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Li W, Chen X, Yu J, Zhu Y. Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance. Sci China Life Sci 2024:10.1007/s11427-024-2580-3. [PMID: 38763999 DOI: 10.1007/s11427-024-2580-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/26/2024] [Indexed: 05/21/2024]
Abstract
Durian (Durio zibethinus) is a tropical fruit that has a unique flavor and aroma. It occupies a significant phylogenetic position within the Malvaceae family. Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling, resulting in an abundant genomic diversity. However, the ancestral karyotypes of the Malvaceae family, as well as the evolution trajectory leading to the 28 chromosomes in durian, remain poorly understood. Here, we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses. By analyzing the collinear blocks between cacao and durian, we inferred 11 Malvaceae ancestral karyotypes. These blocks were present in a single-copy form in cacao and mainly in triplicates in durian, possibly resulting from a recent whole genome triplication (WGT) event that led to hexaploidization of the durian genome around 20 (17-24) million years ago. A large proportion of the duplicated genes in durian, such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis, are derived directly from whole genome duplication, which makes it an important force in reshaping its genomic architecture. Transcriptome studies have revealed that genes involved in feruloyl-CoA formations were highly preferentially expressed in fruit peels, indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins. Among all the analyzed transcription factors (TFs), members of the heat shock factor family (HSF) were the most significantly upregulated under heat stress. All subfamilies of genes encoding heat shock proteins (HSPs) in the durian genome appear to have undergone expansion. The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified. Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome. We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.
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Affiliation(s)
- Wanwan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xin Chen
- The State Key Laboratory of Protein and Gene Research, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jianing Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
| | - Yuxian Zhu
- The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China.
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Gu T, Hu J, Yu L. Evolution and conservation genetics of pangolins. Integr Zool 2024; 19:426-441. [PMID: 38146613 DOI: 10.1111/1749-4877.12796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Pangolins (Pholidota, Manidae) are classified as an evolutionarily distinct and globally endangered mammal due to their unique morphology (nail-like scales and a myrmecophagous diet) and being the victim of heavy poaching and worldwide trafficking. As such, pangolins serve as a textbook example for studying the special phenotypic evolutionary adaptations and conservation genetics of an endangered species. Recent years have demonstrated significant advancements in the fields of molecular genetics and genomics, which have translated to a series of important research achievements and breakthroughs concerning the evolution and conservation genetics of pangolins. This review comprehensively presents the hitherto advances in phylogeny, adaptive evolution, conservation genetics, and conservation genomics that are related to pangolins, which will provide an ample understanding of their diversity, molecular adaptation mechanisms, and evolutionary potentials. In addition, we highlight the priority of investigating species/population diversity among pangolins and suggest several avenues of research that are highly relevant for future pangolin conservation.
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Affiliation(s)
- Tongtong Gu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Jingyang Hu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Li Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resource in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
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3
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Wu M, Wang D, Li MH, Lv F. Artificial selection shapes the lower genomic diversity and higher selective pressures on the sex chromosomes of domestic animals. Sci China Life Sci 2024; 67:1072-1075. [PMID: 38277069 DOI: 10.1007/s11427-023-2478-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 01/27/2024]
Affiliation(s)
- Meiming Wu
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dongfeng Wang
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Science (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Meng-Hua Li
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
- Sanya Institute of China Agricultural University, Sanya, 572024, China.
| | - Fenghua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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Zhou X, Li Z, Chen K, Wei Y, Cao Z, Yu D. The expansion of oligopeptide transporters in Melampsora larici-populina may reflect its adaptation to a phytoparasitic lifestyle. Gene 2024; 920:148506. [PMID: 38670390 DOI: 10.1016/j.gene.2024.148506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/13/2024] [Accepted: 04/23/2024] [Indexed: 04/28/2024]
Abstract
The acquisition of nutrients from host plants by phytopathogenic fungi is critically important for their invasion success. Melampsora larici-populina, an obligate biotrophic pathogenic fungus, causes the poplar leaf rust disease and can severely damage host poplar plants. Previously, we found that oligopeptide transporters (OPTs) have undergone a convergent expansion, which might reflect adaptation to a phytoparasitic lifestyle. Here, we used various methods to evaluate this hypothesis, including conserved motif identification, positive selection signal mining, expression pattern clustering analysis, and neutral selection tests. The motif composition of the five clades in the OPT family differed, and positive selection was observed during clade differentiation. This suggests that OPTs in these five clades may be functionally differentiated, which would increase the range of transported substrates and promote the absorption of more types of nitrogen compounds from the hosts. According to clustering analysis of gene expression patterns, the expression of most genes from the two expanded clades (clade 2 and 4) was up-regulated during the infection of poplar trees, indicating that the expansion of OPTs likely occurred to promote the uptake of oligopeptides from host poplar plants. The MellpOPT4g gene was determined to be under significant balancing selection based on the neutral selection tests, suggesting that it plays a role in the pathogenic process. In conclusion, these three observations provide preliminary evidence supporting our hypothesis, as they indicate that the expansion of OPTs in M. larici-populina has aided the ability of this pathogen to acquire nutrients from host plants.
