Post by Vodmeister on Feb 10, 2016 12:39:19 GMT 5
The tiger genome and comparative analysis with lion and snow leopard genomes
Abstract
Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.
Introduction
The tiger (Panthera tigris), the largest felid species on Earth and a widely recognized symbol for wildlife conservation1, is one of the world’s most endangered species. Tigers are a keystone species and natural indicators of the health of the ecological communities in which they are found2. The current estimates of wild tigers range from just 3,050 to 3,950 individuals. It is postulated that without conservation measures tigers will soon become extinct in the wild, thus turning the preservation of existing wild tiger populations into a major goal of conservation efforts3, 4. Tigers comprise of nine genetically validated subspecies1, 5, 6. Four of these went extinct in the wild during the last century (Javan, Balinese, South China and Caspian tigers), leaving five extant subspecies (Amur, Bengal, Indochinese, Malayan and Sumatran tigers)5. The Amur tiger (Panthera tigris altaica) is the largest in overall size and the only subspecies inhabiting snow-covered regions.
Previous genetic studies using mitochondrial and nuclear loci have helped to elucidate the phylogeography and population genetics of tigers1, 5, 6, 7, and the low coverage genome (1.8 × ) of the domestic cat (Felis catus) has provided insights into felid evolution8, 9. However, no whole-genome reference sequence has been reported for the tiger, or any of the Panthera species, thus limiting current understanding of genetic diversity and demography10, 11, 12.
We report the first tiger genome sequence assembly and annotation as well as a comparative analysis of the lion (Panthera leo) and snow leopard (Panthera uncia) genomes. We describe genotypic variation and genotype association analyses with species-specific phenotypes and adaptation. Panthera whole-genome sequences provide valuable information on genome organization, evolutionary divergence and overall endemic diversity.
See full study here
www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html
Natural Born Killers
"Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct," Bhak said.
Some gene differences are apparent in the mapping, such as two genes likely involved in adaptation to high altitudes and thin air in snow leopards and white fur in white African lions.
But overall, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein, the study shows, seen widely across the study species. The genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago, the study authors suggest.
"I take this to indicate that have evolved to fill a very particular carnivorous niche in the environment that is predicated on the advantages in hunting these genes provide," said Bhak.
Domestic cats also have many of these same genes, he said. "All the cats are unparalleled hunters, and here we are seeing some of the genetic reasons."
news.nationalgeographic.com/news/2013/13/130917-tiger-genome-sequenced-siberian-lion-cats-science/
Abstract
Tigers and their close relatives (Panthera) are some of the world’s most endangered species. Here we report the de novo assembly of an Amur tiger whole-genome sequence as well as the genomic sequences of a white Bengal tiger, African lion, white African lion and snow leopard. Through comparative genetic analyses of these genomes, we find genetic signatures that may reflect molecular adaptations consistent with the big cats’ hypercarnivorous diet and muscle strength. We report a snow leopard-specific genetic determinant in EGLN1 (Met39>Lys39), which is likely to be associated with adaptation to high altitude. We also detect a TYR260G>A mutation likely responsible for the white lion coat colour. Tiger and cat genomes show similar repeat composition and an appreciably conserved synteny. Genomic data from the five big cats provide an invaluable resource for resolving easily identifiable phenotypes evident in very close, but distinct, species.
Introduction
The tiger (Panthera tigris), the largest felid species on Earth and a widely recognized symbol for wildlife conservation1, is one of the world’s most endangered species. Tigers are a keystone species and natural indicators of the health of the ecological communities in which they are found2. The current estimates of wild tigers range from just 3,050 to 3,950 individuals. It is postulated that without conservation measures tigers will soon become extinct in the wild, thus turning the preservation of existing wild tiger populations into a major goal of conservation efforts3, 4. Tigers comprise of nine genetically validated subspecies1, 5, 6. Four of these went extinct in the wild during the last century (Javan, Balinese, South China and Caspian tigers), leaving five extant subspecies (Amur, Bengal, Indochinese, Malayan and Sumatran tigers)5. The Amur tiger (Panthera tigris altaica) is the largest in overall size and the only subspecies inhabiting snow-covered regions.
Previous genetic studies using mitochondrial and nuclear loci have helped to elucidate the phylogeography and population genetics of tigers1, 5, 6, 7, and the low coverage genome (1.8 × ) of the domestic cat (Felis catus) has provided insights into felid evolution8, 9. However, no whole-genome reference sequence has been reported for the tiger, or any of the Panthera species, thus limiting current understanding of genetic diversity and demography10, 11, 12.
We report the first tiger genome sequence assembly and annotation as well as a comparative analysis of the lion (Panthera leo) and snow leopard (Panthera uncia) genomes. We describe genotypic variation and genotype association analyses with species-specific phenotypes and adaptation. Panthera whole-genome sequences provide valuable information on genome organization, evolutionary divergence and overall endemic diversity.
See full study here
www.nature.com/ncomms/2013/130917/ncomms3433/full/ncomms3433.html
Natural Born Killers
"Genetically all the cats are very close, so we need close genetic mapping to find the small differences that make them distinct," Bhak said.
Some gene differences are apparent in the mapping, such as two genes likely involved in adaptation to high altitudes and thin air in snow leopards and white fur in white African lions.
But overall, the cat family seems to rely on a narrow set of 1,376 genes linked to strong muscle fibers and digestion of protein, the study shows, seen widely across the study species. The genes likely originated in large part with the earliest common ancestor of big felines some 11 million years ago, the study authors suggest.
"I take this to indicate that have evolved to fill a very particular carnivorous niche in the environment that is predicated on the advantages in hunting these genes provide," said Bhak.
Domestic cats also have many of these same genes, he said. "All the cats are unparalleled hunters, and here we are seeing some of the genetic reasons."
news.nationalgeographic.com/news/2013/13/130917-tiger-genome-sequenced-siberian-lion-cats-science/
