Initial sequence and comparative analysis of the cat genome.
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 approximately 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.
Pontius
Joan U
JU
Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA. Pontiusj@ncifcrf.gov
Mullikin
James C
JC
Smith
Douglas R
DR
Lindblad-Toh
Kerstin
K
Gnerre
Sante
S
Clamp
Michele
M
Chang
Jean
J
Stephens
Robert
R
Neelam
Beena
B
Volfovsky
Natalia
N
Schäffer
Alejandro A
AA
Agarwala
Richa
R
Narfström
Kristina
K
Murphy
William J
WJ
Giger
Urs
U
Roca
Alfred L
AL
Antunes
Agostinho
A
Menotti-Raymond
Marilyn
M
Yuhki
Naoya
N
Pecon-Slattery
Jill
J
Johnson
Warren E
WE
Bourque
Guillaume
G
Tesler
Glenn
G
O'Brien
Stephen J
SJ
D000818:Animals; D002415:Cats / Q000235:genetics*; D004285:Dogs; D016678:Genome; D023281:Genomics; D006801:Humans; D051379:Mice; D035683:MicroRNAs; D018895:Microsatellite Repeats; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D051381:Rats; D012091:Repetitive Sequences, Nucleic Acid
D035683:MicroRNAs