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Weng YM, Kavanaugh DH, Schoville SD. Evidence for Admixture and Rapid Evolution During Glacial Climate Change in an Alpine Specialist. Mol Biol Evol 2024; 41:msae130. [PMID: 38935588 PMCID: PMC11247348 DOI: 10.1093/molbev/msae130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 05/30/2024] [Accepted: 06/14/2024] [Indexed: 06/29/2024] Open
Abstract
The pace of current climate change is expected to be problematic for alpine flora and fauna, as their adaptive capacity may be limited by small population size. Yet, despite substantial genetic drift following post-glacial recolonization of alpine habitats, alpine species are notable for their success surviving in highly heterogeneous environments. Population genomic analyses demonstrating how alpine species have adapted to novel environments with limited genetic diversity remain rare, yet are important in understanding the potential for species to respond to contemporary climate change. In this study, we explored the evolutionary history of alpine ground beetles in the Nebria ingens complex, including the demographic and adaptive changes that followed the last glacier retreat. We first tested alternative models of evolutionary divergence in the species complex. Using millions of genome-wide SNP markers from hundreds of beetles, we found evidence that the N. ingens complex has been formed by past admixture of lineages responding to glacial cycles. Recolonization of alpine sites involved a distributional range shift to higher elevation, which was accompanied by a reduction in suitable habitat and the emergence of complex spatial genetic structure. We tested several possible genetic pathways involved in adaptation to heterogeneous local environments using genome scan and genotype-environment association approaches. From the identified genes, we found enriched functions associated with abiotic stress responses, with strong evidence for adaptation to hypoxia-related pathways. The results demonstrate that despite rapid demographic change, alpine beetles in the N. ingens complex underwent rapid physiological evolution.
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Affiliation(s)
- Yi-Ming Weng
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
- Okinawa Institute of Science and Technology, Graduate University, Okinawa, Japan
| | - David H Kavanaugh
- California Academy of Sciences, Department of Entomology, San Francisco, CA, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI, USA
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2
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Tregub PP, Komleva YK, Kulikov VP, Chekulaev PA, Tregub OF, Maltseva LD, Manasova ZS, Popova IA, Andriutsa NS, Samburova NV, Salmina AB, Litvitskiy PF. Relationship between Hypoxia and Hypercapnia Tolerance and Life Expectancy. Int J Mol Sci 2024; 25:6512. [PMID: 38928217 PMCID: PMC11204369 DOI: 10.3390/ijms25126512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
The review discusses the potential relationship between hypoxia resistance and longevity, the influence of carbon dioxide on the mechanisms of aging of the mammalian organism, and intermittent hypercapnic-hypoxic effects on the signaling pathways of aging mechanisms. In the article, we focused on the potential mechanisms of the gero-protective efficacy of carbon dioxide when combined with hypoxia. The review summarizes the possible influence of intermittent hypoxia and hypercapnia on aging processes in the nervous system. We considered the perspective variants of the application of hypercapnic-hypoxic influences for achieving active longevity and the prospects for the possibilities of developing hypercapnic-hypoxic training methods.
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Affiliation(s)
- Pavel P. Tregub
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
- Brain Science Institute, Research Center of Neurology, 125367 Moscow, Russia; (Y.K.K.)
- Scientific and Educational Resource Center “Innovative Technologies of Immunophenotyping, Digital Spatial Profiling and Ultrastructural Analysis”, RUDN University, 117198 Moscow, Russia
| | - Yulia K. Komleva
- Brain Science Institute, Research Center of Neurology, 125367 Moscow, Russia; (Y.K.K.)
| | - Vladimir P. Kulikov
- Department of Ultrasound and Functional Diagnostics, Altay State Medical University, 656040 Barnaul, Russia
| | - Pavel A. Chekulaev
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | | | - Larisa D. Maltseva
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Zaripat Sh. Manasova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Inga A. Popova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Natalia S. Andriutsa
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Natalia V. Samburova
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Alla B. Salmina
- Brain Science Institute, Research Center of Neurology, 125367 Moscow, Russia; (Y.K.K.)
| | - Peter F. Litvitskiy
- Department of Pathophysiology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
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3
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Dong JH, Xu X, Ren ZX, Zhao YH, Zhang Y, Chen L, Wu Y, Chen G, Cao R, Wu Q, Wang H. The adaptation of bumblebees to extremely high elevation associated with their gut microbiota. mSystems 2024; 9:e0121923. [PMID: 38329353 PMCID: PMC10949452 DOI: 10.1128/msystems.01219-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/09/2024] [Indexed: 02/09/2024] Open
Abstract
Bumblebees are among the most abundant and important pollinators for sub-alpine and alpine flowering plant species in the Northern Hemisphere, but little is known about their adaptations to high elevations. In this article, we focused on two bumblebee species, Bombus friseanus and Bombus prshewalskyi, and their respective gut microbiota. The two species, distributed through the Hengduan Mountains of southwestern China, show species replacement at different elevations. We performed genome sequencing based on 20 worker bee samples of each species. Applying evolutionary population genetics and metagenomic approaches, we detected genes under selection and analyzed functional pathways between bumblebees and their gut microbes. We found clear genetic differentiation between the two host species and significant differences in their microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. These extremely high-elevation bumblebees show evidence of positive selection related to diverse biological processes. Positively selected genes involved in host immune systems probably contributed to gut microbiota changes, while the butyrate generated by gut microbiota may influence both host energy metabolism and immune systems. This suggests a close association between the genomes of the host species and their microbiomes based on some degree of natural selection.IMPORTANCETwo closely related and dominant bumblebee species, distributed at different elevations through the Hengduan Mountains of southwestern China, showed a clear genomic signature of adaptation to elevation at the molecular level and significant differences in their respective microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. Bumblebees' adaptations to higher elevations are closely associated with their gut microbiota through two biological processes: energy metabolism and immune response. Information allowing us to understand the adaptive mechanisms of species to extreme conditions is implicit if we are to conserve them as their environments change.
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Affiliation(s)
- Jiu-Hong Dong
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Xin Xu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zong-Xin Ren
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yan-Hui Zhao
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Yaran Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Chen
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - You Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guotao Chen
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruiqing Cao
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qi Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hong Wang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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4
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Li H, Peng Y, Wu C, Li Z, Zou L, Mao K, Ping J, Buck R, Monahan S, Sethuraman A, Xiao Y. Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens. INSECT SCIENCE 2024. [PMID: 38204333 DOI: 10.1111/1744-7917.13320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Understanding the genetic basis of adaptive evolution following habitat expansion can have important implications for pest management. The pink rice borer (PRB), Sesamia inferens (Walker), is a destructive pest of rice that was historically restricted to regions south of 34° N latitude in China. However, with changes in global climate and farming practices, the distribution of this moth has progressively expanded, encompassing most regions in North China. Here, 3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural variant datasets across China, corresponding to northern, southern China regions, and the Yunnan-Guizhou Plateau, with significant patterns of isolation by geographic and environmental distances. Our estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 subpopulations. Selective sweep analyses estimated strong selection at insect cuticle glycine-rich cuticular protein genes which are associated with enhanced desiccation adaptability in the northern group, and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong population. Our findings have significant implications for the development of effective strategies to control this pest.
