Bioinformatics approaches to deciphering alien gene transfer: A comprehensive analysis

Abstract

A large number of bioinformatics methods have been developed in recent years for detecting gene transfers between distantly related or unrelated organisms. These have been mainly classified as parametric and phylogenetic methods. While the former methods have been frequently invoked for detecting recent gene transfers, detection of ancient gene transfers have relied upon phylogenetic methods. Numerous evidences emerging from the applications of these methods have firmly established interspecies gene transfer as a significant force-driving prokaryotic genome evolution. The focus is now shifting to assessing the extent and impact of this mechanismin eukaryotic genome evolution. The methods developed for detecting alien genes in unicellular organisms have been adapted for identifying and cataloging instances of gene transfers in multicellular organisms. A significantinterest is in cataloging gene transfers in plants which have more leaky barriers to gene transfer than highly evolved animals. We review the advances in this field with a focus on alien gene transfer in plants and the bioinformatics methods frequently used to detect such transfers.