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Chai S, Chong Y, Yin D, Qiu Q, Xu S, Yang G. Genomic insights into adaptation to bipedal saltation and desert-like habitats of jerboas. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2516-9. [PMID: 38902451 DOI: 10.1007/s11427-023-2516-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/20/2023] [Indexed: 06/22/2024]
Abstract
Jerboas is a lineage of small rodents displaying atypical mouse-like morphology with elongated strong hindlimbs and short forelimbs. They have evolved obligate bipedal saltation and acute senses, and been well-adapted to vast desert-like habitats. Using a newly sequenced chromosome-scale genome of the Mongolian five-toed jerboa (Orientallactaga sibirica), our comparative genomic analyses and in vitro functional assays showed that the genetic innovations in both protein-coding and non-coding regions played an important role in jerboa morphological and physiological adaptation. Jerboa-specific amino acid substitutions, and segment insertions/deletions (indels) in conserved non-coding elements (CNEs) were found in components of proteoglycan biosynthesis pathway (XYLT1 and CHSY1), which plays an important role in limb development. Meanwhile, we found specific evolutionary changes functionally associated with energy or water metabolism (e.g., specific amino acid substitutions in ND5 and indels in CNEs physically near ROR2) and senses (e.g., expansion of vomeronasal receptors and the FAM136A gene family) in jerboas. Further dual-luciferase reporter assay verified that some of the CNEs with jerboa-specific segment indels exerted a significantly different influence on luciferase activity, suggesting changes in their regulatory function in jerboas. Our results revealed the potential molecular mechanisms underlying jerboa adaptation since the divergence from the Eocene-Oligocene transition, and provided more resources and new insights to enhance our understanding of the molecular basis underlying the phenotypic diversity and the environmental adaptation of mammals.
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Affiliation(s)
- Simin Chai
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Yujie Chong
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Daiqing Yin
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710072, China.
| | - Shixia Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
| | - Guang Yang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, School of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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Huang G, Zhang Y, Zhang W, Wei F. Genetic mechanisms of animal camouflage: an interdisciplinary perspective. Trends Genet 2024:S0168-9525(24)00073-8. [PMID: 38644132 DOI: 10.1016/j.tig.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/23/2024]
Abstract
Camouflage is a classic example of a trait wherein animals respond to natural selection to avoid predation or attract prey. This unique phenomenon has attracted significant recent attention and the rapid development of integrative research methods is facilitating advances in our understanding of the in-depth genetic mechanisms of camouflage. In this review article, we revisit camouflage definitions and strategies and then we examine the underlying mechanisms of the two most common forms of camouflage, crypsis and masquerade, that have recently been elucidated using multiple approaches. We also discuss unresolved questions related to camouflage. Ultimately, we highlight the implications of camouflage for informing various key issues in ecology and evolution.
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Affiliation(s)
- Guangping Huang
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yubo Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wei Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fuwen Wei
- Jiangxi Provincial Key Laboratory of Conservation Biology, College of Forestry, Jiangxi Agricultural University, Nanchang 330045, China; CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China.
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Song X, Jiang Y, Zhao L, Jin L, Yan C, Liao W. Predicting the Potential Distribution of the Szechwan Rat Snake ( Euprepiophis perlacea) and Its Response to Climate Change in the Yingjing Area of the Giant Panda National Park. Animals (Basel) 2023; 13:3828. [PMID: 38136865 PMCID: PMC10740900 DOI: 10.3390/ani13243828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Climate change is a significant driver of changes in the distribution patterns of species and poses a threat to biodiversity, potentially resulting in species extinctions. Investigating the potential distribution of rare and endangered species is crucial for understanding their responses to climate change and for the conservation of biodiversity and ecosystem management. The Szechwan rat snake (Euprepiophis perlacea) is an endemic and endangered species co-distributed with giant pandas, and studying its potential distribution contributes to a better understanding of the distribution pattern of endangered species. In this study, we confirmed seven presence points of this species in the Yingjing Area of the Giant Panda National Park, and selected eleven key factors to predict the potential distribution of E. perlacea under current and future scenarios using MaxEnt models. Our study consistently achieved AUC values exceeding 0.79, meeting the precision requirements of the models. The results indicated that the high potential distribution area of E. perlacea is mainly located near Yunwu mountain and the giant panda rewilding and reintroduction base, accounting for approximately 12% of the protected area. Moreover, we identified the primary environmental factors influencing the distribution of E. perlacea as the distance from streams and the slope degree, with their contribution rates exceeding 41% and 31%, respectively. In comparison to the current scenario, the potential habitat range for E. perlacea did not show an overall reduction in the context of future climate scenarios. To ensure the long-term preservation of E. perlacea, it is advisable to validate its actual distribution based on the models' results. Particular attention should be given to safeguarding its core distribution areas and raising awareness among residents within the potential distribution range about the conservation of E. perlacea.