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Affiliation(s)
- Hongran Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Yan Peng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Chao Wu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Zhimin Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Luming Zou
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Kaikai Mao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Junfen Ping
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
| | - Ryan Buck
- Department of Biology, San Diego State University, CA, USA
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, CA, USA
| | - Scott Monahan
- Department of Biology, San Diego State University, CA, USA
| | | | - Yutao Xiao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Gene Editing Technologies (Hainan), Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong Province, China
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5
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Chen Y, Ni P, Fu R, Murphy KJ, Wyeth RC, Bishop CD, Huang X, Li S, Zhan A. (Epi)genomic adaptation driven by fine geographical scale environmental heterogeneity after recent biological invasions. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2024; 34:e2772. [PMID: 36316814 DOI: 10.1002/eap.2772] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Elucidating processes and mechanisms involved in rapid local adaptation to varied environments is a poorly understood but crucial component in management of invasive species. Recent studies have proposed that genetic and epigenetic variation could both contribute to ecological adaptation, yet it remains unclear on the interplay between these two components underpinning rapid adaptation in wild animal populations. To assess their respective contributions to local adaptation, we explored epigenomic and genomic responses to environmental heterogeneity in eight recently colonized ascidian (Ciona intestinalis) populations at a relatively fine geographical scale. Based on MethylRADseq data, we detected strong patterns of local environment-driven DNA methylation divergence among populations, significant epigenetic isolation by environment (IBE), and a large number of local environment-associated epigenetic loci. Meanwhile, multiple genetic analyses based on single nucleotide polymorphisms (SNPs) showed genomic footprints of divergent selection. In addition, for five genetically similar populations, we detected significant methylation divergence and local environment-driven methylation patterns, indicating the strong effects of local environments on epigenetic variation. From a functional perspective, a majority of functional genes, Gene Ontology (GO) terms, and biological pathways were largely specific to one of these two types of variation, suggesting partial independence between epigenetic and genetic adaptation. The methylation quantitative trait loci (mQTL) analysis showed that the genetic variation explained only 18.67% of methylation variation, further confirming the autonomous relationship between these two types of variation. Altogether, we highlight the complementary interplay of genetic and epigenetic variation involved in local adaptation, which may jointly promote populations' rapid adaptive capacity and successful invasions in different environments. The findings here provide valuable insights into interactions between invaders and local environments to allow invasive species to rapidly spread, thus contributing to better prediction of invasion success and development of management strategies.
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Affiliation(s)
- Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ping Ni
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Ruiying Fu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Kieran J Murphy
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Cory D Bishop
- Department of Biology, St. Francis Xavier University, Antigonish, Nova Scotia, Canada
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, China
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6
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Shi J, Jia Z, Sun J, Wang X, Zhao X, Zhao C, Liang F, Song X, Guan J, Jia X, Yang J, Chen Q, Yu K, Jia Q, Wu J, Wang D, Xiao Y, Xu X, Liu Y, Wu S, Zhong Q, Wu J, Cui S, Bo X, Wu Z, Park M, Kellis M, He K. Structural variants involved in high-altitude adaptation detected using single-molecule long-read sequencing. Nat Commun 2023; 14:8282. [PMID: 38092772 PMCID: PMC10719358 DOI: 10.1038/s41467-023-44034-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/27/2023] [Indexed: 12/17/2023] Open
Abstract
Structural variants (SVs), accounting for a larger fraction of the genome than SNPs/InDels, are an important pool of genetic variation, enabling environmental adaptations. Here, we perform long-read sequencing data of 320 Tibetan and Han samples and show that SVs are highly involved in high-altitude adaptation. We expand the landscape of global SVs, apply robust models of selection and population differentiation combining SVs, SNPs and InDels, and use epigenomic analyses to predict enhancers, target genes and biological functions. We reveal diverse Tibetan-specific SVs affecting the regulatory circuitry of biological functions, including the hypoxia response, energy metabolism and pulmonary function. We find a Tibetan-specific deletion disrupts a super-enhancer and downregulates EPAS1 using enhancer reporter, cellular knock-out and DNA pull-down assays. Our study expands the global SV landscape, reveals the role of gene-regulatory circuitry rewiring in human adaptation, and illustrates the diverse functional roles of SVs in human biology.
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Affiliation(s)
- Jinlong Shi
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
| | - Zhilong Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
- Medical Artificial Intelligence Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinxiu Sun
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xiaoreng Wang
- Laboratory of Nuclear and Radiation Injury, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- State Key Laboratory of Experimental Hematology, Beijing, 100853, China
| | - Xiaojing Zhao
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
- Translational Medicine Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Chenghui Zhao
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Research Center for Biomedical Engineering, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Fan Liang
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Xinyu Song
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
- Medical Artificial Intelligence Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jiawei Guan
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Xue Jia
- Laboratory of Nuclear and Radiation Injury, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Yang
- Laboratory of Nuclear and Radiation Injury, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
| | - Qi Chen
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Kang Yu
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qian Jia
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jing Wu
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Depeng Wang
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Yuhui Xiao
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Xiaoman Xu
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Yinzhe Liu
- NextOmics Biosciences Inc, Wuhan, 430000, China
| | - Shijing Wu
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qin Zhong
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China
| | - Jue Wu
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China
| | - Saijia Cui
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing, 100850, China
| | | | | | - Manolis Kellis
- Massachusetts Institute of Technology; MIT Computer Science and Artificial Intelligence Laboratory, Broad Institute of MIT and Harvard, Cambridge, 02139, MA, USA
| | - Kunlun He
- Medical Big Data Research Center, Medical Innovation Research Division of Chinese PLA General Hospital, Beijing, 100853, China.
- National Engineering Research Center of Medical Big Data, Chinese PLA General Hospital, Beijing, 100853, China.
- Key Laboratory of Biomedical Engineering and Translational Medicine, Ministry of Industry and Information Technology, Chinese PLA General Hospital, Beijing, 100853, China.
- Beijing Key Laboratory for Precision Medicine of Chronic Heart Failure, Chinese PLA General Hospital, Beijing, China.
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7
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Wang Z, Liu Y, Wang H, Roy A, Liu H, Han F, Zhang X, Lu Q. Genome and transcriptome of Ips nitidus provide insights into high-altitude hypoxia adaptation and symbiosis. iScience 2023; 26:107793. [PMID: 37731610 PMCID: PMC10507238 DOI: 10.1016/j.isci.2023.107793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/15/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023] Open
Abstract
Ips nitidus is a well-known conifer pest that has contributed significantly to spruce forest disturbance in the Qinghai-Tibet Plateau and seriously threatens the ecological balance of these areas. We report a chromosome-level genome of I. nitidus determined by PacBio and Hi-C technology. Phylogenetic inference showed that it diverged from the common ancestor of I. typographus ∼2.27 mya. Gene family expansion in I. nitidus was characterized by DNA damage repair and energy metabolism, which may facilitate adaptation to high-altitude hypoxia. Interestingly, differential gene expression analysis revealed upregulated genes associated with high-altitude hypoxia adaptation and downregulated genes associated with detoxification after feeding and tunneling in fungal symbiont Ophiostoma bicolor-colonized substrates. Our findings provide evidence of the potential adaptability of I. nitidus to conifer host, high-altitude hypoxia and insight into how fungal symbiont assist in this process. This study enhances our understanding of insect adaptation, symbiosis, and pest management.
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Affiliation(s)
- Zheng Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | - Ya Liu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Huimin Wang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, EXTEMIT-K and EVA.4.0 Unit, Czech University of Life Sciences, Kamýcká 1176, Prague 6, 165 00 Suchdol, Czech Republic
| | - Huixiang Liu
- Shandong Research Center for Forestry Harmful Biological Control Engineering and Technology, College of Plant Protection, Shandong Agricultural University, Tai’an 271018, China
| | | | - Xingyao Zhang
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
| | - Quan Lu
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration, Ecology and Nature Conservation Institute, Chinese Academy of Forestry, Beijing 100091, China
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8
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Jacobs PJ, Hart DW, Merchant HN, Voigt C, Bennett NC. The Evolution and Ecology of Oxidative and Antioxidant Status: A Comparative Approach in African Mole-Rats. Antioxidants (Basel) 2023; 12:1486. [PMID: 37627481 PMCID: PMC10451868 DOI: 10.3390/antiox12081486] [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: 06/14/2023] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
The naked mole-rat of the family Bathyergidae has been the showpiece for ageing research as they contradict the traditional understanding of the oxidative stress theory of ageing. Some other bathyergids also possess increased lifespans, but there has been a remarkable lack of comparison between species within the family Bathyergidae. This study set out to investigate how plasma oxidative markers (total oxidant status (TOS), total antioxidant capacity (TAC), and the oxidative stress index (OSI)) differ between five species and three subspecies of bathyergids, differing in their maximum lifespan potential (MLSP), resting metabolic rate, aridity index (AI), and sociality. We also investigated how oxidative markers may differ between captive and wild-caught mole-rats. Our results reveal that increased TOS, TAC, and OSI are associated with increased MLSP. This pattern is more prevalent in the social-living species than the solitary-living species. We also found that oxidative variables decreased with an increasing AI and that wild-caught individuals typically have higher antioxidants. We speculate that the correlation between higher oxidative markers and MLSP is due to the hypoxia-tolerance of the mole-rats investigated. Hormesis (the biphasic response to oxidative stress promoting protection) is a likely mechanism behind the increased oxidative markers observed and promotes longevity in some members of the Bathyergidae family.
