Synteny

Synteny refers to the preserved arrangement of genes on chromosomes across different species or within a genome. It originally described the observation that certain groups of genes tend to stay linked on the same chromosome, and in comparative genomics it is used to denote blocks of genes that have been inherited from a single ancestral chromosome segment with limited rearrangement. Syntenic blocks can vary in size and integrity, and may be interrupted by genomic rearrangements over evolutionary time.

In relation to related concepts, synteny is often distinguished from collinearity. Synteny broadly means that a set of genes remains on the same chromosome in the compared genomes, whereas collinearity emphasizes the preserved linear order and orientation of those genes. In practice, many studies use the terms together, but collinearity refers to a stricter preservation of gene order, while synteny can accommodate some rearrangements within a block.

Detection and analysis of synteny involve identifying orthologous genes between genomes and mapping their relative positions. Synteny blocks are defined when several neighboring genes retain conserved order and proximity, though small-scale rearrangements such as inversions, translocations, duplications, or gene loss can modify block boundaries. Synteny tends to be more conserved among closely related species and erodes with increasing evolutionary distance.

Applications of synteny include reconstructing ancestral karyotypes, studying genome evolution and rearrangements, guiding gene annotation transfer between species, and assisting in the assembly and scaffolding of new genomes. Synteny analyses thus provide a framework for understanding how chromosome structure has evolved and how it influences gene function and organization.