Initial Sequence and Comparative Analysis of the Cat Genome

Authors

• J. U. Pontius, National Cancer Institute at Frederick
• James C. Mullikin, National Human Genome Research Institute
• Douglas R. Smith, Agencourt Bioscience Corporation
• Agencourt Bioscience Corporation
• Kerstin Lindblad-Toh, Broad Institute
• Sante Gnerre, Broad Institute
• Michele Clamp, Broad Institute
• Jean Chang, Broad Institute
• R. Stephens, National Cancer Institute at Frederick
• Beena A. Neelam, National Cancer Institute at Frederick
• Natalia Volfovsky, National Cancer Institute at Frederick
• Alejandro A. Schaffer, National Institutes of Health - Bethesda
• R. Agarwala, National Institutes of Health - Bethesda
• Kristina Narfstrom, University of Missouri - Columbia
• William J. Murphy, Texas A&M University
• Urs Giger, University of Pennsylvania
• Alfred L. Roca, National Cancer Institute at Frederick
• Agostinho Antunes, National Cancer Institute at Frederick; Universidade do Porto
• Marilyn Menotti-Raymond, National Cancer Institute at Frederick
• Naoya Yuhki, National Cancer Institute at Frederick
• Jill Pecon-Slattery, National Cancer Institute at Frederick
• Warren E. Johnson, National Cancer Institute at Frederick
• Guillaume Bourque, Genome Institute of Singapore
• Glenn Tesler, University of California - San Diego
• NISC Comparative Sequencing Program
• Stephen J. O'Brien, National Cancer Institute at FrederickFollow

ORCID

0000-0001-7353-8301

ResearcherID

N-1726-2015

Document Type

Article

Publication Title

Genome Research

ISSN

1088-9051

Publication Date

11-2007

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.

Volume

17

Issue

11

First Page

1675

Last Page

1689

Comments

©2007 by Cold Spring Harbor Laboratory Press

Additional Comments

National Cancer Institute contract #: N01-CO-12400; NIH grant #: NIH RR 02512

NSUWorks Citation

Pontius, J. U.; James C. Mullikin; Douglas R. Smith; Agencourt Bioscience Corporation; Kerstin Lindblad-Toh; Sante Gnerre; Michele Clamp; Jean Chang; R. Stephens; Beena A. Neelam; Natalia Volfovsky; Alejandro A. Schaffer; R. Agarwala; Kristina Narfstrom; William J. Murphy; Urs Giger; Alfred L. Roca; Agostinho Antunes; Marilyn Menotti-Raymond; Naoya Yuhki; Jill Pecon-Slattery; Warren E. Johnson; Guillaume Bourque; Glenn Tesler; NISC Comparative Sequencing Program; and Stephen J. O'Brien. 2007. "Initial Sequence and Comparative Analysis of the Cat Genome." Genome Research 17, (11): 1675-1689. https://nsuworks.nova.edu/cnso_bio_facarticles/782