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.

Figure 1.

Homologous synteny blocks (HSBs) of the cat genome as compared to corresponding syntenic blocks in five mammalian species: (Cfa) Canis familiaris, (Hsa) Homo sapiens, (Ptr) Pan troglodytes, (Mmu) Mus musculus, and (Rno) Rattus norvegicus. The empty line between blocks indicates ambiguous regions, which may arise, for example from gaps in the genome assemblies. White regions with red borders represent alignments to unplaced contigs. Black triangle represents approximate centromere position.

Figure 2.

Counts and rates of chromosome rearrangements detected among human, chimpanzee, cat, dog, mouse, and rat genomes, based on HSBs of at least 500 kb. Branches are labeled on the top with the estimated minimum number of intrachromosomal rearrangements (inversions) plus interchromosomal rearrangements (translocations, fissions, and fusions). Branches are labeled on the bottom with the estimated minimum rates of intrachromosomal plus interchromosomal rearrangements per million yr. The ancestors are BA (Boreoeutherian), EA (Euarchontoglires), CDA (cat/dog), MRA (mouse/rat), and PHA (chimpanzee/human).

Figure 3.

Phylogenetic analyses of felid mitochondrial (cymt) and homologous domestic cat numt sequences. Divergence dates of numt lineages-defining nodes were estimated following Lopez et al. (1994). Divergence dates (in gray boxes) assumed for the Felidae radiation and the represented species of the domestic cat lineage were retrieved from Johnson et al. (2006). Bootstrap values, calculated from 1000 replications, are placed at each branchpoint. (A) Minimum-evolution condensed tree (50% cutoff value) of a 570-bp segment of the mtDNA NADH dehydrogenase subunit I (NDI is a gene segment represented in the Lopez-numt) and homologous numt detected by BLAST searches in F. catus. (Black rectangle) The phylogenetically informative 10-bp deletion shared by all representatives of the Lopez-numt lineage. The symbols (+) and (−) represent the orientation of the genomic DNA sequence. The numt sequences are labeled using trace (ti), scaffold, GenBank accession, and chromosome. (B) Minimum-evolution condensed tree (50% cutoff value) of a 426-bp segment of the mtDNA cytochrome b (CytB is a gene segment not represented in the Lopez-numt) and several homologous numts detected by BLAST searches in F. catus. The cymt sequences are labeled with a three-letter code: (Fca) F. catus, domestic cat; (Fsi) Felis silvestris, European wild cat; (Fli) Felis libyca, African wild cat; (Fbi) Felis bieti, Chinese desert cat; (Nne) Neofelis nebulosa, clouded leopard; (Pti) Panthera tigris, tiger; (Pun) Panthera uncia, snow leopard; (Ple) Panthera leo, lion; and outgroup (Ccr) Crocuta crocuta, spotted hyena.

Figure 4.

Phylogenetic relationship among endogenous retroviruses. (A) Endogenous FeLV present in the genome of the domestic cat. Analysis is based on a 274-bp alignment of 13 previously published proviral LTRs (GenBank accessions) and 47 cat genomic sequences (trace IDs). Strong bootstrap support suggests that the proviral sequences fall into two groups, as labeled. The maximum parsimony tree is shown (length = 39, CI = 0.923, RC = 0.911). Bootstrap support (>70%) is indicated for maximum parsimony, neighbor joining, and maximum likelihood methods. (B) FERV-1. Phylogenetic relationships among previously identified retroviruses and a novel retroelement sequence in the cat genome. One copy of the novel provirus (FERV-1) in an unpublished BAC sequence was used to generate the maximum parsimony (MP) tree (length = 142, CI = 0.915, RC = 0.851), based on the predicted sequence of 205 amino acids of Pol. The number of steps is listed above the branches, while MP bootstrap support is indicated below the branches of the major clades.

Figure 5.

Homozygosity across Cinnamon’s chromosomes represented in non-overlapping windows of 100 kb. (Red) Regions with more than two SNPs per 100 kb; (green) homozygous regions (<2 SNPs/100 kb); (white gaps) gaps in the chromosome assembly.

Figure 6.

Gene Annotation Region Field (GARFIELD genome browser; http://lgd.abcc.ncifcrf.gov) showing the region of the cat genome corresponding to the taste receptor gene TAS1R2 on chromosome C1 at two levels of resolution. (A) Chromosome view showing homologous synteny blocks (HSBs) for dog, human, and mouse; representation of G+C density; density of repetitive elements; and heterozygosity of chromosome C1. (B) A 110-kb view, CSBs, putative cat genes, regions that align to annotated genes in other mammalian genomes, STRs, fosmid reads with their partners, and contigs and scaffolds for the region. The GARFIELD name and image are used with permission from TM & Paws, Inc. All Rights Reserved; http://www.garfield.com.

Figure 7.

FLA annotation from finished BAC sequence (RPCI 86 BAC library constructed from the DNA of a domestic cat, Gus) and 1.9× WGS contigs alignment with three MHC models (Yuhki et al. 2003; Beck et al. 2005). Two segments of cat MHC (FLA) sequences—2.976-Mb B2cen MHC sequence and 0.0362-Mb B2ter MHC sequence—were assembled based on the human HLA sequence (The MHC Sequencing Consortium 1999). Gene annotation of this FLA sequence was performed using the GENSCAN (Burge and Karlin 1997) program. Genes with forward and reverse orientations were placed as solid blocks above and below the line, respectively. A gap position of these two FLA sequences is indicated as double slash lines. Contigs from the 1.9× WGS genome sequence were aligned using the Cross_match program with three models—FLA, DLA (canFam2), and HLA (hg17 assembly), respectively. These three sets of contig alignments were compared and highlighted with different colors with the following categories: (red) conserved sequence blocks with the same order between FLA and DLA shown on FLA and DLA lines or between FLA and HLA shown on the HLA line; (green) nonconserved sequences between FLA/DLA or FLA/HLA but a part of FLA sequences conserved in other genomic regions in dog and human and translocated to MHC regions in DLA or HLA; (multiple colors) conserved sequence blocks between FLA/DLA or FLA/HLA with different order; (pink) FLA-specific blocks; (white) no 2× WGS contigs were aligned in DLA or HLA.