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Affiliation(s)
- Xianzhen Zhou
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Ziye Li
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Kaiyue Chen
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Yefan Wei
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Zhimin Cao
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, China.
| | - Dan Yu
- College of Forestry (Northwest A&F University), No. 3 Taicheng Road, Yangling, Shaanxi 712100, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Guo B, Sun Y, Wang Y, Zhang Y, Zheng Y, Xu S, Yang G, Ren W. Evolutionary genetics of pulmonary anatomical adaptations in deep-diving cetaceans. BMC Genomics 2024; 25:339. [PMID: 38575860 PMCID: PMC10993460 DOI: 10.1186/s12864-024-10263-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/27/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Cetaceans, having experienced prolonged adaptation to aquatic environments, have undergone evolutionary changes in their respiratory systems. This process of evolution has resulted in the emergence of distinctive phenotypic traits, notably the abundance of elastic fibers and thickened alveolar walls in their lungs, which may facilitate alveolar collapse during diving. This structure helps selective exchange of oxygen and carbon dioxide, while minimizing nitrogen exchange, thereby reducing the risk of DCS. Nevertheless, the scientific inquiry into the mechanisms through which these unique phenotypic characteristics govern the diving behavior of marine mammals, including cetaceans, remains unresolved. RESULTS This study entails an evolutionary analysis of 42 genes associated with pulmonary fibrosis across 45 mammalian species. Twenty-one genes in cetaceans exhibited accelerated evolution, featuring specific amino acid substitutions in 14 of them. Primarily linked to the development of the respiratory system and lung morphological construction, these genes play a crucial role. Moreover, among marine mammals, we identified eight genes undergoing positive selection, and the evolutionary rates of three genes significantly correlated with diving depth. Specifically, the SFTPC gene exhibited convergent amino acid substitutions. Through in vitro cellular experiments, we illustrated that convergent amino acid site mutations in SFTPC contribute positively to pulmonary fibrosis in marine mammals, and the presence of this phenotype can induce deep alveolar collapse during diving, thereby reducing the risk of DCS during diving. CONCLUSIONS The study unveils pivotal genetic signals in cetaceans and other marine mammals, arising through evolution. These genetic signals may influence lung characteristics in marine mammals and have been linked to a reduced risk of developing DCS. Moreover, the research serves as a valuable reference for delving deeper into human diving physiology.
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Affiliation(s)
- Boxiong Guo
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yixuan Sun
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yuehua Wang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Ya Zhang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Yu Zheng
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Shixia Xu
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Guang Yang
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China
| | - Wenhua Ren
- Jiangsu Key Laboratory for Bioaffiliationersity and Biotechnology, College of Life Sciences, Nanjing Normal University, 210023, Nanjing, China.
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7
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Xu S, Shao S, Feng X, Li S, Zhang L, Wu W, Liu M, Tracy ME, Zhong C, Guo Z, Wu CI, Shi S, He Z. Adaptation in Unstable Environments and Global Gene Losses: Small but Stable Gene Networks by the May-Wigner Theory. Mol Biol Evol 2024; 41:msae059. [PMID: 38507653 PMCID: PMC10991078 DOI: 10.1093/molbev/msae059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/07/2024] [Accepted: 03/15/2024] [Indexed: 03/22/2024] Open
Abstract
Although gene loss is common in evolution, it remains unclear whether it is an adaptive process. In a survey of seven major mangrove clades that are woody plants in the intertidal zones of daily environmental perturbations, we noticed that they generally evolved reduced gene numbers. We then focused on the largest clade of Rhizophoreae and observed the continual gene set reduction in each of the eight species. A great majority of gene losses are concentrated on environmental interaction processes, presumably to cope with the constant fluctuations in the tidal environments. Genes of the general processes for woody plants are largely retained. In particular, fewer gene losses are found in physiological traits such as viviparous seeds, high salinity, and high tannin content. Given the broad and continual genome reductions, we propose the May-Wigner theory (MWT) of system stability as a possible mechanism. In MWT, the most effective solution for buffering continual perturbations is to reduce the size of the system (or to weaken the total genic interactions). Mangroves are unique as immovable inhabitants of the compound environments in the land-sea interface, where environmental gradients (such as salinity) fluctuate constantly, often drastically. Extending MWT to gene regulatory network (GRN), computer simulations and transcriptome analyses support the stabilizing effects of smaller gene sets in mangroves vis-à-vis inland plants. In summary, we show the adaptive significance of gene losses in mangrove plants, including the specific role of promoting phenotype innovation and a general role in stabilizing GRN in unstable environments as predicted by MWT.
