what can a tiger’s genome tell us about mammalian evolution?
TRANSCRIPT
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What can a tiger’s genome tell us about mammalian evolution?
A review of Cho, et al. 2013. The tiger genome and comparative analysis with lion and snow leopard genomes. Nature. 4:2433. by Courtney Dunn
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Introduction▪ Panthera tigris exists as the largest
felid species on Earth as well as one of the most endangered species known, functioning as a keystone species.
▪ Population estimates range from 3,050 to 3,950 individuals
▪ Nine genetically identifiable subspecies have been named of which four have went extinct in the last century
▪ The Amur subspecies is the largest and the only one which does not live in a tropical, warm climate.
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A New Genetic Realm▪ Previous studies have elucidated the
phylogeography and population genetics of tigers▪ Relied primarily on mitochondrial and nuclear
loci▪ Domestic cat (Felis catus), although a low
coverage genome, has provided further insights.▪ No whole-genome reference sequences have
been reported for any Panthera species
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Objectives1. Sequence the first tiger genome
through assembly and annotation.2. Compare sequences to Panthera uncia
to determine genetic adaptations specific to high-altitude habitats.
3. Determine mutations responsible for white coat coloration in Panthera leo and Panthera tigris.
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Methods▪Genome sequence assembly and annotation▪Orthologous gene families▪Gene evolution▪ Chromosomal rearrangement▪Demographic history
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Genome Sequence Assembly and Annotation▪ Blood samples for Amur tiger, white Bengal
tiger, African lion, and African lion acquired from the Everland Zoo of Korea.▪ Muscle sample for a Mongolian snow leopard
was obtained from the Conservation Genome Resource Bank at Seoul National University▪ Sequenced using HiSeq2000 with read and
insert lengths of approx. 90 bp and 400 bp. ▪ Assembled by SOAPdenovo▪ De novo prediction using AUGUSTUS (version
2.5.5) and GENSCAN (version 1.0)
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Orthologous gene families▪ The expansion and contraction of the orthologous
protein families using seven mammalian species (tiger, cat, dog, human, mouse, giant panda and opossum) via CAFE´ 2.2 and Fisher’s exact test.▪ Multiple sequence alignment (CLUSTALW2)▪ Chromosomal rearrangement from SyMap and
LASTZ software.▪ Markovian coalescent model for population size
history analysis
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The Amur tiger genome▪ Core eukaryotic genes revealed
homologues for >93.4% of conserved genes.▪ Tiger genome has 95.6%
similarity to the domestic cat – evolutionary divergence 10.8 million years ago (MYA)▪ Such a similarity was used to
improve the tiger genome assembly via a recently completed high coverage domestic cat genome.
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Adaptation of the big cats▪ Assembled Amur genome predicted
to contain 2,935 non-coding RNAs and 20,226 protein-coding genes.
▪ Gene clusters constructed using seven mammalian genomes
▪ Tiger proteome contained 14,954 orthologous gene families – of which:▪ 14,425 shared by all seven comparison
genomes▪ 103 exclusively shared by the cat and
tiger▪ Amur tiger genome displays 381
expanded and 1,70 contracted gene families compared with the feline common ancestor
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Genome Enrichment Areas
▪ Olfactory receptor activity▪ G-protein coupled receptor
signaling pathway▪ Signal transducer activity▪ Amino-acid transport▪ Protein metabolic process
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Lineage-specific amino acid changes
▪ Compared to human, dog, and mouse▪ 3,646 gene changes specific to big cats▪ 5,882 gene changes unique to the felid lineage▪ 1,376 related to protein function changes
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Metabolism Pathway Alteration▪ Panthera specific changes associated with
proteins and fatty acids a.k.a energy acquisition.▪ Histidine, beta-alanine, phenylalanine
valine, leucine and isoleucine degradation, cysteine and methoionine , fatty acid, and fat digestion and absorption.▪ Reflective of an obligatory carnivorous diet.
