New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger
<i>Panthera tigris</i> is a top predator that maintains the integrity of forest ecosystems and is an integral part of biodiversity. No more than 400 Amur tigers (<i>P. t. altaica</i>) are left in the wild, whereas the South China tiger (<i>P. t. amoyensis</i>) is...
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MDPI AG
2022-07-01
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| Series: | Animals |
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| Online Access: | https://www.mdpi.com/2076-2615/12/14/1817 |
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| author | Hairong Du Jingjing Yu Qian Li Minghai Zhang |
| author_facet | Hairong Du Jingjing Yu Qian Li Minghai Zhang |
| author_sort | Hairong Du |
| collection | DOAJ |
| description | <i>Panthera tigris</i> is a top predator that maintains the integrity of forest ecosystems and is an integral part of biodiversity. No more than 400 Amur tigers (<i>P. t. altaica</i>) are left in the wild, whereas the South China tiger (<i>P. t. amoyensis</i>) is thought to be extinct in the wild, and molecular biology has been widely used in conservation and management. In this study, the genetic information of Amur tigers and South China tigers was studied by whole-genome sequencing (WGS). A total of 647 Gb of high-quality clean data was obtained. There were 6.3 million high-quality single-nucleotide polymorphisms (SNPs), among which most (66.3%) were located in intergenic regions, with an average of 31.72% located in coding sequences. There were 1.73 million insertion-deletions (InDels), among which there were 2438 InDels (0.10%) in the coding region, and 270 thousand copy number variations (CNVs). Significant genetic differences were found between the Amur tiger and the South China tiger based on a principal component analysis and phylogenetic tree. The linkage disequilibrium analysis showed that the linkage disequilibrium attenuation distance of the South China tiger and the Amur tiger was almost the same, whereas the r<sup>2</sup> of the South China tiger was 0.6, and the r<sup>2</sup> of the Amur tiger was 0.4. We identified functional genes and regulatory pathways related to reproduction, disease, predation, and metabolism and characterized functional genes related to survival in the wild, such as smell, vision, muscle, and predatory ability. The data also provide new evidence for the adaptation of Amur tigers to cold environments. <i>PRKG1</i> is involved in temperature regulation in a cold climate. <i>FOXO1</i> and <i>TPM4</i> regulate body temperature to keep it constant. Our results can provide genetic support for precise interspecies conservation and management planning in the future. |
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| last_indexed | 2024-03-09T10:23:55Z |
| publishDate | 2022-07-01 |
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| series | Animals |
| spelling | doaj.art-2e47c45b6669414eb6ebc6a6ab54fc1f2023-12-01T21:48:33ZengMDPI AGAnimals2076-26152022-07-011214181710.3390/ani12141817New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China TigerHairong Du0Jingjing Yu1Qian Li2Minghai Zhang3College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, ChinaCollege of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang 550025, ChinaCollege of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China<i>Panthera tigris</i> is a top predator that maintains the integrity of forest ecosystems and is an integral part of biodiversity. No more than 400 Amur tigers (<i>P. t. altaica</i>) are left in the wild, whereas the South China tiger (<i>P. t. amoyensis</i>) is thought to be extinct in the wild, and molecular biology has been widely used in conservation and management. In this study, the genetic information of Amur tigers and South China tigers was studied by whole-genome sequencing (WGS). A total of 647 Gb of high-quality clean data was obtained. There were 6.3 million high-quality single-nucleotide polymorphisms (SNPs), among which most (66.3%) were located in intergenic regions, with an average of 31.72% located in coding sequences. There were 1.73 million insertion-deletions (InDels), among which there were 2438 InDels (0.10%) in the coding region, and 270 thousand copy number variations (CNVs). Significant genetic differences were found between the Amur tiger and the South China tiger based on a principal component analysis and phylogenetic tree. The linkage disequilibrium analysis showed that the linkage disequilibrium attenuation distance of the South China tiger and the Amur tiger was almost the same, whereas the r<sup>2</sup> of the South China tiger was 0.6, and the r<sup>2</sup> of the Amur tiger was 0.4. We identified functional genes and regulatory pathways related to reproduction, disease, predation, and metabolism and characterized functional genes related to survival in the wild, such as smell, vision, muscle, and predatory ability. The data also provide new evidence for the adaptation of Amur tigers to cold environments. <i>PRKG1</i> is involved in temperature regulation in a cold climate. <i>FOXO1</i> and <i>TPM4</i> regulate body temperature to keep it constant. Our results can provide genetic support for precise interspecies conservation and management planning in the future.https://www.mdpi.com/2076-2615/12/14/1817Amur tigerSouth China tigerwhole-genome sequencingenvironmental adaptationgenetic evolution |
| spellingShingle | Hairong Du Jingjing Yu Qian Li Minghai Zhang New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger Animals Amur tiger South China tiger whole-genome sequencing environmental adaptation genetic evolution |
| title | New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger |
| title_full | New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger |
| title_fullStr | New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger |
| title_full_unstemmed | New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger |
| title_short | New Evidence of Tiger Subspecies Differentiation and Environmental Adaptation: Comparison of the Whole Genomes of the Amur Tiger and the South China Tiger |
| title_sort | new evidence of tiger subspecies differentiation and environmental adaptation comparison of the whole genomes of the amur tiger and the south china tiger |
| topic | Amur tiger South China tiger whole-genome sequencing environmental adaptation genetic evolution |
| url | https://www.mdpi.com/2076-2615/12/14/1817 |
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