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Affiliation(s)
- Shaohua Xu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Shao Shao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Xiao Feng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Sen Li
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Lingjie Zhang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Weihong Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Min Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Miles E Tracy
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Cairong Zhong
- Institute of Wetland Research, Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
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Zhang H, Niu H, Steele MA, Peng L, He H, Li A, Yi X, Li H, Zhang Z. Masting promotes transformation from predation to mutualism in an oak-weevil-rodent system. Sci China Life Sci 2024:10.1007/s11427-023-2517-1. [PMID: 38558376 DOI: 10.1007/s11427-023-2517-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/21/2023] [Indexed: 04/04/2024]
Abstract
The significance of ecological non-monotonicity (a function whose first derivative changes signs) in shaping the structure and functions of the ecosystem has recently been recognized, but such studies involving high-order interactions are rare. Here, we have proposed a three-trophic conceptual diagram on interactions among trees, rodents, and insects in mast and non-mast years and tested the hypothesis that oak (Quercus wutaishanica) masting could result in increased mutualism and less predation in an oak-weevil-rodent system in a warm temperate forest of China. Our 14-year dataset revealed that mast years coincided with a relatively low rodent abundance but a high weevil abundance. Masting not only benefited seedling recruitment of oaks through increased dispersal by rodents but also a decrease in predation by rodents and weevils, as well as an increase in the overwintering survival of rodents. Masting appeared to have increased weevil survival by reducing predation of infested acorns by rodents. These results suggest that masting benefits all participants in the plant-insect-rodent system by increasing mutualism and reducing predation behavior (i.e., a non-monotonic function). Our study highlights the significance of masting in maintaining the diversity and function of the forest ecosystem by facilitating the transformation from predation to mutualism among trophic species.
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Affiliation(s)
- Hongmao Zhang
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China.
| | - Hongyu Niu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Michael A Steele
- Department of Biology, Wilkes University, Wilkes-Barre, 18766, USA
| | - Liqing Peng
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Huimin He
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Aoqiang Li
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan, 430079, China
| | - Xianfeng Yi
- School of Life Sciences, Qufu Normal University, Qufu, 273165, China
| | - Hongjun Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhibin Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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9
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Lu S, Zeng H, Xiong F, Yao M, He S. Advances in environmental DNA monitoring: standardization, automation, and emerging technologies in aquatic ecosystems. Sci China Life Sci 2024:10.1007/s11427-023-2493-5. [PMID: 38512561 DOI: 10.1007/s11427-023-2493-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/30/2023] [Indexed: 03/23/2024]
Abstract
Environmental DNA (eDNA) monitoring, a rapidly advancing technique for assessing biodiversity and ecosystem health, offers a noninvasive approach for detecting and quantifying species from various environmental samples. In this review, a comprehensive overview of current eDNA collection and detection technologies is provided, emphasizing the necessity for standardization and automation in aquatic ecological monitoring. Furthermore, the intricacies of water bodies, from streams to the deep sea, and the associated challenges they pose for eDNA capture and analysis are explored. The paper delineates three primary eDNA survey methods, namely, bringing back water, bringing back filters, and bringing back data, each with specific advantages and constraints in terms of labor, transport, and data acquisition. Additionally, innovations in eDNA sampling equipment, including autonomous drones, subsurface samplers, and in-situ filtration devices, and their applications in monitoring diverse taxa are discussed. Moreover, recent advancements in species-specific detection and eDNA metabarcoding are addressed, highlighting the integration of novel techniques such as CRISPR-Cas and nanopore sequencing that enable precise and rapid detection of biodiversity. The implications of environmental RNA and epigenetic modifications are considered for future applications in providing nuanced ecological data. Lastly, the review stresses the critical role of standardization and automation in enhancing data consistency and comparability for robust long-term biomonitoring. We propose that the amalgamation of these technologies represents a paradigm shift in ecological monitoring, aligning with the urgent call for biodiversity conservation and sustainable management of aquatic ecosystems.
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Affiliation(s)
- Suxiang Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Honghui Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Fan Xiong
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Meng Yao
- Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China.
