Biology Faculty Articles
Document Type
Article
Publication Date
11-2007
Publication Title
Genome Research
ISSN
1088-9051
Volume
17
Issue/No.
11
First Page
1675
Last Page
1689
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.
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
ORCID ID
0000-0001-7353-8301
ResearcherID
N-1726-2015
Comments
©2007 by Cold Spring Harbor Laboratory Press