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Affiliation(s)
- Paul. J. Jacobs
- Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa;
| | - Daniel W. Hart
- Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa;
| | - Hana N. Merchant
- Department of Biological Sciences, School of Life and Environmental Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey TW20 0EX, UK;
| | - Cornelia Voigt
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa; (C.V.); (N.C.B.)
| | - Nigel C. Bennett
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Pretoria 0002, South Africa; (C.V.); (N.C.B.)
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9
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Huang X, Du Q, Wang L, Chen B. Impacts of oxygen deficiency on embryo life-history traits of migratory locust Locusta migratoria from low and high altitudes. INSECT SCIENCE 2023; 30:867-879. [PMID: 36325760 DOI: 10.1111/1744-7917.13129] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 10/13/2022] [Indexed: 06/15/2023]
Abstract
Hypoxia challenges aerobic organisms in numerous environments, and hypoxic conditions may become more severe under future climate-change scenarios. The impact of hypoxia on the development of terrestrial insect embryos is not well understood. Here, to address this gap, embryonic life-history traits of migratory locust Locusta migratoria from low-altitude and high-altitude regions were compared under 2 oxygen levels: normoxia (i.e., 21 kPa oxygen partial pressure and mild hypoxia (i.e., 10 kPa oxygen partial pressure). Our results demonstrated that, whether reared under normoxia or mild hypoxia, L. migratoria from high-altitude populations had longer developmental times, reduced weight, and lower mean relative growth rate as compared with those from low-altitude populations. When transferred from normoxia to mild hypoxia, nearly all the tested life-history traits presented significant negative changes in the low-altitude populations, but not in the high-altitude populations. The factor 'strain' alone explained 18.26%-54.59% of the total variation for traits, suggesting that the phenotypic differences between L. migratoria populations from the 2 altitudes could be driven by genetic variation. Significant genetic correlations were found between life-history traits, and most of these showed differentiation between the 2 altitudinal gradients. G-matrix comparisons showed significant structural differences between L. migratoria from the 2 regions, as well as several negative covariances (i.e., trade-offs) between traits in the low-altitude populations. Overall, our study provides clear evidence that evolutionary divergence of embryonic traits between L. migratoria populations from different altitudes has occurred.
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Affiliation(s)
- Xianliang Huang
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, Hebei Province, China
| | - Qianli Du
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, Hebei Province, China
| | - Lijing Wang
- Kenli Municipal Bureau of Agriculture and Rural Affairs, Dongying, Shandong Province, China
| | - Bing Chen
- School of Life Science, Institutes of Life Science and Green Development, Hebei University, Baoding, Hebei Province, China
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10
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Biological Characteristics and Energy Metabolism of Migrating Insects. Metabolites 2023; 13:metabo13030439. [PMID: 36984878 PMCID: PMC10055822 DOI: 10.3390/metabo13030439] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 03/19/2023] Open
Abstract
Through long-distance migration, insects not only find suitable breeding locations and increase the survival space and opportunities for the population but also facilitate large-scale material, energy, and information flow between regions, which is important in maintaining the stability of agricultural ecosystems and wider natural ecosystems. In this study, we summarize the changes in biological characteristics such as morphology, ovarian development, reproduction, and flight capability during the seasonal migration of the insect. In consideration of global research work, the interaction between flight and reproduction, the influence and regulation of the insulin-like and juvenile hormone on the flight and reproductive activities of migrating insects, and the types of energy substances, metabolic processes, and hormone regulation processes during insect flight are elaborated. This systematic review of the latest advances in the studies on insect migration biology and energy metabolism will help readers to better understand the biological behavior and regulation mechanism of the energy metabolism of insect migration.
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11
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Liang C, Liu D, Song P, Zhou Y, Yu H, Sun G, Ma X, Yan J. Transcriptomic Analyses Suggest the Adaptation of Bumblebees to High Altitudes. INSECTS 2022; 13:1173. [PMID: 36555083 PMCID: PMC9783775 DOI: 10.3390/insects13121173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/15/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Determining the adaptive mechanisms by which bumblebees adapt to high altitudes can help us to better understand their distribution, providing a basis for the future protection and utilization of bumblebee resources. For this study, the adaptive mechanisms of two dominant bumblebee species in the northeastern Qinghai-Tibet Plateau-Bombus kashmirensis and B. waltoni-were studied through transcriptomics methods. For each species, enrichment analysis of the differentially expressed genes and gene set enrichment analysis were carried out between samples collected at different altitudes (4000 m, 4500 m, and 5000 m). The results indicate that these bumblebees tend to up-regulate energy metabolism-related genes when facing extremely high-altitude environments. Of the enriched pathways up-regulated in higher altitudes, the pentose and glucuronate interconversions pathway presented the most severe up-regulation in multiple comparisons of different altitudes for B. kashmirensis, as well as the AMPK signaling pathway, which was found to be up-regulated in both species. Notably, limited by the extreme hypoxic conditions in this study, oxidative phosphorylation was found to be down-regulated with increasing altitude, which is uncommon in studies on bumblebee adaptation to high altitudes.
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Affiliation(s)
- Chengbo Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Daoxin Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Kunlun College, Qinghai University, Xining 810016, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Pengfei Song
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001, China
| | - Yuantao Zhou
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Hongyan Yu
- Qinghai Service Guarantee Center of Qilian Mountain National Park, Xining 810001, China
| | - Guo Sun
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Xiaoxuan Ma
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
| | - Jingyan Yan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- College of Agriculture and Animal Husbandry, Qinghai University, Xining 810016, China
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12
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Lyu T, Zhou S, Fang J, Wang L, Shi L, Dong Y, Zhang H. Convergent Genomic Signatures of High-Altitude Adaptation among Six Independently Evolved Mammals. Animals (Basel) 2022; 12:ani12243572. [PMID: 36552492 PMCID: PMC9774524 DOI: 10.3390/ani12243572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/08/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
The species living in the Qinghai-Tibet Plateau provide an excellent model system for studying the relationship between molecular convergent evolution and adaptation. Distant species experiencing the same selection pressure (i.e., hypoxia, low temperature and strong ultraviolet radiation) are likely to evolve similar genetic adaptations independently. Here, we performed comparative genomics studies on six independently evolved high-altitude species. The results also showed that the convergent evolution of the six species was mainly reflected at the level of rapidly evolving genes, and the functions of these rapidly evolving genes were mainly related to hypoxia response and DNA damage repair. In addition, we found that high-altitude species had more gene family changes than their low-altitude relatives, except for the order Lagomorpha. The results also show that the convergence of the gene family contraction of high-altitude species is much greater than that of expansion, revealing a possible pattern of species in adapting to high-altitude. Furthermore, we detected a positive selection signature in four genes related to hypoxia response and ultraviolet radiation damage in these six species (FYCO1, ERBIN, SCAMP1 and CXCL10). Our study reveals that hypoxia response might play an important role in the adaptation of independently evolved species to a high-altitude environment, providing a basic perspective for further exploring the high-altitude adaptation mechanism of different related species in the future.
