Comparative Genomics

We offer comprehensive comparative genomics analysis to explore genome-wide differences and conserved elements across species, strains, or isolates. Our pipeline supports synteny detection, ortholog clustering, gene family expansion/contraction, and pan-genome analysis using high-quality genome assemblies.

Workflow Summary

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flowchart LR
    subgraph Input["`**Input & QC**`"]
        direction TB
        Genomes["Assembled Genomes"]
        Annot["Structural/Functional Annotation"]
        QC["Annotation Quality Check"]
        Genomes --> Annot --> QC
    end

    subgraph Core["`**Comparative Analysis**`"]
        direction TB
        Ortho["Ortholog Detection (e.g., OrthoFinder)"]
        Pan["Pan-Genome Construction"]
        Synteny["Synteny Block Detection"]
        Collinearity["Collinearity Visualization"]
        Func["Functional Enrichment"]
        Ortho --> Pan --> Func
        Ortho --> Synteny --> Collinearity
    end

    subgraph Evolution["`**Evolutionary Inference**`"]
        direction TB
        Phylo["Phylogenetic Tree Construction"]
        Expansion["Gene Family Expansion/Contraction"]
        Positive["Positive Selection Analysis"]
        Phylo --> Expansion --> Positive
    end

    Input --> Core --> Evolution

Input & QC

1. Assembled Genomes: Input of high-quality genome assemblies (FASTA + GFF or GenBank).
2. Structural/Functional Annotation: Gene prediction and functional annotation via Prokka, MAKER, or EggNOG-mapper.
3. Annotation QC: Evaluate genome completeness using BUSCO, check gene counts and annotation statistics.

Comparative Analysis

1. Ortholog Detection: Identify orthologous and paralogous genes using OrthoFinder or OrthoMCL.
2. Pan-Genome Construction: Define core, accessory, and unique gene sets across genomes.
3. Synteny Detection: Identify conserved genomic blocks using tools like MCScanX, SyRI, or LASTZ.
4. Collinearity Visualization: Generate dotplots, circos plots, or synteny heatmaps.
5. Functional Enrichment: Assess enriched pathways or GO terms among gene subsets (e.g., unique, expanded).

Evolutionary Inference

1. Phylogenetic Tree Construction: Build species or gene trees using concatenated alignments or core gene presence/absence matrices.
2. Gene Family Expansion/Contraction: Analyze gain/loss dynamics using tools like CAFE.
3. Positive Selection Analysis: Identify rapidly evolving genes via dN/dS ratio (e.g., PAML, HyPhy).

Example

Dotplots reveal genome-level collinearity and structural rearrangements across species.

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Pan-genome curves summarize the distribution of core and accessory genes.

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Ortholog clustering heatmaps highlight gene family distributions across strains.

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Phylogenetic trees based on core genes reflect evolutionary relationships among genomes.

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For detailed options and customization, contact us.