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Positive Selection Genes
▪ Over-represented in muscle filament sliding (MYH7, TPM4, MYO1A), stress fiber (MYH7, TPM4, and ACTN4)▪ Significantly altered Ka/Ks ratios
of non-synonymous to synonymous substitutions revealed evidence of rapid evolution for muscle strength, energy metabolism, and sensory nerves.
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Genetic Landscape of the Snow Leopard▪ The study investigated the
genetic basis of several unique physiological and phenotypic traits.▪ Snow leopards are adapted to life
in extreme alpine areas in Central Asia▪ Previous genome-wide association
studies have revealed two human loci responsible for high-altitude adaptation – EGLN1 and EPAS1 - as well as in Naked mole rats.
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Genetic Landscape of the Snow Leopard
▪ The study revealed Snow Leopards have unique amino-acid changes in both which were not found in any other species including Lys39 (Polar) -> Met39 (Non-Polar)▪ Lys39 has been shown to occur
monomorphically in Panthera and Neofelis individuals.▪ Variants may have contributed to this species
acquisition of a unique ecological niche.
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White Tigers and Lions – Mystery solved?
▪ Tyrosinase (TYR) variants are responsible for albinism in humans and white coats in domestic cats.
▪ However, an amino-acid change in the transporter protein SLC45A2 was found responsible for White tigers.
▪ Examination of pigment-associated gene for White lion revealed a change from +Arg87 to Gln87, a mutation known as TYR260G>A.
▪ The concordance between the expected and observed genotype was 100% for the mutation in 47 examined lions.
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Genomic Comparison between Tiger and other Mammals
▪ Tiger and cat genomes showed very similar repeat compositions – 39.3% vs 39.2% respectively – as well as transposable elements and repeat components suggesting a similar genome architecture. ▪ Alignment of tiger scaffolds to cat
genomes revealed 571 out of 674 tiger scaffolds were alignment – 98.8% gene-coding regions and 98.3% of conserved synteny blocks.▪ High level of genomic synteny – six
breaks with large chromosomal segment rearrangement.
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Synteny and Collinear Rearrangement
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Genomic Comparison between Tiger and other Mammals
▪Divergence among closely-related species is an important factor underlying species diversification.▪Gene flow requires recombination in collinear chromosomes.▪ Such recombination results in a partial reproductive barrier.
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Within-Species Diversity▪ Measured by the rate of heterozygous
SNVS – single nucleotide variants▪ Tiger (0.00049 – 0.00073), Lion (0.00048
– 0.00058), Human (0.00066).▪ Diversity of Snow leopard genomes was
nearly half that of other Panthera species and slightly lower than that of the Tasmanian devil.
▪ Based on mitochondrial DNA coalescence, a marked bottleneck occurred around the last glacial maximum 20,000 years ago and 72-108,000 years ago
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Within-Species Diversity
▪White lion (0.00048)▪Domestic cat (0.00012)▪Multiple rounds of close in-breeding may have resulted in such low SNV diversity.
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Discussion▪ The Amur tiger genome was the first reference genome
for the Panthera lineage and only the second for Felidae species.▪ Predicted possible molecular adaptations consistent with
big cats obligatory meat diet, muscle strength, and predatory behavior.▪ Similarity between cat and tiger genomes could be
supported by their recent species divergence – approx. 11 million years ago.▪ Breaks in synteny could be due to rare, sporadic
accumulated exchanges over evolutionary time.▪ Close species comparative genomics approach with one
reference species heralds a new level of genomic studies.
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Discussion▪ If sufficiently distinct phenotypes are
biologically curated, genetic mutations causing species specificity can be systematically detected using next generation sequencing.▪ e.g. phenotypic analysis of White lions using
47 individuals▪ Utilizing whole genomes for variation
comparison has and can provide valuable insight for a whole family’s conservation – especially related to local adaptation and potential inbreeding/outbreeding.
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Questions?