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Affiliation(s)
- Tianshu Lyu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150000, China
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Shengyang Zhou
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Jiaohui Fang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lidong Wang
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Lupeng Shi
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Yuehuan Dong
- College of Life Science, Qufu Normal University, Qufu 273165, China
| | - Honghai Zhang
- College of Life Science, Qufu Normal University, Qufu 273165, China
- Correspondence:
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13
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Lyu T, Yang X, Zhao C, Wang L, Zhou S, Shi L, Dong Y, Dou H, Zhang H. Comparative transcriptomics of high-altitude Vulpes and their low-altitude relatives. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.999411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The harsh environment of Qinghai-Tibet Plateau (QTP) imposes strong selective stresses (e.g., hypoxia, high UV-radiation, and extreme temperature) to the native species, which have driven striking phenotypic and genetic adaptations. Although the mechanisms of high-altitude adaptation have been explored for many plateau species, how the phylogenetic background contributes to genetic adaption to high-altitude of Vulpes is largely unknown. In this study, we sequenced transcriptomic data across multiple tissues of two high-altitude Vulpes (Vulpes vulpes montana and Vulpes ferrilata) and their low-altitude relatives (Vulpes corsac and Vulpes lagopus) to search the genetic and gene expression changes caused by high-altitude environment. The results indicated that the positive selection genes (PSGs) identified by both high-altitude Vulpes are related to angiogenesis, suggesting that angiogenesis may be the result of convergent evolution of Vulpes in the face of hypoxic selection pressure. In addition, more PSGs were detected in V. ferrilata than in V. v. montana, which may be related to the longer adaptation time of V. ferrilata to plateau environment and thus more genetic changes. Besides, more PSGs associated with high-altitude adaptation were identified in V. ferrilata compared with V. v. montana, indicating that the longer the adaptation time to the high-altitude environment, the more genetic alterations of the species. Furthermore, the result of expression profiles revealed a tissue-specific pattern between Vulpes. We also observed that differential expressed genes in the high-altitude group exhibited species-specific expression patterns, revealed a convergent expression pattern of Vulpes in high-altitude environment. In general, our research provides a valuable transcriptomic resource for further studies, and expands our understanding of high-altitude adaptation within a phylogenetic context.
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14
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Analysis of genome and methylation changes in Chinese indigenous chickens over time provides insight into species conservation. Commun Biol 2022; 5:952. [PMID: 36097156 PMCID: PMC9467985 DOI: 10.1038/s42003-022-03907-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/26/2022] [Indexed: 11/08/2022] Open
Abstract
Conservation of natural resources is a vital and challenging task. Numerous animal genetic resources have been effectively conserved worldwide. However, the effectiveness of conservation programmes and the variation information of species have rarely been evaluated. Here, we performed whole-genome and whole-genome bisulfite sequencing of 90 Chinese indigenous chickens, which belonged to the Tibetan, Wenchang and Bian chicken breeds, and have been conserved under different conservation programmes. We observed that low genetic diversity and high DNA methylation variation occurs during ex situ in vivo conservation, while higher genetic diversity and differentiation occurs during in situ conservation. Further analyses revealed that most DNA methylation signatures are unique within ex situ in vivo conservation. Moreover, a high proportion of differentially methylated regions is found in genomic selection regions, suggesting a link between the effects of genomic variation and DNA methylation. Altogether our findings provide valuable information about genetic and DNA methylation variations during different conservation programmes, and hold practical relevance for species conservation. Comparisons of genomic and methylomic changes during the conservation of indigenous chicken breeds in China provide insight into conservation programmes for these breeds and their adaptations to unique environments.
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15
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Ding D, Zhang J, Du B, Wang X, Hou L, Guo S, Chen B, Kang L. Non-canonical function of an Hif-1α splice variant contributes to the sustained flight of locusts. eLife 2022; 11:74554. [PMID: 36039636 PMCID: PMC9427102 DOI: 10.7554/elife.74554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 07/11/2022] [Indexed: 12/30/2022] Open
Abstract
The hypoxia inducible factor (Hif) pathway is functionally conserved across metazoans in modulating cellular adaptations to hypoxia. However, the functions of this pathway under aerobic physiological conditions are rarely investigated. Here, we show that Hif-1α2, a locust Hif-1α isoform, does not induce canonical hypoxic responses but functions as a specific regulator of locust flight, which is a completely aerobic physiological process. Two Hif-1α splice variants were identified in locusts, a ubiquitously expressed Hif-1α1 and a muscle-predominantly expressed Hif-1α2. Hif-1α1 that induces typical hypoxic responses upon hypoxia exposure remains inactive during flight. By contrast, the expression of Hif-1α2, which lacks C-terminal transactivation domain, is less sensitive to oxygen tension but induced extensively by flying. Hif-1α2 regulates physiological processes involved in glucose metabolism and antioxidation during flight and sustains flight endurance by maintaining redox homeostasis through upregulating the production of a reactive oxygen species (ROS) quencher, DJ-1. Overall, this study reveals a novel Hif-mediated mechanism underlying prolonged aerobic physiological activity.
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Affiliation(s)
- Ding Ding
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Baozhen Du
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xuanzhao Wang
- School of Life Science, Hebei University, Baoding, China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Bing Chen
- School of Life Science, Hebei University, Baoding, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,School of Life Science, Hebei University, Baoding, China
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16
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Repeated genetic adaptation to altitude in two tropical butterflies. Nat Commun 2022; 13:4676. [PMID: 35945236 PMCID: PMC9363431 DOI: 10.1038/s41467-022-32316-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 07/26/2022] [Indexed: 01/02/2023] Open
Abstract
Repeated evolution can provide insight into the mechanisms that facilitate adaptation to novel or changing environments. Here we study adaptation to altitude in two tropical butterflies, Heliconius erato and H. melpomene, which have repeatedly and independently adapted to montane habitats on either side of the Andes. We sequenced 518 whole genomes from altitudinal transects and found many regions differentiated between highland (~ 1200 m) and lowland (~ 200 m) populations. We show repeated genetic differentiation across replicate populations within species, including allopatric comparisons. In contrast, there is little molecular parallelism between the two species. By sampling five close relatives, we find that a large proportion of divergent regions identified within species have arisen from standing variation and putative adaptive introgression from high-altitude specialist species. Taken together our study supports a role for both standing genetic variation and gene flow from independently adapted species in promoting parallel local adaptation to the environment. Here, the authors study adaptation to altitude in 518 whole genomes from two species of tropical butterflies. They find repeated genetic differentiation within species, little molecular parallelism between these species, and introgression from closely related species, concluding that standing genetic variation promotes parallel local adaptation.
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17
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Gao Y, Chen Y, Li S, Huang X, Hu J, Bock DG, MacIsaac HJ, Zhan A. Complementary genomic and epigenomic adaptation to environmental heterogeneity. Mol Ecol 2022; 31:3598-3612. [PMID: 35560847 DOI: 10.1111/mec.16500] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 04/18/2022] [Accepted: 05/05/2022] [Indexed: 12/01/2022]
Abstract
While adaptation is commonly thought to result from selection on DNA sequence-based variation, recent studies have highlighted an analogous epigenetic component as well. However, the relative roles of these mechanisms in facilitating population persistence under environmental heterogeneity remain unclear. To address the underlying genetic and epigenetic mechanisms and their relationship during environmental adaptation, we screened the genomes and epigenomes of nine global populations of a predominately sessile marine invasive tunicate, Botryllus schlosseri, using reduced-representation methods. We detected clear population differentiation at the genetic and epigenetic levels. Patterns of genetic and epigenetic structure were significantly influenced by local environmental variables. Among these variables, minimum annual sea surface temperature was identified as the top explanatory variable for both genetic and epigenetic variation. However, patterns of population structure driven by genetic and epigenetic variation were somewhat distinct, suggesting possible autonomy of epigenetic variation. We found both shared and specific genes and biological pathways among genetic and epigenetic loci associated with environmental factors, consistent with complementary and independent contributions of genetic and epigenetic variation to environmental adaptation in this system. Collectively, these mechanisms may facilitate population persistence under environmental change and sustain successful invasions across novel environments.
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Affiliation(s)
- Yangchun Gao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China.,Guangdong Key Laboratory of Animal Conservation and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Science, Guangzhou, 510260, China
| | - Yiyong Chen
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Shiguo Li
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuena Huang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Juntao Hu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Dan G Bock
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Hugh J MacIsaac
- School of Ecology and Environmental Science, Yunnan University, Yunnan, 650091, China.,Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, N9B 3P4, Canada
| | - Aibin Zhan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.,University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing, 100049, China
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18
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Wang H, Jiang F, Liu X, Liu Q, Fu Y, Li R, Hou L, Zhang J, He J, Kang L. Piwi/piRNAs control food intake by promoting neuropeptide F expression in locusts. EMBO Rep 2022; 23:e50851. [PMID: 34985794 PMCID: PMC8892266 DOI: 10.15252/embr.202050851] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/18/2022] Open
Abstract
Animal feeding, which directly affects growth and metabolism, is an important physiological process. However, the contribution of PIWI proteins and PIWI‐interacting RNAs (piRNAs) to the regulatory mechanism of animal feeding is unknown. Here, we report a novel function of Piwi and piRNAs in regulating food intake in locusts. Our study shows that the locust can serve as a representative species for determining PIWI function in insects. Knockdown of Piwi1 expression suppresses anabolic processes and reduces food consumption and body weight. The reduction in food intake by knockdown of Piwi1 expression results from decreased expression of neuropeptide NPF1 in a piRNA‐dependent manner. Mechanistically, intronic piRNAs might enhance RNA splicing of NPF1 by preventing hairpin formation at the branch point sites. These results suggest a novel nuclear PIWI/piRNA‐mediated mechanism that controls food intake in the locust nervous system.