- School of Life Sciences, Peking University, Beijing, 100871, China.
| | - Shunping He
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China.
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10
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Guan D, Sun S, Song L, Zhao P, Nie Y, Huang X, Zhou W, Yan L, Lei Y, Hu Y, Wei F. Taking a color photo: A homozygous 25-bp deletion in Bace2 may cause brown-and-white coat color in giant pandas. Proc Natl Acad Sci U S A 2024; 121:e2317430121. [PMID: 38437540 PMCID: PMC10945837 DOI: 10.1073/pnas.2317430121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/30/2023] [Indexed: 03/06/2024] Open
Abstract
Brown-and-white giant pandas (hereafter brown pandas) are distinct coat color mutants found exclusively in the Qinling Mountains, Shaanxi, China. However, its genetic mechanism has remained unclear since their discovery in 1985. Here, we identified the genetic basis for this coat color variation using a combination of field ecological data, population genomic data, and a CRISPR-Cas9 knockout mouse model. We de novo assembled a long-read-based giant panda genome and resequenced the genomes of 35 giant pandas, including two brown pandas and two family trios associated with a brown panda. We identified a homozygous 25-bp deletion in the first exon of Bace2, a gene encoding amyloid precursor protein cleaving enzyme, as the most likely genetic basis for brown-and-white coat color. This deletion was further validated using PCR and Sanger sequencing of another 192 black giant pandas and CRISPR-Cas9 edited knockout mice. Our investigation revealed that this mutation reduced the number and size of melanosomes of the hairs in knockout mice and possibly in the brown panda, further leading to the hypopigmentation. These findings provide unique insights into the genetic basis of coat color variation in wild animals.
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Affiliation(s)
- Dengfeng Guan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang330045, China
| | - Shuyan Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Lingyun Song
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Pengpeng Zhao
- Shaanxi (Louguantai) Rescue and Breeding Center for Rare Wildlife, Xi’an710402, China
| | - Yonggang Nie
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Xin Huang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
| | - Li Yan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
| | - Yinghu Lei
- Shaanxi (Louguantai) Rescue and Breeding Center for Rare Wildlife, Xi’an710402, China
| | - Yibo Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- University of Chinese Academy of Sciences, Beijing100049, China
| | - Fuwen Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing100101, China
- Jiangxi Provincial Key Laboratory of Conservation Biology, Jiangxi Agricultural University, Nanchang330045, China
- University of Chinese Academy of Sciences, Beijing100049, China
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou511458, China
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11
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He J, Kang L. Regulation of insect behavior by non-coding RNAs. Sci China Life Sci 2024:10.1007/s11427-023-2482-2. [PMID: 38443665 DOI: 10.1007/s11427-023-2482-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 03/07/2024]
Abstract
The adaptation of insects to environments relies on a sophisticated set of behaviors controlled by molecular and physiological processes. Over the past several decades, accumulating studies have unveiled the roles of non-coding RNAs (ncRNAs) in regulating insect behaviors. ncRNAs assume particularly pivotal roles in the behavioral plasticity of insects by rapidly responding to environmental stimuli. ncRNAs also contribute to the maintenance of homeostasis of insects by fine-tuning the expression of target genes. However, a comprehensive review of ncRNAs' roles in regulating insect behaviors has yet to be conducted. Here, we present the recent progress in our understanding of how ncRNAs regulate various insect behaviors, including flight and movement, social behavior, reproduction, learning and memory, and feeding. We refine the intricate mechanisms by which ncRNAs modulate the function of neural, motor, reproductive, and other physiological systems, as well as gene expression in insects like fruit flies, social insects, locusts, and mosquitos. Furthermore, we discuss potential avenues for future studies in ncRNA-mediated insect behaviors.
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Affiliation(s)
- Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, Hebei University, Baoding, 071002, China.
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12
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Hu Y, Hu Y, Zhou W, Wei F. Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild. Annu Rev Anim Biosci 2024; 12:69-89. [PMID: 37863091 DOI: 10.1146/annurev-animal-021022-054730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species.
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Affiliation(s)
- Yisi Hu
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yibo Hu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Wenliang Zhou
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Fuwen Wei
- College of Forestry, Jiangxi Agricultural University, Nanchang, China;
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
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13
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Huang G, Qi D, Yang Z, Hou R, Shi W, Zhao F, Li Z, Yan L, Wei F. Gut microbiome as a key monitoring indicator for reintroductions of captive animals. Conserv Biol 2024; 38:e14173. [PMID: 37650395 DOI: 10.1111/cobi.14173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 07/04/2023] [Accepted: 07/15/2023] [Indexed: 09/01/2023]
Abstract
Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.
