1
|
Lan T, Yang S, Li H, Zhang Y, Li R, Sahu SK, Deng W, Liu B, Shi M, Wang S, Du H, Huang X, Lu H, Liu S, Deng T, Chen J, Wang Q, Han L, Zhou Y, Li Q, Li D, Kristiansen K, Wan QH, Liu H, Fang SG. Large-scale genome sequencing of giant pandas improves the understanding of population structure and future conservation initiatives. Proc Natl Acad Sci U S A 2024; 121:e2406343121. [PMID: 39186654 PMCID: PMC11388402 DOI: 10.1073/pnas.2406343121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/23/2024] [Indexed: 08/28/2024] Open
Abstract
The extinction risk of the giant panda has been demoted from "endangered" to "vulnerable" on the International Union for Conservation of Nature Red List, but its habitat is more fragmented than ever before, resulting in 33 isolated giant panda populations according to the fourth national survey released by the Chinese government. Further comprehensive investigations of the genetic background and in-depth assessments of the conservation status of wild populations are still necessary and urgently needed. Here, we sequenced the genomes of 612 giant pandas with an average depth of ~26× and generated a high-resolution map of genomic variation with more than 20 million variants covering wild individuals from six mountain ranges and captive representatives in China. We identified distinct genetic clusters within the Minshan population by performing a fine-grained genetic structure. The estimation of inbreeding and genetic load associated with historical population dynamics suggested that future conservation efforts should pay special attention to the Qinling and Liangshan populations. Releasing captive individuals with a genetic background similar to the recipient population appears to be an advantageous genetic rescue strategy for recovering the wild giant panda populations, as this approach introduces fewer deleterious mutations into the wild population than mating with differentiated lineages. These findings emphasize the superiority of large-scale population genomics to provide precise guidelines for future conservation of the giant panda.
Collapse
Affiliation(s)
- Tianming Lan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shangchen Yang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haimeng Li
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin 150040, China
| | - Yi Zhang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Rengui Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Wenwen Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Boyang Liu
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Minhui Shi
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Shiqing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Hanyu Du
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyu Huang
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Haorong Lu
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Shanlin Liu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Deng
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Jin Chen
- China National GeneBank, BGI Research, Beijing Genomics Institute, Shenzhen 518120, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Lei Han
- Wildlife Evolution and Conservation Omics Laboratory, College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China
| | - Yajie Zhou
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Qiye Li
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- BGI Research, Beijing Genomics Institute, Wuhan 430074, China
| | - Desheng Li
- Key Laboratory of State Forestry and Grassland Administration (State Park Administration) on Conservation Biology of Rare Animals in the Giant Panda National Park, China Conservation and Research Center of Giant Panda, Dujiangyan 611830, China
| | - Karsten Kristiansen
- Department of Biology, University of Copenhagen, Copenhagen DK-2100, Denmark
- Qingdao-Europe Advanced Institute for Life Sciences, Qingdao 266555, China
| | - Qiu-Hong Wan
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
- Heilongjiang Key Laboratory of Complex Traits and Protein Machines in Organisms, Harbin 150040, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Beijing Genomics Institute, Shenzhen 518083, China
| | - Sheng-Guo Fang
- Key Laboratory of Biosystems Homeostasis & Protection (Ministry of Education), State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
2
|
Wei S, Fan H, Zhou W, Huang G, Hua Y, Wu S, Wei X, Chen Y, Tan X, Wei F. Conservation genomics of the critically endangered Chinese pangolin. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2540-y. [PMID: 38970727 DOI: 10.1007/s11427-023-2540-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/07/2024] [Indexed: 07/08/2024]
Abstract
The Chinese pangolin (Manis pentadactyla, MP) has been extensively exploited and is now on the brink of extinction, but its population structure, evolutionary history, and adaptive potential are unclear. Here, we analyzed 94 genomes from three subspecies of the Chinese pangolin and identified three distinct genetic clusters (MPA, MPB, and MPC), with MPB further divided into MPB1 and MPB2 subpopulations. The divergence of these populations was driven by past climate change. For MPB2 and MPC, recent human activities have caused dramatic population decline and small population size as well as increased inbreeding, but not decrease in genomic variation and increase in genetic load probably due to strong gene flow; therefore, it is crucial to strengthen in situ habitat management for these two populations. By contrast, although human activities have a milder impact on MPA, it is at high risk of extinction due to long-term contraction and isolation, and genetic rescue is urgently needed. MPB1 exhibited a relatively healthy population status and can potentially serve as a source population. Overall, our findings provide novel insights into the conservation of the Chinese pangolin and biogeography of the mammals of eastern Asia.