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Affiliation(s)
- Huimin Wang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Feng Jiang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
| | - Xiang Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Qing Liu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- Sino‐Danish College University of Chinese Academy of Sciences Beijing China
| | - Yunyun Fu
- College of Life Science Hebei University Baoding China
| | - Ran Li
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Jie Zhang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
| | - Jing He
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
| | - Le Kang
- Beijing Institutes of Life Science Chinese Academy of Sciences Beijing China
- CAS Center for Excellence in Biotic Interactions University of Chinese Academy of Sciences Beijing China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents Institute of Zoology Chinese Academy of Sciences Beijing China
- College of Life Science Hebei University Baoding China
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19
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Galván I, Schwartz TS, Garland T. Evolutionary physiology at 30+: Has the promise been fulfilled?: Advances in Evolutionary Physiology: Advances in Evolutionary Physiology. Bioessays 2021; 44:e2100167. [PMID: 34802161 DOI: 10.1002/bies.202100167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022]
Abstract
Three decades ago, interactions between evolutionary biology and physiology gave rise to evolutionary physiology. This caused comparative physiologists to improve their research methods by incorporating evolutionary thinking. Simultaneously, evolutionary biologists began focusing more on physiological mechanisms that may help to explain constraints on and trade-offs during microevolutionary processes, as well as macroevolutionary patterns in physiological diversity. Here we argue that evolutionary physiology has yet to reach its full potential, and propose new avenues that may lead to unexpected advances. Viewing physiological adaptations in wild animals as potential solutions to human diseases offers enormous possibilities for biomedicine. New evidence of epigenetic modifications as mechanisms of phenotypic plasticity that regulate physiological traits may also arise in coming years, which may also represent an overlooked enhancer of adaptation via natural selection to explain physiological evolution. Synergistic interactions at these intersections and other areas will lead to a novel understanding of organismal biology.
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Affiliation(s)
- Ismael Galván
- Department of Evolutionary Ecology, National Museum of Natural Sciences, CSIC, Madrid, Spain
| | - Tonia S Schwartz
- Department of Biological Sciences, Auburn University, Auburn, Alabama, USA
| | - Theodore Garland
- Department of Evolution, Ecology, and Organismal Biology, University of California, Riverside, California, USA
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20
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Omotoso O, Gladyshev VN, Zhou X. Lifespan Extension in Long-Lived Vertebrates Rooted in Ecological Adaptation. Front Cell Dev Biol 2021; 9:704966. [PMID: 34733838 PMCID: PMC8558438 DOI: 10.3389/fcell.2021.704966] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 09/02/2021] [Indexed: 01/21/2023] Open
Abstract
Contemporary studies on aging and longevity have largely overlooked the role that adaptation plays in lifespan variation across species. Emerging evidence indicates that the genetic signals of extended lifespan may be maintained by natural selection, suggesting that longevity could be a product of organismal adaptation. The mechanisms of adaptation in long-lived animals are believed to account for the modification of physiological function. Here, we first review recent progress in comparative biology of long-lived animals, together with the emergence of adaptive genetic factors that control longevity and disease resistance. We then propose that hitchhiking of adaptive genetic changes is the basis for lifespan changes and suggest ways to test this evolutionary model. As individual adaptive or adaptation-linked mutations/substitutions generate specific forms of longevity effects, the cumulative beneficial effect is largely nonrandom and is indirectly favored by natural selection. We consider this concept in light of other proposed theories of aging and integrate these disparate ideas into an adaptive evolutionary model, highlighting strategies in decoding genetic factors of lifespan control.
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Affiliation(s)
- Olatunde Omotoso
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Xuming Zhou
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Beijing, China
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21
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Song K, Gao B, Halvarsson P, Fang Y, Klaus S, Jiang YX, Swenson JE, Sun YH, Höglund J. Demographic history and divergence of sibling grouse species inferred from whole genome sequencing reveal past effects of climate change. BMC Ecol Evol 2021; 21:194. [PMID: 34689746 PMCID: PMC8543876 DOI: 10.1186/s12862-021-01921-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 10/13/2021] [Indexed: 11/23/2022] Open
Abstract
Background The boreal forest is one of the largest biomes on earth, supporting thousands of species. The global climate fluctuations in the Quaternary, especially the ice ages, had a significant influence on the distribution of boreal forest, as well as the divergence and evolution of species inhabiting this biome. To understand the possible effects of on-going and future climate change it would be useful to reconstruct past population size changes and relate such to climatic events in the past. We sequenced the genomes of 32 individuals from two forest inhabiting bird species, Hazel Grouse (Tetrastes bonasia) and Chinese Grouse (T. sewerzowi) and three representatives of two outgroup species from Europe and China. Results We estimated the divergence time of Chinese Grouse and Hazel Grouse to 1.76 (0.46–3.37) MYA. The demographic history of different populations in these two sibling species was reconstructed, and showed that peaks and bottlenecks of effective population size occurred at different times for the two species. The northern Qilian population of Chinese Grouse became separated from the rest of the species residing in the south approximately 250,000 years ago and have since then showed consistently lower effective population size than the southern population. The Chinese Hazel Grouse population had a higher effective population size at the peak of the Last Glacial Period (approx. 300,000 years ago) than the European population. Both species have decreased recently and now have low effective population sizes. Conclusions Combined with the uplift history and reconstructed climate change during the Quaternary, our results support that cold-adapted grouse species diverged in response to changes in the distribution of palaeo-boreal forest and the formation of the Loess Plateau. The combined effects of climate change and an increased human pressure impose major threats to the survival and conservation of both species. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01921-7.
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Affiliation(s)
- Kai Song
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden. .,Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Bin Gao
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Peter Halvarsson
- Unit of Parasitology, Department of Biomedicine and Veterinary Public Health, Swedish University of Agricultural Sciences, PO Box 7036, 75007, Uppsala, Sweden
| | - Yun Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | | | - Ying-Xin Jiang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China
| | - Jon E Swenson
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, 1432, Ås, Norway
| | - Yue-Hua Sun
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 100101, Beijing, People's Republic of China.
| | - Jacob Höglund
- Animal Ecology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.
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22
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Hypoxia Tolerant Species: The Wisdom of Nature Translated into Targets for Stroke Therapy. Int J Mol Sci 2021; 22:ijms222011131. [PMID: 34681788 PMCID: PMC8537001 DOI: 10.3390/ijms222011131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/05/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Human neurons rapidly die after ischemia and current therapies for stroke management are limited to restoration of blood flow to prevent further brain damage. Thrombolytics and mechanical thrombectomy are the available reperfusion treatments, but most of the patients remain untreated. Neuroprotective therapies focused on treating the pathogenic cascade of the disease have widely failed. However, many animal species demonstrate that neurons can survive the lack of oxygen for extended periods of time. Here, we reviewed the physiological and molecular pathways inherent to tolerant species that have been described to contribute to hypoxia tolerance. Among them, Foxo3 and Eif5A were reported to mediate anoxic survival in Drosophila and Caenorhabditis elegans, respectively, and those results were confirmed in experimental models of stroke. In humans however, the multiple mechanisms involved in brain cell death after a stroke causes translation difficulties to arise making necessary a timely and coordinated control of the pathological changes. We propose here that, if we were able to plagiarize such natural hypoxia tolerance through drugs combined in a pharmacological cocktail it would open new therapeutic opportunities for stroke and likely, for other hypoxic conditions.