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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, China
| | - Dunwu Qi
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | | | - Rong Hou
- Sichuan Key Laboratory of Conservation Biology for Endangered Wildlife, Chengdu Research Base of Giant Panda Breeding, Chengdu, China
| | - Wenyu Shi
- College of Biological Science, China Agricultural University, Beijing, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Zitian Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Li Yan
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fuwen Wei
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Forestry, Jiangxi Agricultural University, Nanchang, China
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14
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Yu H, Guo Q, Ji W, Wang H, Tao J, Xu P, Chen X, Ali W, Wu X, Shen X, Xie Y, Xu Z. Transcriptome Expression Profiling Reveals the Molecular Response to Salt Stress in Gossypium anomalum Seedlings. Plants (Basel) 2024; 13:312. [PMID: 38276767 PMCID: PMC10819910 DOI: 10.3390/plants13020312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/21/2023] [Accepted: 01/15/2024] [Indexed: 01/27/2024]
Abstract
Some wild cotton species are remarkably tolerant to salt stress, and hence represent valuable resources for improving salt tolerance of the domesticated allotetraploid species Gossypium hirsutum L. Here, we first detected salt-induced stress changes in physiological and biochemical indexes of G. anomalum, a wild African diploid cotton species. Under 350 mmol/L NaCl treatment, the photosynthetic parameters declined significantly, whereas hydrogen peroxide (H2O2) and malondialdehyde (MDA) contents increased. Catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activity and proline (PRO) content also significantly increased, reaching peak values at different stages of salt stress. We used RNA-Seq to characterize 15,476 differentially expressed genes in G. anomalum roots after 6, 12, 24, 72, and 144 h of salt stress. Gene Ontology enrichment analysis revealed these genes to be related to sequence-specific DNA and iron ion binding and oxidoreductase, peroxidase, antioxidant, and transferase activity; meanwhile, the top enriched pathways from the Kyoto Encyclopedia of Genes and Genomes database were plant hormone signal transduction, phenylpropanoid biosynthesis, fatty acid degradation, carotenoid biosynthesis, zeatin biosynthesis, starch and sucrose metabolism, and MAPK signaling. A total of 1231 transcription factors were found to be expressed in response to salt stress, representing ERF, MYB, WRKY, NAC, C2H2, bZIP, and HD-ZIP families. Nine candidate genes were validated by quantitative real-time PCR and their expression patterns were found to be consistent with the RNA-Seq data. These data promise to significantly advance our understanding of the molecular response to salt stress in Gossypium spp., with potential value for breeding applications.
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Affiliation(s)
- Huan Yu
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Qi Guo
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wei Ji
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Heyang Wang
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Jingqi Tao
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Peng Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xianglong Chen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Wuzhimu Ali
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xuan Wu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Xinlian Shen
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
| | - Yinfeng Xie
- Co-Innovation Centre for Sustainable Forestry in Southern China, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China;
| | - Zhenzhen Xu
- Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture and Rural Affairs, The Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Q.G.); (W.J.); (H.W.); (J.T.); (P.X.); (X.C.); (W.A.); (X.W.); (X.S.)
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15
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Zhang W, Lohman DJ. Uncovering the functional basis of mantids that resemble plants. Sci China Life Sci 2024; 67:215-216. [PMID: 37946066 DOI: 10.1007/s11427-023-2450-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 11/12/2023]
Affiliation(s)
- 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.
| | - David J Lohman
- Biology Department, City College of New York, City University of New York, New York, 10031, USA
- PhD Program in Biology, City University of New York, New York, 10016, USA
- Entomology Section, National Museum of Natural History, Manila, 1000, Philippines
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16
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Tan Y, Yao B, Kang Y, Shi S, Shi Z, Su J. Emerging role of the crosstalk between gut microbiota and liver metabolome of subterranean herbivores in response to toxic plants. Ecotoxicol Environ Saf 2024; 269:115902. [PMID: 38171231 DOI: 10.1016/j.ecoenv.2023.115902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/05/2024]
Abstract
Plant secondary metabolites (PSMs) are a defense mechanism against herbivores, which in turn use detoxification metabolism to process ingested and absorbed PSMs. The feeding environment can cause changes in liver metabolism patterns and the gut microbiota. Here, we compared gut microbiota and liver metabolome to investigate the response mechanism of plateau zokors (Eospalax baileyi) to toxic plant Stellera chamaejasme (SC) in non-SC and SC grassland (-SCG and +SCG). Our results indicated that exposure to SC in the -SCG population increased liver inflammatory markers including prostaglandin (PG) in the Arachidonic acid pathway, while exposure to SC in the +SCG population exhibited a significant downregulation of PGs. Secondary bile acids were significantly downregulated in +SCG plateau zokors after SC treatment. Of note, the microbial taxa Veillonella in the -SCG group was significantly correlated with liver inflammation markers, while Clostridium innocum in the +SCG group had a significant positive correlation with secondary bile acids. The increase in bile acids and PGs can lead to liver inflammatory reactions, suggesting that +SCG plateau zokors may mitigate the toxicity of SC plants by reducing liver inflammatory markers including PGs and secondary bile acids, thereby avoiding liver damage. This provides new insight into mechanisms of toxicity by PSMs and counter-mechanisms for toxin tolerance by herbivores.
