Initial sequence and comparative analysis of the cat genome (original) (raw)

  1. Joan U. Pontius1,17,
  2. James C. Mullikin2,
  3. Douglas R. Smith3,
  4. Agencourt Sequencing Team3,16,
  5. Kerstin Lindblad-Toh4,
  6. Sante Gnerre4,
  7. Michele Clamp4,
  8. Jean Chang4,
  9. Robert Stephens5,
  10. Beena Neelam5,
  11. Natalia Volfovsky5,
  12. Alejandro A. Schäffer6,
  13. Richa Agarwala6,
  14. Kristina Narfström7,
  15. William J. Murphy8,
  16. Urs Giger9,
  17. Alfred L. Roca1,
  18. Agostinho Antunes10,11,12,
  19. Marilyn Menotti-Raymond10,
  20. Naoya Yuhki10,
  21. Jill Pecon-Slattery10,
  22. Warren E. Johnson10,
  23. Guillaume Bourque13,
  24. Glenn Tesler14,
  25. NISC Comparative Sequencing Program15, and
  26. Stephen J. O’Brien10,17
  27. 1 Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA;
  28. 2 Comparative Genomics Unit, National Human Genome Research Institute, Rockville, Maryland 20892, USA;
  29. 3 Agencourt Bioscience Corporation, Beverly, Massachusetts 01915, USA;
  30. 4 Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02141, USA;
  31. 5 Advanced Biomedical Computing Center, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA;
  32. 6 National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, Maryland 20894, USA;
  33. 7 Department of Ophthalmology (Mason Eye Institute), Department of Veterinary Medicine & Surgery, University of Missouri–Columbia, Columbia, Missouri 65211, USA;
  34. 8 Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas 77843, USA;
  35. 9 Section of Medical Genetics, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA;
  36. 10 Laboratory of Genomic Diversity, National Cancer Institute, Frederick, Maryland 21702, USA;
  37. 11 REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, 687, 4169-007 Porto, Portugal;
  38. 12 CIMAR, Centro Interdisciplinar de Investigação Marinha e Ambiental, Universidade do Porto, Rua dos Bragas, 177, 4050-123 Porto, Portugal;
  39. 13 Genome Institute of Singapore, Singapore 138672, Republic of Singapore;
  40. 14 Department of Mathematics, University of California, San Diego, California 92093-0112, USA;
  41. 15 NISC, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA

Abstract

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence.

Footnotes