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23
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Sanno R, Kataoka K, Hayakawa S, Ide K, Nguyen CN, Nguyen TP, Le BTN, Kim OTP, Mineta K, Takeyama H, Takeda M, Sato T, Suzuki T, Yura K, Asahi T. Comparative Analysis of Mitochondrial Genomes in Gryllidea (Insecta: Orthoptera): Implications for Adaptive Evolution in Ant-Loving Crickets. Genome Biol Evol 2021; 13:evab222. [PMID: 34554226 PMCID: PMC8511664 DOI: 10.1093/gbe/evab222] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2021] [Indexed: 12/24/2022] Open
Abstract
Species of infraorder Gryllidea, or crickets, are useful invertebrate models for studying developmental biology and neuroscience. They have also attracted attention as alternative protein sources for human food and animal feed. Mitochondrial genomic information on related invertebrates, such as katydids, and locusts, has recently become available in attempt to clarify the controversial classification schemes, although robust phylogenetic relationships with emphasis on crickets remain elusive. Here, we report newly sequenced complete mitochondrial genomes of crickets to study their phylogeny, genomic rearrangements, and adaptive evolution. First, we conducted de novo assembly of mitochondrial genomes from eight cricket species and annotated protein-coding genes and transfer and ribosomal RNAs using automatic annotations and manual curation. Next, by combining newly described protein-coding genes with public data of the complete Gryllidea genomes and gene annotations, we performed phylogenetic analysis and found gene order rearrangements in several branches. We further analyzed genetic signatures of selection in ant-loving crickets (Myrmecophilidae), which are small wingless crickets that inhabit ant nests. Three distinct approaches revealed two positively selected sites in the cox1 gene in these crickets. Protein 3D structural analyses suggested that these selected sites could influence the interaction of respiratory complex proteins, conferring benefits to ant-loving crickets with a unique ecological niche and morphology. These findings enhance our understanding of the genetic basis of cricket evolution without relying on estimates based on a limited number of molecular markers.
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Affiliation(s)
- Ryuto Sanno
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Kosuke Kataoka
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
| | - Shota Hayakawa
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Keigo Ide
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Department of Health Data Science Research, Healthy Aging Innovation Center, Tokyo Metropolitan Geriatric Medical Center, Tokyo, Japan
| | - Chuong N Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Thao P Nguyen
- Applied Biotechnology for Crop Development Research Unit, School of Biotechnology, International University, Ho Chi Minh City, Vietnam
- Vietnam National University, Ho Chi Minh City, Vietnam
| | - Binh T N Le
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Oanh T P Kim
- Institute of Genome Research, Vietnam Academy of Science and Technology, Cau Giay, Hanoi, Vietnam
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Haruko Takeyama
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
| | - Makio Takeda
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Hyogo, Japan
| | - Toshiyuki Sato
- Faculty of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Takeshi Suzuki
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Japan
| | - Kei Yura
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology, Tokyo, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, Tokyo, Japan
| | - Toru Asahi
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
- Comprehensive Research Organization, Waseda University, Tokyo, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
- Research Organization for Nano & Life Innovation, Waseda University, Tokyo, Japan
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24
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Upadhyay M, Kunz E, Sandoval-Castellanos E, Hauser A, Krebs S, Graf A, Blum H, Dotsev A, Okhlopkov I, Shakhin A, Bagirov V, Brem G, Fries R, Zinovieva N, Medugorac I. Whole genome sequencing reveals a complex introgression history and the basis of adaptation to subarctic climate in wild sheep. Mol Ecol 2021; 30:6701-6717. [PMID: 34534381 DOI: 10.1111/mec.16184] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 09/01/2021] [Accepted: 09/07/2021] [Indexed: 11/29/2022]
Abstract
To predict species responses to anthropogenic disturbances and climate change, it is reasonable to use species with high sensitivity to such factors. Snow sheep (Ovis nivicola) could represent a good candidate for this; as the only large herbivore species adapted to the cold and alpine habitats of northeastern Siberia, it plays a crucial role in its ecosystem. Despite having an extensive geographical distribution among all ovine species, it is one of the least studied. In this study, we sequenced and analysed six genomes of snow sheep in combination with all other wild sheep species to infer key aspects of their evolutionary history and unveil the genetic basis of their adaptation to subarctic environments. Despite their large census population size, snow sheep genomes showed remarkably low heterozygosity, which could reflect the effect of isolation and historical bottlenecks that we inferred using the pairwise sequential Markovian coalescent and runs of homozygosity. F4 -statistics indicated instances of introgression involving snow sheep with argali (Ovis ammon) and Dall (Ovis dalli) sheep, suggesting that these species might have been more widespread during the Pleistocene. Furthermore, the introgressed segments, which were identified using mainly minimum relative node depth, covered genes associated with immunity, adipogenesis and morphology-related traits, representing potential targets of adaptive introgression. Genes related to mitochondrial functions and thermogenesis associated with adipose tissue were identified to be under selection. Overall, our data suggest introgression as a mechanism facilitating adaptation in wild sheep species and provide insights into the genetic mechanisms underlying cold adaptation in snow sheep.
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Affiliation(s)
- Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | - Elisabeth Kunz
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
| | | | - Andreas Hauser
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Alexander Graf
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis, Gene Center, LMU Munich, Munich, Germany
| | - Arsen Dotsev
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | | | - Alexey Shakhin
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Vugar Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, VMU, Vienna, Austria
| | - Ruedi Fries
- Lehrstuhl für Tierzucht, Technische Universität München, Freising, Germany
| | - Natalia Zinovieva
- L.K. Ernst Federal Science Center for Animal Husbandry, Podolsk, Russia
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Munich, Germany
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25
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Liu Q, Jiang F, Zhang J, Li X, Kang L. Transcription initiation of distant core promoters in a large-sized genome of an insect. BMC Biol 2021; 19:62. [PMID: 33785021 PMCID: PMC8011201 DOI: 10.1186/s12915-021-01004-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/16/2021] [Indexed: 12/30/2022] Open
Abstract
Background Core promoters have a substantial influence on various steps of transcription, including initiation, elongation, termination, polyadenylation, and finally, translation. The characterization of core promoters is crucial for exploring the regulatory code of transcription initiation. However, the current understanding of insect core promoters is focused on those of Diptera (especially Drosophila) species with small genome sizes. Results Here, we present an analysis of the transcription start sites (TSSs) in the migratory locust, Locusta migratoria, which has a genome size of 6.5 Gb. The genomic differences, including lower precision of transcription initiation and fewer constraints on the distance from transcription factor binding sites or regulatory elements to TSSs, were revealed in locusts compared with Drosophila insects. Furthermore, we found a distinct bimodal log distribution of the distances from the start codons to the core promoters of locust genes. We found stricter constraints on the exon length of mRNA leaders and widespread expression activity of the distant core promoters in locusts compared with fruit flies. We further compared core promoters in seven arthropod species across a broad range of genome sizes to reinforce our results on the emergence of distant core promoters in large-sized genomes. Conclusions In summary, our results provide novel insights into the effects of genome size expansion on distant transcription initiation. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01004-5.