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Affiliation(s)
- Yuchen Tan
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou 730070, China
| | - Baohui Yao
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou 730070, China
| | - Yukun Kang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou 730070, China
| | - Shangli Shi
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou 730070, China
| | - Zunji Shi
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, China.
| | - Junhu Su
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou 730070, China.
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17
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Ishita Y, Onodera A, Ekino T, Chihara T, Okumura M. Co-option of an Astacin Metalloprotease Is Associated with an Evolutionarily Novel Feeding Morphology in a Predatory Nematode. Mol Biol Evol 2023; 40:msad266. [PMID: 38105444 PMCID: PMC10753534 DOI: 10.1093/molbev/msad266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 10/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Animals consume a wide variety of food sources to adapt to different environments. However, the genetic mechanisms underlying the acquisition of evolutionarily novel feeding morphology remain largely unknown. While the nematode Caenorhabditis elegans feeds on bacteria, the satellite species Pristionchus pacificus exhibits predatory feeding behavior toward other nematodes, which is an evolutionarily novel feeding habit. Here, we found that the astacin metalloprotease Ppa-NAS-6 is required for the predatory killing by P. pacificus. Ppa-nas-6 mutants were defective in predation-associated characteristics, specifically the tooth morphogenesis and tooth movement during predation. Comparison of expression patterns and rescue experiments of nas-6 in P. pacificus and C. elegans suggested that alteration of the spatial expression patterns of NAS-6 may be vital for acquiring predation-related traits. Reporter analysis of the Ppa-nas-6 promoter in C. elegans revealed that the alteration in expression patterns was caused by evolutionary changes in cis- and trans-regulatory elements. This study suggests that the co-option of a metalloprotease is involved in an evolutionarily novel feeding morphology.
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Affiliation(s)
- Yuuki Ishita
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Ageha Onodera
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Taisuke Ekino
- School of Agriculture, Meiji University, Kawasaki 214-8571, Japan
| | - Takahiro Chihara
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Misako Okumura
- Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
- Program of Basic Biology, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
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18
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Muniz AC, de Oliveira Buzatti RS, de Lemos-Filho JP, Heuertz M, Nazareno AG, Lovato MB. Genomic signatures of ecological divergence between savanna and forest populations of a Neotropical tree. Ann Bot 2023; 132:523-540. [PMID: 37642427 PMCID: PMC10667007 DOI: 10.1093/aob/mcad120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND AND AIMS In eastern Neotropical South America, the Cerrado, a large savanna vegetation, and the Atlantic Forest harbour high biodiversity levels, and their habitats are rather different from each other. The biomes have intrinsic evolutionary relationships, with high lineage exchange that can be attributed, in part, to a large contact zone between them. The genomic study of ecotypes, i.e. populations adapted to divergent habitats, can be a model to study the genomic signatures of ecological divergence. Here, we investigated two ecotypes of the tree Plathymenia reticulata, one from the Cerrado and the other from the Atlantic Forest, which have a hybrid zone in the ecotonal zone of Atlantic Forest-Cerrado. METHODS The ecotypes were sampled in the two biomes and their ecotone. The evolutionary history of the divergence of the species was analysed with double-digest restriction site-associated DNA sequencing. The genetic structure and the genotypic composition of the hybrid zone were determined. Genotype-association analyses were performed, and the loci under putative selection and their functions were investigated. KEY RESULTS High divergence between the two ecotypes was found, and only early-generation hybrids were found in the hybrid zone, suggesting a partial reproductive barrier. Ancient introgression between the Cerrado and Atlantic Forest was not detected. The soil and climate were associated with genetic divergence in Plathymenia ecotypes and outlier loci were found to be associated with the stress response, with stomatal and root development and with reproduction. CONCLUSIONS The high genomic, ecological and morphophysiological divergence between ecotypes, coupled with partial reproductive isolation, indicate that the ecotypes represent two species and should be managed as different evolutionary lineages. We advise that the forest species should be re-evaluated and restated as vulnerable. Our results provide insights into the genomic mechanisms underlying the diversification of species across savanna and forest habitats and the evolutionary forces acting in the species diversification in the Neotropics.
