| Title: | Comparative genomics of odorant and pheromone receptor genes in rodents |
| Author(s): | Zhang X; Zhang X; Firestein S; |
| Address: | "Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA" |
| DOI: | 10.1016/j.ygeno.2007.01.002 |
| ISSN/ISBN: | 0888-7543 (Print) 1089-8646 (Electronic) 0888-7543 (Linking) |
| Abstract: | "We applied a comprehensive data-mining strategy to examine the repertoires of rat and mouse odorant receptors (ORs) and type 1 pheromone receptors (V1Rs) using the mm5 (mouse) and rn3 (rat) genomes. We identified 1576 rat OR genes, including 292 pseudogenes. The rat V1R repertoire is composed of 115 intact genes and 72 pseudogenes. The mouse OR and V1R databases were updated using the new assembly mm5, from which 1375 mouse ORs and 308 V1Rs were identified, with more than 100 putative pseudogenes from mm2 now identified as intact because of the higher sequence quality. With these new data we have conducted a series of genomic analyses of the OR and V1R genes from mouse and rat. Orthologous OR clusters were identified in mouse and rat and comparison analysis was performed at three incremental levels: families, coding sequences, and motifs. At the family level, we found that V1R genes have more species-specific families than OR genes. About 20% of intact V1R genes have no orthologous counterpart in the same family, whereas less than 1% of intact ORs are similarly isolated. At the coding sequence level, OR genes are more conserved between mouse and rat than V1R genes. OR genes share greater similarity with their orthologous counterparts than with their closest neighbor, whereas V1R genes show the opposite tendency. Motifs were identified to obtain biological insights. Motifs specific for species or families were found in OR and V1R genes, which may result in the differential pheromone-dependent behaviors and perception of odors between mouse and rat" |
| Keywords: | "Animals Chromosomes/genetics Databases, Genetic Genome *Genomics Mice Multigene Family Phylogeny Pseudogenes Rats Receptors, Odorant/*genetics Receptors, Pheromone/*genetics Rodentia/genetics;" |
| Notes: | "MedlineZhang, Xiaohong Zhang, Xinmin Firestein, Stuart eng R01 DC006713-02/DC/NIDCD NIH HHS/ R01 DC003159/DC/NIDCD NIH HHS/ R01 DC006713-03/DC/NIDCD NIH HHS/ R01 DC006713/DC/NIDCD NIH HHS/ R01 DC006713-01/DC/NIDCD NIH HHS/ R01 DC006713-04/DC/NIDCD NIH HHS/ Comparative Study 2007/02/17 Genomics. 2007 Apr; 89(4):441-50. doi: 10.1016/j.ygeno.2007.01.002. Epub 2007 Feb 15" |
