A Cat Genome Model For Discovery Of Traits Of Human Disease Significance

A female Abyssinian cat, served as the DNA source for all sequencing reads.  From this source: 6.7 million plasmid, 1.3 million fosmid end reads (Sanger), 6x fragments, 6x 3 kb paired reads (454), BAC ends (Sanger), and 20x 300bp insert (Illumina) sequences were generated.  As a starting point, we have produced a reference genome Felis catus 6.2 with an N50 contig and scaffold length of 21 kb and 4.7 Mb, respectively.  There are 2.43 Gb (including Ns in gaps) on ordered/oriented chromosomes (n=19), nearly 15.4 M bases with random chromosome positions (unlocalized), and more than 11 M unplaced bases.  This version 6.2 has a preliminary gene set of 17,780 mostly predicted from human gene evidence.  In the most recent iteration of the cat reference assembly, all reads were assembled (Celera assembler) resulting in increased contiguity, N50 of 25 kb and 20 Mb contig and scaffold length, respectively.  This Felis catus version 7.0 is being prepared for submission as a set of chromosomal sequences.  At present, we are examining the presence of disruptive somatic gene mutations in several fancy breeds (Maine Coon, Norwegian Forest, Birman, Egyptian Mau, Turkish Van, and Japanese Bobtail) and a wildcat mix (Felis silvestris), derived from mapped Illumina reads using our variant calling pipeline on the Felis catus 6.2 version.  Finally, we plan to estimate copy number variants as a possible source of normal and pathogenic differences in various cat breeds.