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Affiliation(s)
- André Carneiro Muniz
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | | | - José Pires de Lemos-Filho
- Departamento de Botânica, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-901, Brazil
| | - Myriam Heuertz
- Biogeco, INRAE, Univ. Bordeaux, 69 route d’Arcachon, 33610 Cestas, France
| | - Alison Gonçalves Nazareno
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
| | - Maria Bernadete Lovato
- Departamento de Genética, Ecologia e Evolução, Universidade Federal de Minas Gerais, CP 486, Belo Horizonte, MG 31270-901, Brazil
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19
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Zu X, Luo L, Wang Z, Gong J, Yang C, Wang Y, Xu C, Qiao X, Deng X, Song X, Chen C, Tan BC, Cao X. A mitochondrial pentatricopeptide repeat protein enhances cold tolerance by modulating mitochondrial superoxide in rice. Nat Commun 2023; 14:6789. [PMID: 37880207 PMCID: PMC10600133 DOI: 10.1038/s41467-023-42269-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 10/04/2023] [Indexed: 10/27/2023] Open
Abstract
Cold stress affects rice growth and productivity. Defects in the plastid-localized pseudouridine synthase OsPUS1 affect chloroplast ribosome biogenesis, leading to low-temperature albino seedlings and accumulation of reactive oxygen species (ROS). Here, we report an ospus1-1 suppressor, sop10. SOP10 encodes a mitochondria-localized pentatricopeptide repeat protein. Mutations in SOP10 impair intron splicing of the nad4 and nad5 transcripts and decrease RNA editing efficiency of the nad2, nad6, and rps4 transcripts, resulting in deficiencies in mitochondrial complex I, thus decrease ROS generation and rescuing the albino phenotype. Overexpression of different compartment-localized superoxide dismutases (SOD) genes in ospus1-1 reverses the ROS over-accumulation and albino phenotypes to various degrees, with Mn-SOD reversing the best. Mutation of SOP10 in indica rice varieties enhances cold tolerance with lower ROS levels. We find that the mitochondrial superoxide plays a key role in rice cold responses, and identify a mitochondrial superoxide modulating factor, informing efforts to improve rice cold tolerance.
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Affiliation(s)
- Xiaofeng Zu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lilan Luo
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Zhen Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jie Gong
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- The Municipal Key Laboratory of the Molecular Genetics of Hybrid Wheat, Institute of Hybrid Wheat, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Chao Yang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yong Wang
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Chunhui Xu
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xinhua Qiao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xian Deng
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Xianwei Song
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chang Chen
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bao-Cai Tan
- Key Laboratory of Plant Development and Environmental Adaptation Biology, Ministry of Education, School of Life Sciences, Shandong University, Qingdao, 266237, China
| | - Xiaofeng Cao
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Huang G, Shi W, Wang L, Qu Q, Zuo Z, Wang J, Zhao F, Wei F. PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation. Microbiome 2023; 11:221. [PMID: 37805557 PMCID: PMC10559513 DOI: 10.1186/s40168-023-01657-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/23/2023] [Indexed: 10/09/2023]
Abstract
BACKGROUND The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. RESULTS The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. CONCLUSIONS Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.
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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
| | - Wenyu Shi
- Microbial Resource and Big Data Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qingyue Qu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhenqiang Zuo
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jinfeng Wang
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fangqing Zhao
- Laboratory for Computational Genomics, Beijing Institutes of Life Science, 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.
