Comparative Genomics
One-Sentence Definition
Comparative genomics analyses similarities and differences between genomes to infer taxonomy, evolution, gene function, and the genetic basis of phenotypes.
Simple Explanation
Put genomes side by side: what is shared, what is unique, and what does that difference do?
Detailed Scientific Explanation
- Whole-genome distance: ANI (average nucleotide identity) — ~95% ANI is the common species boundary heuristic; digital DDH as complement
- Synteny and rearrangements; insertion sequence expansions
- Orthologs vs paralogs; gene gain/loss along a tree
- Genomic islands (pathogenicity, resistance, metabolic) — often atypical GC/codon usage
- Downstream: Pangenome Analysis, bacterial GWAS, phenotype association
Mechanism
Alignment-based (progressiveMauve, nucmer) or alignment-free sketching (mash, sourmash) → distance matrices, dot plots, gene-content comparisons.
Clinical Importance
- Identifies what distinguishes an outbreak clone from background flora
- Supports species reassignment when phenotype tests are ambiguous
Research Importance
- Evolution of virulence and resistance; host adaptation; reductive evolution in obligate pathogens
Diagnostic Relevance
- ANI-based species ID complements MALDI/biochemicals in Culture and Isolation workflows
AMR Relevance
- Locates resistance islands and their mobility context
Related MOCs
Active Recall Questions
- What ANI value is commonly used as a species cutoff?
- Ortholog vs paralog?
- What signals a horizontally acquired genomic island?