Comparative genomics compares genomes to identify shared sequences, lineage-specific changes and differences in genome organization. For example, conservation across related species can help identify a candidate regulatory element or evaluate a predicted gene model. Interpretation depends on shared ancestry and correct correspondence between regions: similarity can reflect gene duplication as well as common species ancestry. [ref]
Comparative Genomics Fact Sheet by NHGRI. NHGRI, Comparative Genomics Fact Sheet: shared sequences, function and evolutionary relationships
Synteny describes the occurrence of genomic loci on the same chromosome; comparative usage often additionally concerns conserved neighbourhoods or order between genomes. A block containing corresponding genes can support assignment of an uncertain region even when individual sequences have diverged. Rearrangements such as a chromosomal inversion can preserve membership of a block while reversing its internal orientation. The intended sense of conserved location versus conserved order should be stated. [ref]