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Affiliation(s)
- Qing Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,Sino-Danish College, University of Chinese Academy of Sciences, Beijing, China.,Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Feng Jiang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Xiao Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China. .,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
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26
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Li S, Wang J, Cui D, Hao K, Chen J, Tu X, Zhang Z. Antagonism between PTP1B and PTK Mediates Adults' Insulin-Like Signaling Regulation of Egg Diapause in the Migratory Locust. INSECTS 2021; 12:insects12030253. [PMID: 33802986 PMCID: PMC8002652 DOI: 10.3390/insects12030253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/23/2022]
Abstract
Simple Summary It was reported that insulin-like and fork head transcription factor (FOXO) are involved in the regulation of diapause in insects. However, the upstream modulators of the insulin-like signaling pathway (ISP) involved in diapause regulation are still unknown. We used RNAi and an inhibitor to treat PTK and PTP1B in adult tissues and injected Prx V protein or RNAi Prx V under both short and long photoperiod conditions to identify both proteins and broader cellular metabolism influences on diapause regulation. We found that under short photoperiod conditions PTP1B in female adults induces egg diapause, whereas PTK in female adults inhibits egg diapause. Intriguingly, we also found that the antioxidant enzyme Prx V is a negative regulator of NADPH oxidizing reaction, and apparently decreases reactive oxygen species (ROS) production and NADPH-OX activity. Thus, these results indicate that PTP1B, PTK and Prx V are upstream modulators that regulate diapause in eggs via the insulin signaling pathway. Furthermore, these findings have revealed a possible bridge connecting diapause hormone signaling to the insulin-like signaling pathway. Abstract Diapause is a physiological development arrest state that helps insects to adapt to seasonality and overcome adverse environmental conditions. Numerous reports have indicated that insulinlike and fork head transcription factor (FOXO) are involved in the regulation of diapause in insects. However, the upstream modulators of the insulin-like signaling pathway (ISP) involved in diapause regulation are still unknown. Here, we used RNAi and an inhibitor to treat PTK and PTP1B in adult tissues and injected Prx V or RNAi Prx V under both short and long photoperiod conditions and monitored effects on the expression of ISP genes, the phosphorylation levels for IR and IRS, the activity of NADPH oxidase, the accumulation of reactive oxygen species (ROS) and energy metabolism, seeking to identify both proteins and broader cellular metabolism influences on diapause regulation. We found that under short photoperiod conditions PTP1B in female adults induces egg diapause, whereas PTK in female adults inhibits egg diapause. Intriguingly, we also found that the antioxidant enzyme Prx V is a negative regulator of NADPH oxidizing reaction and apparently decreases ROS production and NADPH-OX activity. In contrast, all the eggs laid by adults that were treated with a series of knockdown or purified-protein injection experiments or inhibitor studies and that were reared under long photoperiod conditions hatched successfully. Thus, our results suggest a mechanism wherein diapause-related proteins (PTP1B, PTK, and Prx V) of female adults are the upstream modulators that regulate offspring eggs’ diapause process through the insulin-like signaling pathway under short photoperiod conditions.
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Affiliation(s)
- Shuang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
| | - Jie Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
- School of Resources and Environmental Sciences, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Dongnan Cui
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
| | - Kun Hao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
| | - Jun Chen
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
| | - Xiongbing Tu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
- Correspondence: (X.T.); (Z.Z.); Tel.: +86-010-8210-9569 (X.T. & Z.Z.)
| | - Zehua Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (S.L.); (J.W.); (D.C.); (K.H.); (J.C.)
- Correspondence: (X.T.); (Z.Z.); Tel.: +86-010-8210-9569 (X.T. & Z.Z.)
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27
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Miocene Diversification and High-Altitude Adaptation of Parnassius Butterflies (Lepidoptera: Papilionidae) in Qinghai-Tibet Plateau Revealed by Large-Scale Transcriptomic Data. INSECTS 2020; 11:insects11110754. [PMID: 33153157 PMCID: PMC7693471 DOI: 10.3390/insects11110754] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/01/2022]
Abstract
Simple Summary Parnassius butterflies have contributed to fundamental studies in biogeography, insect–plant interactions, and other fields of conservation biology and ecology. However, the early evolutionary pattern and molecular adaptation mechanism of this alpine butterfly group to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now. In this study, we report for the first time, a relatively large-scale transcriptomic dataset of eight Parnassius species and their two closely related papilionid species, a dated phylogeny based on hundreds of gene sequences, and potential genetic mechanisms underlying the high-altitude adaptation by investigating changes in evolutionary rates and positively selected genes. Overall, our findings indicate that the transcriptome data sets reported here can provide some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, and will support further expressional and functional studies that will help interested researchers to address evolution, biodiversity and conservation questions concerning Parnassius and other butterfly species. Abstract The early evolutionary pattern and molecular adaptation mechanism of alpine Parnassius butterflies to high altitudes in Qinghai–Tibet Plateau are poorly understood up to now, due to difficulties in sampling, limited sequence data, and time calibration issues. Here, we present large-scale transcriptomic datasets of eight representative Parnassius species to reveal the phylogenetic timescale and potential genetic basis for high-altitude adaptation with multiple analytic strategies using 476 orthologous genes. Our phylogenetic results strongly supported that the subgenus Parnassius formed a well-resolved basal clade, and the subgenera Tadumia and Kailasius were closely related in the phylogenetic trees. In addition, molecular dating analyses showed that the Parnassius began to diverge at about 13.0 to 14.3 million years ago (middle Miocene), correlated with their hostplant’s spatiotemporal distributions, as well as geological and palaeoenvironmental changes of the Qinghai–Tibet Plateau. Moreover, the accelerated evolutionary rate, candidate positively selected genes and their potentially functional changes were detected, probably contributed to the high-altitude adaptation of Parnassius species. Overall, our study provided some new insights into the spatiotemporally evolutionary pattern and high altitude adaptation of Parnassius butterflies from the extrinsic and intrinsic view, which will help to address evolution, biodiversity, and conservation questions concerning Parnassius and other butterfly species.
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28
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Talaminos-Barroso A, Roa-Romero LM, Ortega-Ruiz F, Cejudo-Ramos P, Márquez-Martín E, Reina-Tosina J. Effects of genetics and altitude on lung function. CLINICAL RESPIRATORY JOURNAL 2020; 15:247-256. [PMID: 33112470 DOI: 10.1111/crj.13300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/11/2020] [Accepted: 10/23/2020] [Indexed: 12/13/2022]
Abstract
OBJECTIVES The aim of this work is to present a review on the impact of genetics and altitude on lung function from classic and recent studies. DATA SOURCE A systematic search has been carried out in different databases of scientific studies, using keywords related to lung volumes, spirometry, altitude and genetics. RESULTS The results of this work have been structured into three parts. First, the relationship between genes and lung function. Next, a review of the genetic predispositions related to respiratory adaptation of people who inhabit high-altitude regions for millennia. Finally, temporary effects and long-term acclimatisation on respiratory physiology at high altitude are presented. CONCLUSIONS The works focused on the influence of genetics and altitude on lung function are currently of interest in terms of studying the interactions between genetic, epigenetic and environmental factors in the configuration of the pathophysiological adaptation patterns.
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Affiliation(s)
| | | | - Francisco Ortega-Ruiz
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocio, Seville, Spain.,Spanish Networking Center on Biomedical Research, Area of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Pilar Cejudo-Ramos
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocio, Seville, Spain.,Spanish Networking Center on Biomedical Research, Area of Respiratory Diseases (CIBERES), Madrid, Spain
| | - Eduardo Márquez-Martín
- Medical-Surgical Unit of Respiratory Diseases, University Hospital Virgen del Rocio, Seville, Spain
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29
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Xu KK, Pan BY, Wang YY, Ren QQ, Li C. Roles of the PTP61F Gene in Regulating Energy Metabolism of Tribolium castaneum (Coleoptera: Tenebrionidae). Front Physiol 2020; 11:1071. [PMID: 32973565 PMCID: PMC7468486 DOI: 10.3389/fphys.2020.01071] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/04/2020] [Indexed: 12/17/2022] Open
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a negative regulator in the insulin signaling pathway. It belongs to a class of non-receptor phosphatases of protein tyrosine phosphatase and can catalyze the dephosphorylation of tyrosine to regulate cell differentiation, growth, and metabolism. However, few studies have focused on the role of PTP1B in regulating energy metabolism of insects. In this study, we investigated the expression profiles and the functions of a PTP1B gene (designated TcPTP61F) in the red flour beetle Tribolium castaneum. Quantitative real-time PCR analyzed showed that TcPTP61F was highly expressed in the pupal and adult stages. In adult tissues, TcPTP61F was prominently expressed in the tarsus and head. RNA interference-mediated silencing of TcPTP61F reduced the expression of eight genes in trehalose metabolic and glycolytic pathways. TcPTP61F depletion also caused a significant change in the distribution of trehalose, glucose, and glycogen. Additionally, knockdown of TcPTP61F inhibited the pyruvate kinase (PK) activity and significantly decreased the adenosine triphosphate (ATP) level. The results suggest that TcPTP61F is indispensible for trehalose and energy metabolism of T. castaneum.
