Initial sequence and comparative analysis of the cat genome

Joan U. Pontius, James C. Mullikin, Douglas R. Smith, Kerstin Lindblad-Toh, Sante Gnerre, Michele Clamp, Jean Chang, Robert Stephens, Beena Neelam, Natalia Volfovsky, Alejandro A. Schäffer, Richa Agarwala, Kristina Narfström, William J. Murphy, Urs Giger, Alfred L. Roca, Agostinho Antunes, Marilyn Menotti-Raymond, Naoya Yuhki, Jill Pecon-SlatteryWarren E. Johnson, Guillaume Bourque, Glenn Tesler, Stephen J. O'Brien, Adrianne Brand, Heather Ebling, David J. Saranga, Marc Rubenfield, Matthew J. Parisi, Wei Tao, Nadeem Tusneem, Robert David, Erick Gustafson, Jason Tsolas, Keven McKernan

Research output: Contribution to journalArticlepeer-review

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.

Original languageEnglish (US)
Pages (from-to)1675-1689
Number of pages15
JournalGenome Research
Volume17
Issue number11
DOIs
StatePublished - Nov 2007
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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