Annotation, Orthologues and Comparative Genomics

An assembled genome is only useful once genes are located and their likely functions assigned. New genes are usually named by matching them to genes already studied in other species. That transfer is powerful but provisional. A match says the two genes look alike, not that they do the same thing. Every transferred annotation is a prediction waiting for a test.

Orthologues are genes in different species that descend from one gene in their last common ancestor. They split because the species split, and they usually keep the ancestral job. Paralogues instead come from a duplication inside one genome, leaving two or more copies in the same lineage. The spare copies are free to mutate and take on new jobs. Trees built from shared DNA tell the two histories apart.

Line genomes up side by side and some stretches match closely across distant relatives. Those conserved stretches flag DNA that evolution refused to change. If a sequence is unchanged, mutations there were probably harmful, which suggests the sequence does something important. But the argument has limits: some sequences persist for structural reasons, and similarity alone never proves function. Only experiments settle it.