Dog genetics and whole genome mapping. UMR-CNRS 6061

dog genetics

- These data are Additional data files for :

The Dog and Rat Olfactory Receptor Repertoires

Pascale Quignon^1,4, Mathieu Giraud², Maud Rimbault¹, Patricia Lavigne¹, Sandrine Tacher¹, Emmanuelle Morin², Elodie Retout²,
Anne-Sophie Valin², Kerstin Lindblad-Toh³, Jacques Nicolas² and Francis Galibert¹

Genome Biol. 2005;6(10) Sep 28. [-pubmed-] [-full paper-]

Background

Dogs and rats have a highly developed capability to detect and identify odorant molecules, even at minute concentrations. Previous analyses have shown that the olfactory receptors (ORs) that specifically bind odorant molecules are encoded by the largest gene family sequenced in mammals so far.

Results

We identified five amino acid patterns characteristic of ORs in the recently sequenced boxer dog and brown Norway rat genomes. Using these patterns, we retrieved 1,094 dog genes and 1,493 rat genes from these shotgun sequences. The retrieved sequences constitute the olfactory receptor repertoires of these two animals. Subsets of 20.3% (for the dog) and 19.5% (for the rat) of these genes were annotated as pseudogenes as they had one or several mutations interrupting their open reading frames. We performed phylogenetic studies and organized these two repertoires into classes, families and subfamilies.

Conclusion

We have established a complete or almost complete list of OR genes in the dog and the rat and have compared the sequences of these genes within and between the two species. Our results provide insight into the evolutionary development of these genes and the local amplifications that have led to the specific amplification of many subfamilies. We have also compared the human and rat ORs with the human and mouse OR repertoires.

Chromosomal localisation of canine OR genes and pseudogenes. Clusters are named following their position in megabases from the top of each chromosome [Additional_data_file_1.xls]

Chromosomal localisation of rat OR genes and pseudogenes. Clusters are named following their position in megabases from the top of each chromosome [Additional_data_file_2.xls]

Number of rat and dog OR genes and pseudogenes per family and subfamily. Families 2 to 21 belong to ClassII and families 51 to 57 to ClassI [Additional_data_file_3.xls]

Phylogenetic trees [Additional data files 4 to 20] :
Dog and rat OR proteins belonging to the same family were aligned using ClustalW software and a phylogram for each family was constructed using canine ADRB3 gene as outgroup. Subfamilies are indicated by circled letters. Rat genes are noted in red and dog genes in blue.
Dog :
File containing DNA sequences of the dog OR genes in fasta format : [Seq-dog-fasta]
File containing the protein sequences of only the OR genes of the dog in fasta format : [Prot-dog-fasta]
Table summarizing the characteristics of each dog OR sequences : [TableORdog.xls]
Rat :
File containing DNA sequences of the rat OR genes in fasta format : [Seq-rat-fasta]
File containing the protein sequences of only the OR genes of the rat in fasta format : [Prot-rat-fasta]
Table summarizing the characteristics of each rat OR sequences : [TableORrat.xls]

¹Pr Francis GALIBERT group at CNRS-University of Rennes1 - Rennes France
²Pr Jacques NICOLAS group at IRISA-University of Rennes1 - Rennes France
³Dr Kerstin LINDBLAD-TOH group at the BROAD Institute of MIT&Harvard - Cambridge USA
⁴current address : NIH/NHGRI/50 South Drive, MSC 8000, Bethesda, MD 20892-8000, USA