In classical genetics, the term denotes the existence of several genetic loci on the same chromosome, regardless of whether this relationship can be established by conventional tests for genetic linkage. In particular, two loci may be known to be syntenic even if their recombinant frequency cannot be distinguished from unlinked loci by practical experiments. Therefore, all genetically linked loci are syntenic, but not all syntenic loci are genetically linked. Loci located on different chromosomes are non-syntenic.
In comparative genomics, the term describes the preserved order of genes on chromosomes of related species, as a result of descent from a common ancestor. During evolution, chromosome rearrangements result in disruptions of synteny. The analysis of synteny has several applications in genomics. Shared synteny is one of the most reliable criteria for establishing the orthology of genomic regions in different species. Additionally, exceptional conservation of synteny can reflect important functional relationships between genes. For example, the order of genes in the "Hox cluster", which are key determinants of the animal body plan and which interact with each other in critical ways, is essentially preserved throughout the animal kingdom. Patterns of shared synteny or synteny breaks can also be used as characters to infer the phylogenetic relationships among several species, and even to infer the genome organization of extinct ancestral species. When many chromosome rearrangements have taken place after species divergence, synteny at genome-wide scale (macrosynteny) cannot be observed anymore. However in the absence of macrosynteny, microsynteny may still be observed when small clusters of genes in one species exhibit synteny with similar clusters at different positions in the genome of another species.
The genomics usage of the term may be more common today owing to the explosion of interest in this field. Some geneticists regard this as unfortunate, since the term is still needed in its classical sense.
- Synteny server Server for Synteny Identification and Analysis of Genome Rearrangement—the Identification of synteny and calculating reversal distances.
- Comparative Maps NIH's National Library of Medicine NCBI link to Gene Homology resources, and Comparative Chromosome Maps of the Human, Mouse, and Rat.
- NCBI Home Page NIH's National Library of Medicine NCBI (National Center for Biotechnology Information) link to a tremendous number of resources.
- ACT (Artemis Comparison Tool) — Probably the most used synteny software program used in comparative genomics.