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Affiliation(s)
- Xinqiang Song
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
- Daxiangling Provincial Nature Reserve, Ya’an 625200, China
| | - Ying Jiang
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
| | - Li Zhao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong 637009, China
- College of Panda, China West Normal University, Nanchong 637009, China
| | - Long Jin
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
- School of Ecology and Nature Conservation, Beijing Forestry University, Beijing 100083, China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong 637009, China
- College of Panda, China West Normal University, Nanchong 637009, China
| | - Chengzhi Yan
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong 637009, China
- College of Panda, China West Normal University, Nanchong 637009, China
| | - Wenbo Liao
- Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong 637009, China
- Key Laboratory of Artificial Propagation and Utilization in Anurans of Nanchong City, China West Normal University, Nanchong 637009, China
- College of Panda, China West Normal University, Nanchong 637009, China
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Schartl M. What the genome of the leafy seadragon teaches us about rapid evolution of camouflage and adaptations to life in the kelp forest. SCIENCE CHINA. LIFE SCIENCES 2023; 66:2692-2693. [PMID: 37405566 DOI: 10.1007/s11427-023-2368-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 07/06/2023]
Affiliation(s)
- Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Würzburg, Würzburg, 97074, Germany.
- The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, 78666, USA.
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Huang G, Song L, Du X, Huang X, Wei F. Evolutionary genomics of camouflage innovation in the orchid mantis. Nat Commun 2023; 14:4821. [PMID: 37563121 PMCID: PMC10415354 DOI: 10.1038/s41467-023-40355-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/20/2023] [Indexed: 08/12/2023] Open
Abstract
The orchid mantises achieve camouflage with morphological modifications in body color and pattern, providing an interesting model for understanding phenotypic innovation. However, a reference genome is lacking for the order Mantodea. To unveil the mechanisms of plant-mimicking body coloration and patterns, we performed de novo assembly of two chromosome-level genomes of the orchid mantis and its close relative, the dead leaf mantis. Comparative genomic analysis revealed that the Scarlet gene plays an important role in the synthesis of xanthommatin, an important pigment for mantis camouflage coloration. Combining developmental transcriptomic analysis and genetic engineering experiments, we found that the cuticle was an essential component of the 'petal-like' enlargement, and specific expression in the ventral femur was controlled by Wnt signaling. The prolonged expression of Ultrabithorax (Ubx) accompanied by femoral expansion suggested that Ubx determines leg remodeling in the early developmental stage. We also found evidence of evolution of the Trypsin gene family for insectivory adaptation and ecdysone-dependent sexual dimorphism in body size. Overall, our study presents new genome catalogs and reveals the genetic and evolutionary mechanisms underlying the unique camouflage of the praying mantis, providing evolutionary developmental insights into phenotypic innovation and adaptation.
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Affiliation(s)
- Guangping Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lingyun Song
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Du
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Huang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
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Zhang B, Xiao W, Qin G, Chen Z, Qiu L, Wang X, Lin Q. Gene loss and co-option of toll-like receptors facilitate paternal immunological adaptation in the brood pouch of pregnant male seahorses. Front Immunol 2023; 14:1224698. [PMID: 37588592 PMCID: PMC10426278 DOI: 10.3389/fimmu.2023.1224698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/04/2023] [Indexed: 08/18/2023] Open
Abstract
Male pregnancy in syngnathids (seahorses, pipefishes, and sea dragons) is an evolutionary innovation in the animal kingdom. Paternal immune resistance to the fetus is a critical challenge, particularly in seahorses with fully enclosed brood pouches and sophisticated placentas. In this study, comparative genomic analysis revealed that all syngnathid species lost three vertebrate-conserved Toll-like receptors (TLR1, TLR2, and TLR9), of which all play essential roles in immune protection and immune tolerance in the uterus and placenta. Quantitative real-time PCR (qRT-PCR) analysis showed that the TLR paralog genes including TLR18, TLR25, and TLR21 were highly expressed in the placenta inside the seahorse brood pouch and changed dynamically during the breeding cycle, suggesting the potentially important role of the TLRs during male pregnancy. Furthermore, the immune challenge test in vitro showed a remarkable expression response from all three TLR genes to specific pathogenic antigens, confirming their immune function in seahorse brood pouches. Notably, the altered antigen recognition spectrum of these genes appeared to functionally compensate in part for the lost TLRs, in contrast to that observed in other species. Therefore, we suggest that gene loss and co-option of TLRs may be a typical evolutionary strategy for facilitating paternal immunological adaptation during male pregnancy.
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Affiliation(s)
- Bo Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Wanghong Xiao
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, China
| | - Geng Qin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Sanya, China
| | - Zelin Chen
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Lihua Qiu
- Key Laboratory of South China Sea Fishery Resources Exploitation & Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- Key Laboratory of Aquatic Product Processing, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
| | - Xin Wang
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Qiang Lin
- CAS Key Laboratory of Tropical Marine Bio-Resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
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