1
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Alibardi L. Progressive modifications during evolution involving epigenetic changes have determined loss of regeneration mainly in terrestrial animals: A hypothesis. Dev Biol 2024; 515:169-177. [PMID: 39029569 DOI: 10.1016/j.ydbio.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/10/2024] [Accepted: 07/17/2024] [Indexed: 07/21/2024]
Abstract
In order to address a biological explanation for the different regenerative abilities present among animals, a new evolutionary speculation is presented. It is hypothesized that epigenetic mechanisms have lowered or erased regeneration during the evolution of terrestrial invertebrates and vertebrates. The hypothesis indicates that a broad regeneration can only occur in marine or freshwater conditions, and that life on land does not allow for high regeneration. This is due to the physical, chemical and microbial conditions present in the terrestrial environment with respect to those of the aquatic environment. The present speculation provides examples of hypothetic evolutionary animal lineages that colonized the land, such as parasitic annelids, terrestrial mollusks, arthropods and amniotes. These are the animals where regeneration is limited or absent and their injuries are only repaired through limited healing or scarring. It is submitted that this loss derived from changes in the developmental gene pathways sustaining regeneration in the aquatic environment but that cannot be expressed on land. Once regeneration was erased in terrestrial species, re-adaptation to freshwater niches could not reactivate the previously altered gene pathways that determined regeneration. Therefore a broad regeneration was no longer possible or became limited and heteromorphic in the derived, extant animals. Only in few cases extensive healing abilities or regengrow, a healing process where regeneration overlaps with somatic growth, have evolved among arthropods and amniotes. The present paper is an extension of previous speculations trying to explain in biological terms the different regenerative abilities present among metazoans.
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2
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Cappucci U, Proietti M, Casale AM, Schiavo S, Chiavarini S, Accardo S, Manzo S, Piacentini L. Assessing genotoxic effects of plastic leachates in Drosophila melanogaster. CHEMOSPHERE 2024; 361:142440. [PMID: 38821133 DOI: 10.1016/j.chemosphere.2024.142440] [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: 10/19/2023] [Revised: 05/16/2024] [Accepted: 05/24/2024] [Indexed: 06/02/2024]
Abstract
Plastic polymers were largely added with chemical substances to be utilized in the items and product manufacturing. The leachability of these substances is a matter of concern given the wide amount of plastic waste, particularly in terrestrial environments, where soil represents a sink for these novel contaminants and a possible pathway of human health risk. In this study, we integrated genetic, molecular, and behavioral approaches to comparatively evaluate toxicological effects of plastic leachates, virgin and oxodegradable polypropylene (PP) and polyethylene (PE), in Drosophila melanogaster, a novel in vivo model organism for environmental monitoring studies and (eco)toxicological research. The results of this study revealed that while conventional toxicological endpoints such as developmental times and longevity remain largely unaffected, exposure to plastic leachates induces chromosomal abnormalities and transposable element (TE) activation in neural tissues. The combined effects of DNA damage and TE mobilization contribute to genome instability and increase the likelihood of LOH events, thus potentiating tumor growth and metastatic behavior ofRasV12 clones. Collectively, these findings indicate that plastic leachates exert genotoxic effects in Drosophila thus highlighting potential risks associated with leachate-related plastic pollution and their implications for ecosystems and human health.
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Affiliation(s)
- Ugo Cappucci
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Mirena Proietti
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Assunta Maria Casale
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy
| | - Simona Schiavo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Salvatore Chiavarini
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Sara Accardo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy
| | - Sonia Manzo
- ENEA, Department for Sustainability, Division Protection and Enhancement of the Natural Capital, P. le E. Fermi 1, 80055 Portici, Na, Italy.
| | - Lucia Piacentini
- Department of Biology and Biotechnologies "C. Darwin", Sapienza University of Rome, P. le A. Moro 5, 00185 Rome, Italy.
