Elsevier

Genomics

Volume 83, Issue 3, March 2004, Pages 361-372
Genomics

The canine olfactory subgenome☆

https://doi.org/10.1016/j.ygeno.2003.08.009Get rights and content

Abstract

We identified 971 olfactory receptor (OR) genes in the dog genome, estimated to constitute ∼80% of the canine OR repertoire. This was achieved by directed genomic DNA cloning of olfactory sequence tags as well as by mining the Celera canine genome sequences. The dog OR subgenome is estimated to have 12% pseudogenes, suggesting a functional repertoire similar to that of mouse and considerably larger than for humans. No novel OR families were discovered, but as many as 34 gene subfamilies were unique to the dog. “Fish-like” Class I ancient ORs constituted 18% of the repertoire, significantly more than in human and mouse. A set of 122 dog–human–mouse ortholog triplets was identified, with a relatively high fraction of Class I ORs. The elucidation of a large portion of the canine olfactory receptor gene superfamily, with some dog-specific attributes, may help us understand the unique chemosensory capacities of this species.

Section snippets

Canine olfactory sequence tags

To obtain efficient coverage of the canine OR repertoire, we employed the olfactory sequence tag (OST) approach [22], whereby pairs of degenerate primers were used to amplify OR clone sublibraries from canine genomic DNA, followed by subcloning and sequencing. Ten primers were designed according to human full-length OR coding sequences (http://bioinformatics.weizmann.ac.il/HORDE). The resulting combined degeneracy of the primer pairs ranged between 1.2×106 and 2.25×1010 (Table 1). These primers

Discussion

We have employed a comprehensive experimental and in silico approach to decipher a large fraction of the dog OR repertoire. A combination of de novo DNA sequencing and genome-wide data mining enabled us to define 971 OR genes.

A previous implementation of the OST approach, as part of the DEFOG scheme, deciphered successfully a third of the human repertoire [23]. In this study, we have used a set of degenerate primers designed according to human sequences to obtain 246 canine OR sequences. This

Degenerate primers design

Degenerate primers were designed using the HYDEN software (Highly Degenerate Primers: http://www.cs.tau.ac.il/~rshamir/hyden/HYDEN.htm). Given a set of DNA family-related sequences, HYDEN constructs degenerate primer pairs that match many of the given sequences with up to three mismatched bases. The full algorithmic details are described in [46]. For this work we have designed 10 primers, based on 719 human full-length ORs listed in the HORDE database version 38 as described in Table 1. The

Acknowledgements

This work was supported by German–Israel Foundation Grant G-0506-183.0396 (D. Lancet and R. Shamir) and the Israel Science Foundation (Grant 309/09) (R.Shamir) and the Crown Human Genome Center of the Weizmann Institute (D. Lancet).

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    ☆

    Supplementary material is available online at http://bioinformatics.weizmann.ac.il/HORDE/lancetpub/genomics2003

    1

    These authors contributed equally to this article.

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