Collapse
Affiliation(s)
- Shichao Wei
- Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Huizhong Fan
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Guangping Huang
- Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Yan Hua
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, 510520, China
| | - Shibao Wu
- School of Life Science, South China Normal University, Guangzhou, 510631, China
| | - Xiao Wei
- Terrestrial Wildlife Rescue and Epidemic Diseases Surveillance Center of Guangxi, Nanning, 530003, China
| | - Yiting Chen
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Xinyue Tan
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Fuwen Wei
- Jiangxi Province Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
| |
Collapse
|
3
|
Shi M, Chen F, Sahu SK, Wang Q, Yang S, Wang Z, Chen J, Liu H, Hou Z, Fang SG, Lan T. Haplotype-resolved chromosome-scale genomes of the Asian and African Savannah Elephants. Sci Data 2024; 11:63. [PMID: 38212399 PMCID: PMC10784532 DOI: 10.1038/s41597-023-02729-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/07/2023] [Indexed: 01/13/2024] Open
Abstract
The Proboscidea, which includes modern elephants, were once the largest terrestrial animals among extant species. They suffered mass extinction during the Ice Age. As a unique branch on the evolutionary tree, the Proboscidea are of great significance for the study of living animals. In this study, we generate chromosome-scale and haplotype-resolved genome assemblies for two extant Proboscidea species (Asian Elephant, Elephas maximus and African Savannah Elephant, Loxodonta africana) using Pacbio, Hi-C, and DNBSEQ technologies. The assembled genome sizes of the Asian and African Savannah Elephant are 3.38 Gb and 3.31 Gb, with scaffold N50 values of 130 Mb and 122 Mb, respectively. Using Hi-C technology ~97% of the scaffolds are anchored to 29 pseudochromosomes. Additionally, we identify ~9 Mb Y-linked sequences for each species. The high-quality genome assemblies in this study provide a valuable resource for future research on ecology, evolution, biology and conservation of Proboscidea species.
Collapse
Affiliation(s)
- Minhui Shi
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Chen
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming, 650031, China
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming, 650031, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Qing Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
| | - Shangchen Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhihong Wang
- Southwest Survey and Planning Institute of National Forestry and Grassland Administration, Kunming, 650031, China
- Asian Elephant Research Center of National Forestry and Grassland Administration, Kunming, 650031, China
| | - Jin Chen
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
- China National GeneBank, BGI Research, Shenzhen, 518083, China
| | - Huan Liu
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI Research, Shenzhen, 518083, China
| | - Zhijun Hou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Tianming Lan
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, 150040, China.
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen, 518083, China.
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, 150040, China.
| |
Collapse
|
4
|
He K, Zhu Y, Yang SC, Ye Q, Fang SG, Wan QH. Major histocompatibility complex genomic investigation of endangered Chinese alligator provides insights into the evolution of tetrapod major histocompatibility complex and survival of critically bottlenecked species. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1078058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BackgroundThe major histocompatibility complex (MHC) gene family, a vital immune gene family in vertebrates, helps animals defend against pathogens. The polymorphism of MHC genes is important for a species and is considered to be caused by the numerous alleles of MHC antigen-presenting genes. However, the mechanism of this process is unclear due to the lack of data on the MHC structure. The evolutionary trajectories of the tetrapod MHC are also unclear because of insufficient studies on the reptile MHC architecture. Here, we studied the Chinese alligator (Alligator sinensis), which experienced a population bottleneck, but the population increased rapidly in the past 30 years and is proposed to have a unique MHC system to face pathogenic challenges.ResultsWe successfully constructed a 2 Mb MHC region using bacterial artificial chromosome (BAC) library and genome data of the Chinese alligator and checked the antigen-presenting genes using transcriptome data and the rapid amplification of cDNA ends (RACE) technique. The MHC architecture reported here uncovers adjacent Class I and Class II subregions and a unique CD1 subregion. This newly added information suggested that the Class I-II structure pattern was more ancient in tetrapods and helped reconstruct the evolution of the MHC region architecture. We also found multiple groups of MHC class I (MHC-I) (12 duplicated loci, belonging to three groups, two of which were novel) and MHC class II (MHC-II) (11 duplicated loci, belonging to two groups) inside the 2 Mb MHC region, and there were three more duplicated MHC-I loci outside it. These highly duplicated antigen-presenting loci had differences in expression, amino acid length of antigen-presenting exons, and splice signal of exon and intron, which together promoted the polymorphism of duplicated genes. Although the MHC antigen-presenting genes were identified as monomorphic or oligomorphic in our previous population study, the loci with high copy numbers and many differences can make up for this loss, presenting another mechanism for polymorphism in antigen presentation. These MHC-I and MHC-IIB loci with low polymorphism for each locus, but high numbers in all, may also contribute to MHC antigen-presenting binding variability in a population.ConclusionTo summarize, the fine MHC region architecture of reptiles presented in this study completes the evolutionary trajectories of the MHC structure in tetrapods, and these distinctive MHC gene groups in the Chinese alligator may have helped this species to expand rapidly in the past recent years.
Collapse
|