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Dittrich C, Hoelzl F, Smith S, Fouilloux CA, Parker DJ, O’Connell LA, Knowles LS, Hughes M, Fewings A, Morgan R, Rojas B, Comeault AA. Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution. Genome Biol Evol 2024; 16:evae109. [PMID: 38753031 PMCID: PMC11152451 DOI: 10.1093/gbe/evae109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/12/2024] [Indexed: 06/07/2024] Open
Abstract
Genome size varies greatly across the tree of life and transposable elements are an important contributor to this variation. Among vertebrates, amphibians display the greatest variation in genome size, making them ideal models to explore the causes and consequences of genome size variation. However, high-quality genome assemblies for amphibians have, until recently, been rare. Here, we generate a high-quality genome assembly for the dyeing poison frog, Dendrobates tinctorius. We compare this assembly to publicly available frog genomes and find evidence for both large-scale conserved synteny and widespread rearrangements between frog lineages. Comparing conserved orthologs annotated in these genomes revealed a strong correlation between genome size and gene size. To explore the cause of gene-size variation, we quantified the location of transposable elements relative to gene features and find that the accumulation of transposable elements in introns has played an important role in the evolution of gene size in D. tinctorius, while estimates of insertion times suggest that many insertion events are recent and species-specific. Finally, we carry out population-scale mobile-element sequencing and show that the diversity and abundance of transposable elements in poison frog genomes can complicate genotyping from repetitive element sequence anchors. Our results show that transposable elements have clearly played an important role in the evolution of large genome size in D. tinctorius. Future studies are needed to fully understand the dynamics of transposable element evolution and to optimize primer or bait design for cost-effective population-level genotyping in species with large, repetitive genomes.
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Affiliation(s)
- Carolin Dittrich
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Franz Hoelzl
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Chloe A Fouilloux
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
| | - Darren J Parker
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | | | - Lucy S Knowles
- NERC Environmental Omics Facility, University of Sheffield, Sheffield, UK
| | - Margaret Hughes
- Centre for Genomic Research, University of Liverpool, Liverpool, UK
| | - Ade Fewings
- Supercomputing Wales, Digital Services, Bangor University, Bangor, UK
| | - Rhys Morgan
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
| | - Bibiana Rojas
- Department of Biology and Environmental Sciences, University of Jyväskylä, Jyväskylä, Finland
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine, Vienna, Austria
| | - Aaron A Comeault
- School of Environmental and Natural Sciences, Molecular Ecology & Evolution Group, Bangor University, Bangor, UK
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4
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Lin X, Yin J, Wang Y, Yao J, Li QQ, Latzel V, Bossdorf O, Zhang YY. Environment-induced heritable variations are common in Arabidopsis thaliana. Nat Commun 2024; 15:4615. [PMID: 38816460 PMCID: PMC11139905 DOI: 10.1038/s41467-024-49024-3] [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: 10/11/2023] [Accepted: 05/17/2024] [Indexed: 06/01/2024] Open
Abstract
Parental or ancestral environments can induce heritable phenotypic changes, but whether such environment-induced heritable changes are a common phenomenon remains unexplored. Here, we subject 14 genotypes of Arabidopsis thaliana to 10 different environmental treatments and observe phenotypic and genome-wide gene expression changes over four successive generations. We find that all treatments caused heritable phenotypic and gene expression changes, with a substantial proportion stably transmitted over all observed generations. Intriguingly, the susceptibility of a genotype to environmental inductions could be predicted based on the transposon abundance in the genome. Our study thus challenges the classic view that the environment only participates in the selection of heritable variation and suggests that the environment can play a significant role in generating of heritable variations.
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Affiliation(s)
- Xiaohe Lin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Yifan Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Jing Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
| | - Qingshun Q Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, USA
| | - Vit Latzel
- Institute of Botany of the CAS, Zamek 1, 252 43, Pruhonice, Czech Republic
| | - Oliver Bossdorf
- Institute of Evolution & Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076, Tübingen, Germany
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, Fujian, China.
