title: Revisiting the missing protein-coding gene catalog of the domestic dog.
abstract: BACKGROUND
  Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog.
  
  
  RESULTS
  Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (d(N)/d(S)), we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates.
  
  
  CONCLUSIONS
  This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.
authors.affiliation: Institut de Génétique et Développement, CNRS UMR6061, Université de Rennes 1, Léon Bernard, Rennes, France. thomas.derrien@crg.es
authors.forename: Thomas
authors.initials: T
authors.lastname: Derrien
authors.forename: Julien
authors.initials: J
authors.lastname: Thézé
authors.forename: Amaury
authors.initials: A
authors.lastname: Vaysse
authors.forename: Catherine
authors.initials: C
authors.lastname: André
authors.forename: Elaine A
authors.initials: EA
authors.lastname: Ostrander
authors.forename: Francis
authors.initials: F
authors.lastname: Galibert
authors.forename: Christophe
authors.initials: C
authors.lastname: Hitte
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004285:Dogs / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D023281:Genomics / Q000379:methods*; D008957:Models, Genetic; D011544:Pseudogenes; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D020539:Sequence Analysis, Protein; D012984:Software; D013045:Species Specificity; D026801:Synteny