# Predicting the Evolution of Syntenies--An Algorithmic Review
## 2 Syntenies Defined as Gene Orders  
The term \"synteny\", first introduced in 1971 [22], arose from the need to refer to Human genes located on the same chromosome, but with a genetic distance that could not be determined by the frequency of recombination inferred from the new gene mapping methods. As recalled in [23], _synteny_ means \"same thread\" (or ribbon), a state of being together in location, as synchrony means being together in time. Thus, according to the original definition, saying that two genes are syntenic only means that they are located on the same chromosome. Today however, the term is largely used by biologists in an evolutionary meaning to design genes or chromosomal segments with a common evolutionary ancestry, i.e., _homologous_ genes, or regions of contiguous genes. For example, CoGe ([[https://genomevolution.org/wiki/index.php/Synteny](https://genomevolution.org/wiki/index.php/Synteny)]([https://genomevolution.org/wiki/index.php/Synteny](https://genomevolution.org/wiki/index.php/Synteny)) (accessed on 8 April 2021)), a platform for performing comparative genomics research, defines a synteny as a valid deduction that two or more genomic regions derived from a single ancestral region. Inferring \"syntenic blocks\" usually relies on inferring pairs of chromosomal regions with a similar gene content and order. The SynMap tool of CoGe identifies such blocks by finding sets of homologous gene pairs and merging them into regions. Such _synteny blocks_ or _regions_ that are more conserved than average in the genomes can reveal regulatory or functional interactions between the involved genes, or combination of alleles that are advantageous when inherited together. Conversely, breakage of conservation in gene order or gene content is an important footprint of the evolution of genomes through global rearrangements [24; 25; 26] that can be used to infer phylogenetic trees [27]. Two chromosomal regions with identical gene content and order can clearly be labeled as syntenic. However, because syntenic regions are largely remodeled during evolution, it is usually necessary to relax this strict conservation requirement, allowing for a certain gene content or gene order disruption. Notice that genes are usually represented as signed (\"+\" for the \(5^{\prime}\to 3^{\prime}\) strand and \"-\" for the \(3^{\prime}\to 5^{\prime}\) strand) units, where the sign or _orientation of a gene_ indicates on which of the two complementary DNA strands the gene is located. Thus, ranging from a strict definition in terms of conserved segments with identical gene content, order and orientation [25] to the most relaxed one in terms of being located on the same chromosome, the notion of two regions being syntenic has been defined in several ways, also depending on the evolutionary events being considered. In fact, during evolution, syntenic regions evolve independently through local gene rearrangements or local events modifying their gene content, such as tandem duplications adding genes or, conversely, losses removing genes. They also evolve collectively through transpositions and translocations splitting a single synteny into two syntenies, or conversely joining two syntenies into one; new syntenies are created through transposed duplications [28] or whole genome duplication, or conversely lost [29]. They are also passed to organisms through speciation or HGTs (see Figure 1). From a combinatorial point of view, various formal definitions of synteny blocks, also called _gene clusters_ have been introduced to allow identifying them in a set of genomes [20; 30] (see Figure 2). Notice first that although we define syntenies as sequences of genes, from a combinatorial or an algorithmic point of view, any other marker or unit can be considered instead of genes. The notion of _common intervals_[31; 32; 33] refers to conserved segments in which we relax the conditions that genes appear in the same order or the same orientation.