Predicting the Evolution of Syntenies—An Algorithmic Review

Abstract

Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties. In addition of being able to identify them, it is also necessary to infer the evolutionary history that has led from the ancestral segment to the extant ones. In this field, most algorithmic studies address the problem of inferring rearrangement scenarios explaining the disruption in gene order between segments with the same gene content, some of them extending the evolutionary model to gene insertion and deletion. However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another. Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization to segmental events and to syntenies. This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees.

Algorithms for the Reconstruction of Genomic Structures with Proofs of Their Low Polynomial Complexity and High Exactness

“…Among the algorithms of genome reconstruction, we highlight [3] a convenient way of visualizing reconstructed genomes when working with databases [4]. In regard to the biological problem of reconstructing genome syntenies, we highlight the review [5]; and among the algorithms of its solution [6,7]. On reconstructing cell types, we highlight the work presented in [8,9]; in the latter, a network class is introduced with node marks that are convenient for describing cell types and their evolution.…”

Evolutionary dynamics of glue gene copy number in Drosophila species

“…Duplicated gene copies are often clustered at speci c genomic locations [14]. Examining the immediate surroundings of gene copies, researchers have often noticed the presence of transposable elements, for example for pigmentation transcription factor genes in maize [15], effector genes in grass powdery mildew [16], insecticide resistance genes in Drosophila [17], amylase genes in Vertebrates [18] and fatty acid metabolic genes in sh [19].…”