Dataset Information

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.

Conclusion

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.

SUBMITTER: Derrien T

PROVIDER: S-EPMC2644713 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature

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Publications

Revisiting the missing protein-coding gene catalog of the domestic dog.

Derrien Thomas T Thézé Julien J Vaysse Amaury A André Catherine C Ostrander Elaine A EA Galibert Francis F Hitte Christophe C

BMC genomics 20090204

<h4>Background</h4>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.<h4>Results</h4>Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise sy ...[more]

PMID: 19193219

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Project description:The domestic dog shows a wide range of morphologies, that humans have selected for in the process of creating unique breeds. Recent studies have revealed correlations between changes in morphology and behaviour as reported by owners. For example, as height and weight decrease, many undesirable behaviours (non-social fear, hyperactivity and attention seeking) become more apparent. The current study aimed to explore more of these correlations, but this time used reports from trained observers. Phenotypic measurements were recorded from a range of common dog breeds (n = 45) and included cephalic index (CI: the ratio of skull width to skull length), bodyweight, height and sex. These data were then correlated with results from the Dog Mentality Assessment (DMA), which involves trained observers scoring a dog's reaction to stimuli presented over 10 standardised subtests. Each subtest is designed to evoke a behavioural response. Backward elimination and weighted step-wise regression revealed that shorter dogs demonstrated more aggressive tendencies, reacting defensively toward both assistants dressed as ghosts (p = 0.045), and to a dummy (p = 0.008). Taller dogs were more affectionate when greeting and being handled by humans (p = 0.007, p = <0.001, respectively). Taller dogs were also more cooperative (p = <0.001), and playful (p = 0.001) with humans than shorter dogs. Heavier dogs were more inquisitive toward a dummy (p = 0.011), to the source of a metallic noise (p = 0.010) and to an assistant (p = 0.003). Heavier dogs were also more attentive to the ghosts (p = 0.013). In comparison, lighter dogs were cautious of a dummy (p = <0.001) and fearful of the sound of a gunshot (p = <0.001). Lighter dogs were also cautious of, and demonstrated prolonged fearfulness toward, the source of metallic noise (p = <0.001, p = <0.034, respectively). With a far larger sample and the advantage of third-party reporting (which overcomes potential owner bias), the current findings build on previous studies in this field, further supporting covariance between morphology and behaviour.

Dataset Information

Revisiting the missing protein-coding gene catalog of the domestic dog.

Background

Results

Conclusion

Publications

Revisiting the missing protein-coding gene catalog of the domestic dog.

Similar Datasets

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