Mouse–Human Orthology Relationships in an Olfactory Receptor Gene Cluster Michal Lapidot,* Yitzhak Pilpel,* ,1 Yoav Gilad,* Ayellet Falcovitz,* Dror Sharon,* ,2 Thomas Haaf,² and Doron Lancet * ,3 * Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel; and ² Max-Planck-Institute of Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany Received July 5, 2000; accepted November 2, 2000 The olfactory receptor (OR) subgenome harbors the largest known gene family in mammals, disposed in clusters on numerous chromosomes. One of the best characterized OR clusters, located at human chromo- some 17p13.3, has previously been studied by us in human and in other primates, revealing a conserved set of 17 OR genes. Here, we report the identification of a syntenic OR cluster in the mouse and the partial DNA sequence of many of its OR genes. A probe for the mouse M5 gene, orthologous to one of the OR genes in the human cluster (OR17-25), was used to isolate six PAC clones, all mapping by in situ hybridization to mouse chromosome 11B3–11B5, a region of shared syn- teny with human chromosome 17p13.3. Thirteen mouse OR sequences amplified and sequenced from these PACs allowed us to construct a putative physical map of the OR gene cluster at the mouse Olfr1 locus. Several points of evidence, including a strong similar- ity in subfamily composition and at least four cases of gene orthology, suggest that the mouse Olfr1 and the human 17p13.3 clusters are orthologous. A detailed comparison of the OR sequences within the two clus- ters helps trace their independent evolutionary his- tory in the two species. Two types of evolutionary scenarios are discerned: cases of “true orthologous genes” in which high sequence similarity suggests a shared conserved function, as opposed to instances in which orthologous genes may have undergone inde- pendent diversification in the realm of “free reign” repertoire expansion. © 2001 Academic Press INTRODUCTION Olfactory receptors (ORs) are seven-transmembrane domain proteins that underlie the recognition and G- protein-mediated transduction of odorant signals (Buck and Axel, 1991; Lancet and Pace, 1987; Mom- baerts, 1999). OR genes are expressed mainly in the olfactory neuroepithelium, but were also found in other tissues (Drutel et al., 1995; Walensky et al., 1998) including mammalian germ cells (Parmentier et al., 1992). Each olfactory sensory neuron expresses one or very few OR genes (Lancet, 1991) and probably just one allele at a given locus (Chess et al., 1994). This expres- sion pattern is believed to provide the molecular basis of odor discrimination by the sensory cells. OR genes were first cloned in the rat (Buck and Axel, 1991) and were later found in the genomes of a wide variety of species including human (Ben-Arie et al., 1994; Parmentier et al., 1992; Schurmans et al., 1993; Selbie et al., 1992), mouse (Ressler et al., 1993; Sulli- van et al., 1996), dog (Issel-Tarver and Rine, 1996), pig (Velten et al., 1998), chicken (Nef and Nef, 1997), Xe- nopus (Freitag et al., 1995), channel catfish (Ngai et al., 1993), zebrafish (Barth et al., 1997), opposum (Kubick et al., 1997), mudpuppy (Zhou et al., 1997), lamprey (Berghard and Dryer, 1998), Caenorhabditis elegans (Troemel et al., 1995), and Drosophila melanogaster (Clyne et al., 1999; Vosshall et al., 1999). ORs are present in the genome of these species in a large germ- line repertoire (the “olfactory subgenome”) with an es- timated 500 –1000 coded proteins (Buck and Axel, 1991; Lancet, 1986; Ressler et al., 1994). They form an outstandingly diverse multigene family, consisting of 32 distinct families (Glusman et al., 2000a; Lancet and Ben-Arie, 1993). While some regions in the OR gene are highly con- served, others show sequence variability. Earlier anal- yses showed that most of the variable amino acid res- idues are clustered within the transmembrane helices TM3, TM4, and TM5 (Buck and Axel, 1991). More recently, an analysis of hundreds of vertebrate OR sequences, along with molecular modeling of the recep- Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under Accession Nos. AF309122– AF309134. 1 Present address: Department of Genetics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115. 2 Present address: Ocular Molecular Genetics Laboratory, Massa- chusetts Eye and Ear Infirmary, Harvard Medical School, 243 Charles Street, Boston, MA 02114. 3 To whom correspondence should be addressed. Telephone: 972-8-9343683 or -934412. Fax: 972-8-9344112. E-mail: doron.lancet@weizmann.ac.il. Genomics 71, 296 –306 (2001) doi:10.1006/geno.2000.6431, available online at http://www.idealibrary.com on 296 0888-7543/01 $35.00 Copyright © 2001 by Academic Press All rights of reproduction in any form reserved.