- College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Zhu R, Shao S, Xie W, Guo Z, He Z, Li Y, Wang W, Zhong C, Shi S, Xu S. High-quality genome of a pioneer mangrove Laguncularia racemosa explains its advantages for intertidal zone reforestation. Mol Ecol Resour 2023. [PMID: 37688468 DOI: 10.1111/1755-0998.13863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/11/2023]
Abstract
Ecological restoration of mangrove ecosystems that became susceptible to recent habitat perturbations is crucial for tropical coast conservation. The white mangrove Laguncularia racemosa, a pioneer species inhabiting intertidal environments of the Atlantic East Pacific (AEP) region, has been used for reforestation in China for decades. However, the molecular mechanisms underlying its fast growth and high adaptive potential remain unknown. Using PacBio single-molecule real-time sequencing, we completed a high-quality L. racemosa genome assembly covering 1105 Mb with scaffold N50 of 3.46 Mb. Genomic phylogeny shows that L. racemosa invaded intertidal zones during a period of global warming. Multi-level genomic convergence analyses between L. racemosa and three native dominant mangrove clades show that they experienced convergent changes in genes involved in nutrient absorption and high salinity tolerance. This may explain successful L. racemosa adaptation to stressful intertidal environments after introduction. Without recent whole-genome duplications or activated transposable elements, L. racemosa has retained many tandem gene duplications. Some of them are involved in auxin biosynthesis, intense light stress and cold stress response pathways, associated with L. racemosa's ability to grow fast under high light or cold conditions when used for reforestation. In summary, our study identifies shared mechanisms of intertidal environmental adaptation and unique genetic changes underlying fast growth in mangrove-unfavourable conditions and sheds light on the molecular mechanisms of the white mangrove utility in ecological restoration.
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Affiliation(s)
- Ranran Zhu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shao Shao
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Wei Xie
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Zixiao Guo
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Ziwen He
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Yulong Li
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
| | - Wenqing Wang
- Key Laboratory of the Coastal and Wetland Ecosystems (Xiamen University), Ministry of Education, College of the Environment & Ecology, Xiamen University, Xiamen, China
| | - Cairong Zhong
- Hainan Academy of Forestry (Hainan Academy of Mangrove), Haikou, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
| | - Shaohua Xu
- State Key Laboratory of Biocontrol, Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Guangzhou, China
- School of Ecology, Sun Yat-sen University, Shenzhen, China
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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23
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Hu Y, Yuan S, Du X, Liu J, Zhou W, Wei F. Comparative analysis reveals epigenomic evolution related to species traits and genomic imprinting in mammals. Innovation (N Y) 2023; 4:100434. [PMID: 37215528 PMCID: PMC10196708 DOI: 10.1016/j.xinn.2023.100434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
DNA methylation is an epigenetic modification that plays a crucial role in various regulatory processes, including gene expression regulation, transposable element repression, and genomic imprinting. However, most studies on DNA methylation have been conducted in humans and other model species, whereas the dynamics of DNA methylation across mammals remain poorly explored, limiting our understanding of epigenomic evolution in mammals and the evolutionary impacts of conserved and lineage-specific DNA methylation. Here, we generated and gathered comparative epigenomic data from 13 mammalian species, including two marsupial species, to demonstrate that DNA methylation plays critical roles in several aspects of gene evolution and species trait evolution. We found that the species-specific DNA methylation of promoters and noncoding elements correlates with species-specific traits such as body patterning, indicating that DNA methylation might help establish or maintain interspecies differences in gene regulation that shape phenotypes. For a broader view, we investigated the evolutionary histories of 88 known imprinting control regions across mammals to identify their evolutionary origins. By analyzing the features of known and newly identified potential imprints in all studied mammals, we found that genomic imprinting may function in embryonic development through the binding of specific transcription factors. Our findings show that DNA methylation and the complex interaction between the genome and epigenome have a significant impact on mammalian evolution, suggesting that evolutionary epigenomics should be incorporated to develop a unified evolutionary theory.
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Affiliation(s)
- Yisi Hu
- 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
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
| | - Shenli Yuan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, 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
| | - Jiang Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, 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
| | - 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
- Center for Evolution and Conservation Biology, Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 511458, China
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24
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Fang W, Li K, Ma S, Wei F, Hu Y. Natural selection and convergent evolution of the HOX gene family in Carnivora. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1107034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
HOX genes play a central role in the development and regulation of limb patterns. For mammals in the order Carnivora, limbs have evolved in different forms, and there are interesting cases of phenotypic convergence, such as the pseudothumb of the giant and red pandas, and the flippers or specialized limbs of the pinnipeds and sea otter. However, the molecular bases of limb development remain largely unclear. Here, we studied the molecular evolution of the HOX9 ~ 13 genes of 14 representative species in Carnivora and explored the molecular evolution of other HOX genes. We found that only one limb development gene, HOXC10, underwent convergent evolution between giant and red pandas and was thus an important candidate gene related to the development of pseudothumbs. No signals of amino acid convergence and natural selection were found in HOX9 ~ 13 genes between pinnipeds and sea otter, but there was evidence of positive selection and rapid evolution in four pinniped species. Overall, few HOX genes evolve via natural selection or convergent evolution, and these could be important candidate genes for further functional validation. Our findings provide insights into potential molecular mechanisms of the development of specialized pseudothumbs and flippers (or specialized limbs).
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