Identification of mammalian orthologs using local synteny

Abstract

Background: Accurate determination of orthology is central to comparative genomics. For vertebrates in particular, very large gene families, high rates of gene duplication and loss, multiple mechanisms of gene duplication, and high rates of retrotransposition all combine to make inference of orthology between genes difficult. Many methods have been developed to identify orthologous genes, mostly based upon analysis of the inferred protein sequence of the genes. More recently, methods have been proposed that use genomic context in addition to protein sequence to improve orthology assignment in vertebrates. Such methods have been most successfully implemented in fungal genomes and have long been used in prokaryotic genomes, where gene order is far less variable than in vertebrates. However, to our knowledge, no explicit comparison of synteny and sequence based definitions of orthology has been reported in vertebrates, or, more specifically, in mammals.

Evolutionary history of the GH3 family of acyl adenylases in rosids

“…The increasing number of sequenced genomes and new comparative genomic tools makes it possible to use synteny to evaluate phylogenetic trees. For example, Jun et al recently evaluated the use of local synteny for identifying orthologous genes in mammals, and found it quite effective, particularly in cases of local duplication and transposition (Jun et al 2009). We used the syntenic data to guide the choice of phylogenetic methods in order to best understand how PBS3 is related to the other GH3 genes.…”

Bioinformatic screening of genes present only in well regenerating vertebrates reveals novel FGF and purinergic signaling modulator - c-Answer

“…At the first step, by using previously developed algorithm (called ClusterZSL) (Lyubetsky et al, 2013;Rubanov et al, 2016;Zverkov et al, 2012Zverkov et al, , 2015 for each gene of X. tropicalis we formed a cluster of the most homologous genes from the selected representatives of cold-and warm-blooded species with well sequenced and annotated genomes. Several orthology inference methods including the local synteny consideration were compared previously using five mammalian genomes (Jun et al, 2009a).…”

Duplication, Rearrangement and Reconciliation: A Follow-Up 13 Years Later

“…Synteny is usually a good way to infer orthologs [72]. As reconciled gene trees also yield orthology relationships, it is possible to compare the results from both independent methods.…”