Synteny

Study of synteny can show how the genome is cut and pasted in the course of evolution.Synteny is a neologism meaning "on the same ribbon"; Greek: σύν, syn "along with" + ταινία, tainiā "band".

During evolution, rearrangements to the genome such as chromosome translocations may separate two loci, 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.

[3] In light of the more recent shift in the meaning of synteny, this conservation of gene content and linkage without preservation of order has also been termed mesosynteny.

[12] Further study found that many cereals are syntenic [13] and thus plants such as rice or the grass Brachypodium could be used as a model to find genes or genetic markers of interest which could be used in wheat breeding and research.

This is typically done using a version of the MCScan algorithm, which finds syntenic blocks between species by comparing their homologous genes and looking for common patterns of collinearity on a chromosomal or contig scale.

Homologies are usually determined on the basis of high bit score BLAST hits that occur between multiple genomes.

Synteny (in the modern sense) between human and mouse chromosomes. Colors in the human chromosomes indicate regions homologous with parts of the mouse chromosome of the same color. For instance, sequences homologous to mouse chromosome 1 are primarily on human chromosomes 1 and 2, but also 6, 8, and 18. The X chromosome is almost completely syntenic in both species. [ 1 ]
Synteny of Hox gene clusters; lines indicate homology