Transcript Genomic legacy of the African cheeta, acinonyx jubatus

Dobrynin et al., Genome Biology, 2015
 The African cheetah
 Fastest land animal
 Ancestors were distributed in
the Americas, Europe and Asia
until ~10,000 – 12,000 years
ago
 Massive extinction reduced
their range to eastern and
southern Africa
 Likely evolved from common
ancestor with the American
puma
 Dramatic reduction in genetic variability due to bottleneck(s)
 Conservation icon symbol
 A model for the impacts of increased inbreeding
 Fastest land animal
 Actually seven genome sequences
 Main subject – Chewbaaka, a male from Namibia
 Seven mate-paired libraries of varying insert sizes (170 bp, 500 bp, 800 bp, 2000 bp,
5000 bp, 10,000 bp, and 20,000 bp)
 Sequenced to ~75x coverage and assembled using SOAPdenovo2
 Used the existing domestic cat genome to help with the assembly and map to
chromosomes
 Other six genomes were sequenced at 5-6X coverage using 500 bp insert libraries
 Genome size = 2.38-2.4 Gb
 N50 contigs = 28.2 kb
 N50 scaffolds = 3.1 Mb
 20,343 coding genes
 39.5% repetitive content
SNV rate in mammals.
 ‘Remarkable reduction in the cheetah’s
genic and genomic variability
 Lowest Single Nucleotide Variants among
11 other sequenced mammals
 90% lower than the domestic cat
Number of SNVs in protein-coding genes in felid
genomes.
 ‘Remarkable reduction in the
cheeta’s genic and genomic
variability
 Lowest Single Nucleotide Variants
among 11 other sequenced mammals
 90% lower than the domestic cat
 Very few variants in coding gene
complement
 ‘Remarkable reduction in the cheeta’s
genic and genomic variability
 Lowest Single Nucleotide Variants
among 11 other sequenced mammals
 90% lower than the domestic cat
 Very few variants in coding gene
complement
 10-15 fold longer stretches of
homozygous DNA when compared to
domestic cat
 93% of the genome is homozygous
The genome of Boris, an outbred feral domestic cat living in St. Petersburg (top) is compared to Cinnamon, a highly inbred Abyssinian
cat (Fca-6.2 reference for domestic cat genome sequence [19, 20], middle) and a cheetah (Chewbacca, bottom) as described here.
Approximately 15,000 regions of 100 Mb across the genome for each species were assessed for SNVs. Regions of high variability (
>40 SNVs/100 kbp) are colored red; highly homozygous regions (≤40 SNVs/100 kbp) are colored green. The first seven chromosome
homologues of the genomes of Boris, Cinnamon and Chewbacca are displayed for direct comparison.
 Population genomic analysis supports
“an expanding population that
subdivides into two bottlenecked
derivative populations”
 Cheetahs have reproductive problems
characteristic of inbreeding
depression
 92 genes with high rates of non-
synonymous mutations.
 18 were associated with reproduction
 946 genes with signatures of selection
 Several associated with cardiac and
muscle function
 Others associated with energy
production
 Are the changes to genes that are apparently adaptive for high-speed pursuit the
same as the genes associated with adaptations to high-altitude living?
 Do you find the same genes under selection in non-mammal speed demons?
 How could you test the hypothesis that the ‘energetic’ genes are actually associated
with high-speed pursuit evolution?