Evolution of gene fusions horizontal transfer versus independent events.docVIP

/2002/3/5/research/0024.1 Research Evolution of gene fusions: horizontal transfer versus independent events Itai Yanai*, Yuri I Wolf? and Eugene V Koonin? Addresses: *Bioinformatics Graduate Program and Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA. ?National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MA 20894, USA. Correspondence: Eugene V Koonin. E-mail: koonin@ Published: 26 April 2002 Received: 12 November 2001 Revised: 7 February 2002 Accepted: 26 March 2002 GenomeBiology 2002, 3(5):research0024.1–0024.13 The electronic version of this article is the complete one and can be found online at /2002/3/5/research/0024 ? 2002 Yanai et al., licensee BioMed Central Ltd (Print ISSN 1465-6906; Online ISSN 1465-6914) Abstract Background: Gene fusions can be used as tools for functional prediction and also as evolutionary markers. Fused genes often show a scattered phyletic distribution, which suggests a role for processes other than vertical inheritance in their evolution. Results: The evolutionary history of gene fusions was studied by phylogenetic analysis of the domains in the fused proteins and the orthologous domains that form stand-alone proteins. Clustering of fusion components from phylogenetically distant species was construed as evidence of dissemination of the fused genes by horizontal transfer. Of the 51 examined gene fusions that are represented in at least two of the three primary kingdoms (Bacteria, Archaea and Eukaryota), 31 were most probably disseminated by cross-kingdom horizontal gene transfer, whereas 14 appeared to have evolved independently in different kingdoms and two were probably inherited from the common ancestor of modern life forms. On many occasions, the evolutionary scenario also involves one or more secondary fissions of the fusion gene. For approxi