title: Initial sequence and comparative analysis of the cat genome.
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 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.
authors.affiliation: Laboratory of Genomic Diversity, SAIC-Frederick, Inc., NCI-Frederick, Frederick, Maryland 21702, USA. Pontiusj@ncifcrf.gov
authors.forename: Joan U
authors.initials: JU
authors.lastname: Pontius
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.forename: Douglas R
authors.initials: DR
authors.lastname: Smith
authors.forename: Kerstin
authors.initials: K
authors.lastname: Lindblad-Toh
authors.forename: Sante
authors.initials: S
authors.lastname: Gnerre
authors.forename: Michele
authors.initials: M
authors.lastname: Clamp
authors.forename: Jean
authors.initials: J
authors.lastname: Chang
authors.forename: Robert
authors.initials: R
authors.lastname: Stephens
authors.forename: Beena
authors.initials: B
authors.lastname: Neelam
authors.forename: Natalia
authors.initials: N
authors.lastname: Volfovsky
authors.forename: Alejandro A
authors.initials: AA
authors.lastname: Schäffer
authors.forename: Richa
authors.initials: R
authors.lastname: Agarwala
authors.forename: Kristina
authors.initials: K
authors.lastname: Narfström
authors.forename: William J
authors.initials: WJ
authors.lastname: Murphy
authors.forename: Urs
authors.initials: U
authors.lastname: Giger
authors.forename: Alfred L
authors.initials: AL
authors.lastname: Roca
authors.forename: Agostinho
authors.initials: A
authors.lastname: Antunes
authors.forename: Marilyn
authors.initials: M
authors.lastname: Menotti-Raymond
authors.forename: Naoya
authors.initials: N
authors.lastname: Yuhki
authors.forename: Jill
authors.initials: J
authors.lastname: Pecon-Slattery
authors.forename: Warren E
authors.initials: WE
authors.lastname: Johnson
authors.forename: Guillaume
authors.initials: G
authors.lastname: Bourque
authors.forename: Glenn
authors.initials: G
authors.lastname: Tesler
authors.forename: Stephen J
authors.initials: SJ
authors.lastname: O'Brien
mesh_terms: 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
chemical_list: D035683:MicroRNAs