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Affiliation(s)
- Kang-Kang Xu
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Bi-Ying Pan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yuan-Yuan Wang
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Qian-Qian Ren
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
| | - Can Li
- Guizhou Provincial Key Laboratory for Rare Animal and Economic Insect of the Mountainous Region, Guizhou Provincial Engineering Research Center for Biological Resources Protection and Efficient Utilization of the Mountainous Region, College of Biology and Environmental Engineering, Guiyang University, Guiyang, China
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30
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Mutations in a Novel Cadherin Gene Associated with Bt Resistance in Helicoverpa zea. G3-GENES GENOMES GENETICS 2020; 10:1563-1574. [PMID: 32179620 PMCID: PMC7202007 DOI: 10.1534/g3.120.401053] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Transgenic corn and cotton produce crystalline (Cry) proteins derived from the soil bacterium Bacillus thuringiensis (Bt) that are toxic to lepidopteran larvae. Helicoverpa zea, a key pest of corn and cotton in the U.S., has evolved widespread resistance to these proteins produced in Bt corn and cotton. While the genomic targets of Cry selection and the mutations that produce resistant phenotypes are known in other lepidopteran species, little is known about how selection by Cry proteins shape the genome of H. zea. We scanned the genomes of Cry1Ac-selected and unselected H. zea lines, and identified twelve genes on five scaffolds that differed between lines, including cadherin-86C (cad-86C), a gene from a family that is involved in Cry1A resistance in other lepidopterans. Although this gene was expressed in the H. zea larval midgut, the protein it encodes has only 17 to 22% identity with cadherin proteins from other species previously reported to be involved in Bt resistance. An analysis of midgut-expressed cDNAs showed significant between-line differences in the frequencies of putative nonsynonymous substitutions (both SNPs and indels). Our results indicate that cad-86C is a likely target of Cry1Ac selection in H. zea. It remains unclear, however, whether genomic changes at this locus directly disrupt midgut binding of Cry1Ac and cause Bt resistance, or indirectly enhance fitness of H. zea in the presence of Cry1Ac by some other mechanism. Future work should investigate phenotypic effects of these nonsynonymous substitutions and their impact on fitness of H. zea larvae that ingest Cry1Ac.
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31
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Ma Q, Hu CT, Yue J, Luo Y, Qiao F, Chen LQ, Zhang ML, Du ZY. High-carbohydrate diet promotes the adaptation to acute hypoxia in zebrafish. FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:665-679. [PMID: 31820205 DOI: 10.1007/s10695-019-00742-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/03/2019] [Indexed: 06/10/2023]
Abstract
Oxygen deprivation (hypoxia) is a common challenge in water environment, which causes lack of energy and oxidative damage in organisms. Many studies have indicated a number of physiological and metabolic changes under hypoxia, but the effects of dietary nutrients on hypoxia tolerance have not been well evaluated. In the present 7-week feeding trial, we fed zebrafish with low-protein diet (LP), high-protein diet (HP), low-fat diet (LF), high-fat diet (HF), low-carbohydrate diet (LC), and high-carbohydrate diet (HC), respectively. Afterward, the resistance to acute hypoxia challenge, growth, body composition, activities of metabolic enzymes, and expressions of energy homeostasis-related genes and six hifαs genes were measured. The results indicated that only the HC diet could significantly improve the resistance to hypoxia challenge. Moreover, the HC diet feeding caused higher glycogen deposition in the liver and muscle, and these glycogens were significantly reduced after 6-h acute hypoxia challenge. Meanwhile, the lactate content in the liver and blood was increased in the HC groups. At hypoxia status, the relative mRNA expressions of the genes related to glycolysis, ATP production, insulin signaling pathway, and hif-3a (hif1al) were all significantly increased in the muscle of the HC diet-fed fish. This study revealed that high-carbohydrate diet could improve the resistance to hypoxia by activating glycolysis and hif/insulin signaling pathway in zebrafish, mainly in the muscle, to efficiently supply energy. Therefore, our results highlight the importance of dietary carbohydrate in resisting hypoxia in fish.
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Affiliation(s)
- Qiang Ma
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Chun-Ting Hu
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Junjiayu Yue
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Yuan Luo
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Fang Qiao
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Li-Qiao Chen
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Mei-Ling Zhang
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China
| | - Zhen-Yu Du
- LANEH, School of Life Sciences, East China Normal University, Shanghai, 200241, People's Republic of China.
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Su Y, Wei L, Tan H, Li J, Li W, Fu L, Wang T, Kang L, Yao XS. Optical coherence tomography as a noninvasive 3D real time imaging tool for the rapid evaluation of phenotypic variations in insect embryonic development. JOURNAL OF BIOPHOTONICS 2020; 13:e201960047. [PMID: 31682322 DOI: 10.1002/jbio.201960047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/24/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Noninvasive visualization of embryos at different development stages is crucial for the understanding of the basic developmental biology. It is therefore desirable to have an imaging tool capable of rapidly evaluating the effects of gene manipulation or genome editing in developing embryos for the studies of gene functions and genetic engineering. Here, we propose and demonstrate a novel use of optical coherence tomography (OCT) to noninvasively exam the embryonic development of the migratory locusts in real time with 3-dimensional (3D) view capability. In particular, we obtain the sufficiently high spatial resolution tomographic 2D and 3D images of live locust embryos throughout their development processes. We show that not only we are able to noninvasively observe all previously known forms of blastokinesis as an embryo develops, such as anatrepsis, katatrepsis, revolution, rotation and diapauses, and determine their precise occurring time or duration, but also discover an unreported rotation form we named "twist." In addition, with the OCT images we determined the exact occurring time of diapauses of the locusts from Tibetan plateau for the first time. Finally, we demonstrate that OCT systems can be used to rapidly capture the development defects of genetically modified embryos in which certain genes essential for embryonic development were suppressed by RNA interference. Our work shows that OCT is an enabling imaging tool with sufficient spatial resolution for the rapid evaluation of embryonic variations of small animals.
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Affiliation(s)
- Ya Su
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Liya Wei
- College of Life Sciences, Hebei University, Baoding, China
| | - Hao Tan
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Jing Li
- College of Life Sciences, Hebei University, Baoding, China
| | - Wenping Li
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Lei Fu
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
| | - Tongxin Wang
- College of Life Sciences, Hebei University, Baoding, China
| | - Le Kang
- College of Life Sciences, Hebei University, Baoding, China
| | - X Steve Yao
- Photonics Information Innovation Center, Hebei Provincial Center for Optical Sensing Innovations, College of Physics Science & Technology, Hebei University, Baoding, China
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Pristimerin inhibits glioma progression by targeting AGO2 and PTPN1 expression via miR-542-5p. Biosci Rep 2019; 39:BSR20182389. [PMID: 31015365 PMCID: PMC6522714 DOI: 10.1042/bsr20182389] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/28/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma multiform is the most common and malignant primary tumor of the central nervous system in adults, the high recurrence rate and poor prognosis are critical priorities. Pristimerin is a naturally occurring quinone methide triterpenoid isolated from the Celastraceae and Hippocrateaceae families. Its anticancer effects have garnered considerable attention; nonetheless, the mechanisms of action remain unknown. To predict the hub genes of pristimerin, PharmMapper and the Coremine database were used to identify 13 potential protein targets; protein-protein interaction, for which functional enrichment analyses were performed. Compound-target, target-pathway, and compound-target-pathway networks were constructed using Cytoscape. Biological process analysis first revealed that enrichment of these target genes correlated with negative regulation of symbiont growth in the host, and regulation of chronic inflammatory response to antigenic stimulus. Survival analysis in cBioPortal showed that protein tyrosine phosphatase, non-receptor type 1 (PTPN1) and Argonaute 2 (AGO2) might be involved in the carcinogenesis, invasion, or recurrence of diffuse glioma. In addition, we observed that low-dose pristimerin inhibited the viability of glioma cells, while miR-542-5p in vitro; and reduced PTPN1 expression. Notably, high-dose pristimerin induced apoptosis. Furthermore, miR-542-5p silence with siRNA in glioma cells lead to the elevation in AGO2, and decreased PTPN1 level. The effect was obviously post pristimerin treatment and miR-542-5p suppression. In conclusion, pristimerin inhibited glioma progression through AGO2 and PTPN1 expression via a canonical miRNA-mediated mechanism.
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