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Journal of Heredity Advance Access first published online on June 15, 2007
This version published online on June 27, 2007
Journal of Heredity, doi:10.1093/jhered/esm027
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© The American Genetic Association. 2007. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org.

Analysis of the Unassembled Part of the Dog Genome Sequence: Chromosomal Localization of 115 Genes Inferred from Multispecies Comparative Genomics

Thomas Derrien, Catherine André, Francis Galibert, and Christophe Hitte

From the CNRS UMR6061 Génétique et Développement, Université de Rennes 1, IFR140, 2 Av du Pr Léon Bernard, CS 34317, 35043, Rennes, France

Address correspondence to C. Hitte at the address above, or e-mail: hitte{at}univ-rennes1.fr.

The identification of dog genes and their accurate localization to chromosomes remain a major challenge in the postgenomics era. The 132 annotated canine genes with human orthologs remaining in the unassembled part (chrUnknown) of the dog sequence assembly (CanFam1) are of limited use for candidate gene approaches or comparative mapping studies. We used a two-step comparative analysis to infer a canine chromosomal interval for localization of the chrUn genes. We first constructed a human–dog synteny map, using 14 456 gene-based comparative anchors. We then mapped the 132 chrUn genes onto the reference (human) synteny map and identified the corresponding, orthologous segment on the canine map, based on conserved gene order. Our results show that 110 chrUn genes could be localized to short intervals on 18 dog chromosomes, whereas 22 genes remained assigned to 2 possible intervals. We extended this comparative analysis to multiple species, using the chimpanzee, mouse, and rat genome sequences. This made it possible to narrow down the intervals concerned and to increase the number of canine chrUn genes with an inferred chromosome location to 115. This study demonstrates that dog chromosomal intervals for chrUn genes can be rapidly inferred, using a reference species, and indicates that comparative strategies based on larger numbers of species may be even more effective.

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