In classical genetics, synteny describes the physical co-localization of genetic loci on the same chromosome within an individual or species. The concept is related to genetic linkage: Linkage between two loci is established by the observation of lower-than-expected recombination frequencies between two or more loci. In contrast, any loci on the same chromosome are by definition syntenic, even if their recombination frequency cannot be distinguished from unlinked loci by practical experiments. Thus, in theory, all linked loci are syntenic, but not all syntenic loci are necessarily linked. Similarly, in genomics, the genetic loci on a chromosome are syntenic regardless of whether this relationship can be established by experimental methods such as DNA sequencing/assembly, genome walking, physical localization or happy mapping.
Shared synteny describes preserved co-localization of genes on chromosomes of related species. During evolution, rearrangements to the genome such as chromosome translocations may separate two loci apart, resulting in the loss of synteny between them. Conversely, translocations can also join two previously separate pieces of chromosomes together, resulting in a gain of synteny between loci. Stronger-than-expected shared synteny can reflect selection for functional relationships between syntenic genes, such as combinations of alleles that are advantageous when inherited together, or shared regulatory mechanisms.
The term is sometimes also used to describe preservation of the precise order of genes on a chromosome passed down from a common ancestor, although many geneticists reject this use of the term. The analysis of synteny in the gene order sense 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. A qualitative distinction is sometimes drawn between macrosynteny, preservation of synteny in large portions of a chromosome, and microsynteny, preservation of synteny for only a few genes at a time.
Conserved synteny of genes between chromosome 15 of Bombyx mori and a chromosome of Manduca sexta shown by five-color BAC-FISH.(NOTE)(Report)
Nov 01, 2007; Abstract: The successful assignment of the existing genetic linkage groups (LGs) to individual chromosomes and the...
Analyses of Synteny between Arabidopsis Thaliana and Species in the Asteraceae Reveal a Complex Network of Small Syntenic Segments and Major Chromosomal Rearrangements
Aug 01, 2006; ABSTRACT Comparative genomic studies among highly divergent species have been problematic because reduced gene similarities make...