upload
Data Retention: Custom genome data stored for 14 days with automatic cleanup

🚀 Quick Start

Atlas-Microsynteny: Start here for quick analysis with database genomes
Pangenome-Microsynteny: Explore microsynteny across plant pangenomes
Custom-Microsynteny: Upload your own genome for analysis
Batch-Microsynteny: Compare multiple custom genomes
Discovery: Search for annotated gene clusters

💡 Powered by: MCscan and JCVI toolkit for synteny detection with LAST algorithm for protein alignments.

Overview

Application Modules

Atlas-Microsynteny

Pangenome-Microsynteny

Custom-Microsynteny

Batch-Microsynteny

Cluster Discovery

Select Query Genome

Input Genes

Select Comparison Genomes

Advanced Search (recommended to use before plotting)

Search Results

Choose Layout

Assign Genomes to Positions

Available Genomes (drag to slots above)

Generate Plot

Results

🔧 Plot Tweaking Options

📏 Window Size Controls

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

🎨 Connection Coloring

Select Pangenome

Select Query Genome

Input Genes

Select Comparison Genomes

Advanced Search (recommended to use before plotting)

Search Results

Choose Layout

Assign Genomes to Positions

Available Genomes (drag to slots above)

Generate Plot

Results

🔧 Plot Tweaking Options

📏 Window Size Controls

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

🎨 Connection Coloring

Run New / Upload MCscan

📋 File Format Requirements

Select Comparison Genomes

Run MCscan Analysis

📋 File Format Requirements

Select Comparison Genomes

Run MCscan Analysis

🔑 Load by Run Key

📁 Available Custom Genomes

Plot Microsynteny

Input Genes

Select Comparison Genomes

Advanced Search (recommended before plotting)

Search Results

Choose Layout

Assign Genomes to Positions

Available Genomes (drag to slots above)

Generate Plot

Results

🔧 Plot Tweaking Options

📏 Window Size Controls

🏷️ Custom Genome (scaffolds) Labels

🔤 Gene Labels on Plot

🎨 Connection Coloring

Setup Multi-Genome Comparison

📤 Central Genome Comparison

Project Settings

📁 Custom Genomes (2-30)

🌿 Include Database Genomes (Optional, max 3)

⚙️ Select Comparisons to Run

📋 Multi-Genome Comparison

Project Settings

📁 Custom Genomes (2-5)

🌿 Include Database Genomes (Optional, max 3)

⚙️ Select Comparisons to Run

🔑 Load by Run Key

📁 Available Batch-Microsynteny Projects

Plot Microsynteny

Select Query Genome

Input Genes

Select Comparison Genomes

Advanced Search (recommended before plotting)