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Phylogenomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting

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Abstract

Canid species (dogs and foxes) have highly rearranged karyotypes and thus represent a challenge for conventional comparative cytogenetic studies. Among them, the domestic dog is one of the best-mapped species in mammals, constituting an ideal reference genome for comparative genomic study. Here we report the results of genome-wide comparative mapping of dog chromosome-specific probes onto chromosomes of the dhole, fennec fox, and gray fox, as well as the mapping of red fox chromosome-specific probes onto chromosomes of the corsac fox. We also present an integrated comparative chromosome map between the species studied here and all canids studied previously. The integrated map demonstrates an extensive conservation of whole chromosome arms across different canid species. In addition, we have generated a comprehensive genome phylogeny for the Canidae on the basis of the chromosome rearrangements revealed by comparative painting. This genome phylogeny has provided new insights into the karyotypic relationships among the canids. Our results, together with published data, allow the formulation of a likely Canidae ancestral karyotype (CAK, 2n = 82), and reveal that at least 6–24 chromosomal fission/fusion events are needed to convert the CAK karyotype to that of the modern canids.

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Authors and Affiliations

  1. Institute of Cytology and Genetics, SB RAS, Novosibirsk, 630090, Russia

    Alexander S. Graphodatsky, Polina L. Perelman, Natalya V. Sokolovskaya, Violetta R. Beklemisheva & Natalya A. Serdukova

  2. Laboratory of Genomic Diversity, National Cancer Institute, Frederick, MD, 21702, USA

    Polina L. Perelman & Stephen J. O’Brien

  3. Institut de Recherche pour le Développement, Centre de Biologie et Gestion des Populations, Campus International de Baillarguet, CS30016, 34988, Montferrier-sur-Lez, France

    Gauthier Dobigny

  4. Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK

    Malcolm A. Ferguson-Smith

  5. The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

    Fengtang Yang

Authors
  1. Alexander S. Graphodatsky
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  2. Polina L. Perelman
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  3. Natalya V. Sokolovskaya
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  4. Violetta R. Beklemisheva
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  5. Natalya A. Serdukova
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  6. Gauthier Dobigny
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  7. Stephen J. O’Brien
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  8. Malcolm A. Ferguson-Smith
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  9. Fengtang Yang
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Corresponding author

Correspondence to Alexander S. Graphodatsky.

Electronic supplementary material

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Supplementary Figure S1

Diploid G-banded karyotype of fennec fox and gray fox. Summary of hybridization pattern of domestic dog probes onto G-banded fennec fox and gray fox chromosomes (JPEG 501 kb)

Supplementary Figure S2

A single tree retrieved from PAUP analysis of 88 characters rooted on bears, with changes mapped onto the topology. Bootstrap values are provided above branches (JPEG 769 kb)

Supplementary Table S1

Matrix of chromosomal characters corresponding to presence (1) or absence (0) of segmental associations of dog chromosomal fragments (XLS 96 kb)

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Graphodatsky, A.S., Perelman, P.L., Sokolovskaya, N.V. et al. Phylogenomics of the dog and fox family (Canidae, Carnivora) revealed by chromosome painting. Chromosome Res 16, 129–143 (2008). https://doi.org/10.1007/s10577-007-1203-5

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  • DOI: https://doi.org/10.1007/s10577-007-1203-5

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