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Dayi M. Diversity and evolution of transposable elements in the plant-parasitic nematodes. BMC Genomics 2024; 25:511. [PMID: 38783171 PMCID: PMC11118728 DOI: 10.1186/s12864-024-10435-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 05/21/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Transposable elements (TEs) are mobile DNA sequences that propagate within genomes, occupying a significant portion of eukaryotic genomes and serving as a source of genetic variation and innovation. TEs can impact genome dynamics through their repetitive nature and mobility. Nematodes are incredibly versatile organisms, capable of thriving in a wide range of environments. The plant-parasitic nematodes are able to infect nearly all vascular plants, leading to significant crop losses and management expenses worldwide. It is worth noting that plant parasitism has evolved independently at least three times within this nematode group. Furthermore, the genome size of plant-parasitic nematodes can vary substantially, spanning from 41.5 Mbp to 235 Mbp. To investigate genome size variation and evolution in plant-parasitic nematodes, TE composition, diversity, and evolution were analysed in 26 plant-parasitic nematodes from 9 distinct genera in Clade IV. RESULTS Interestingly, despite certain species lacking specific types of DNA transposons or retrotransposon superfamilies, they still exhibit a diverse range of TE content. Identification of species-specific TE repertoire in nematode genomes provides a deeper understanding of genome evolution in plant-parasitic nematodes. An intriguing observation is that plant-parasitic nematodes possess extensive DNA transposons and retrotransposon insertions, including recent sightings of LTR/Gypsy and LTR/Pao superfamilies. Among them, the Gypsy superfamilies were found to encode Aspartic proteases in the plant-parasitic nematodes. CONCLUSIONS The study of the transposable element (TE) composition in plant-parasitic nematodes has yielded insightful discoveries. The findings revealed that certain species exhibit lineage-specific variations in their TE makeup. Discovering the species-specific TE repertoire in nematode genomes is a crucial element in understanding the evolution of genomes in plant-parasitic nematodes. It allows us to gain a deeper insight into the intricate workings of these organisms and their genetic makeup. With this knowledge, we are gaining a fundamental piece in the puzzle of understanding the evolution of these parasites. Moreover, recent transpositions have led to the acquisition of new TE superfamilies, especially Gypsy and Pao retrotransposons, further expanding the diversity of TEs in these nematodes. Significantly, the widely distributed Gypsy superfamily possesses proteases that are exclusively associated with parasitism during nematode-host interactions. These discoveries provide a deeper understanding of the TE landscape within plant-parasitic nematodes.
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Affiliation(s)
- Mehmet Dayi
- Forestry Vocational School, Düzce University, Konuralp Campus, 81620, Düzce, Türkiye.
- Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan.
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6
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Göpel T, Burggren WW. Temperature and hypoxia trigger developmental phenotypic plasticity of cardiorespiratory physiology and growth in the parthenogenetic marbled crayfish, Procambarus virginalis Lyko, 2017. Comp Biochem Physiol A Mol Integr Physiol 2024; 288:111562. [PMID: 38113959 DOI: 10.1016/j.cbpa.2023.111562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/06/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
Attempting to differentiate phenotypic variation caused by environmentally-induced alterations in gene expression from that caused by actual allelic differences can be experimentally difficult. Environmental variables must be carefully controlled and then interindividual genetic differences ruled out as sources of phenotypic variation. We investigated phenotypic variability of cardiorespiratory physiology as well as biometric traits in the parthenogenetically-reproducing marbled crayfish Procambarus virginalis Lyko, 2017, all offspring being genetically identical clones. Populations of P. virginalis were reared from eggs tank-bred at four different temperatures (16, 19, 22 and 25 °C) or two different oxygen levels (9.5 and 20 kPa). Then, at Stage 3 and 4 juvenile stages, physiological (heart rate, oxygen consumption) and morphological (carapace length, body mass) variables were measured. Heart rate and oxygen consumption measured at 23 °C showed only small effects of rearing temperature in Stage 3 juveniles, with larger effects evident in older, Stage 4 juveniles. Additionally, coefficients of variation were calculated to compare our data to previously published data on P. virginalis as well as sexually-reproducing crayfish. Comparison revealed that carapace length, body mass and heart rate (but not oxygen consumption) indeed showed lower, yet notable coefficients of variation in clonal crayfish. Yet, despite being genetically identical, significant variation in their morphology and physiology in response to different rearing conditions nonetheless occurred in marbled crayfish. This suggests that epigenetically induced phenotypic variation might play a significant role in asexual but also sexually reproducing species.
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Affiliation(s)
- Torben Göpel
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, TX, USA; Multiscale Biology, Georg-August-Universität Göttingen, Göttingen, Germany.
| | - Warren W Burggren
- Developmental Integrative Biology Research Group, Department of Biological Sciences, University of North Texas, Denton, TX, USA
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Ardelan A, Tsai A, Will S, McGuire R, Amarasekare P. Increase in heat tolerance following a period of heat stress in a naturally occurring insect species. J Anim Ecol 2023; 92:2039-2051. [PMID: 37667662 DOI: 10.1111/1365-2656.13995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 07/28/2023] [Indexed: 09/06/2023]
Abstract
Climate warming is the defining environmental crisis of the 21st century. Elucidating whether organisms can adapt to rapidly changing thermal environments is therefore a crucial research priority. We investigated warming effects on a native Hemipteran insect (Murgantia histrionica) that feeds on an endemic plant species (Isomeris arborea) of the California coastal sage scrub. Experiments conducted in 2009 quantified the temperature responses of juvenile maturation rates and stage-specific and cumulative survivorship. The intervening decade has seen some of the hottest years ever recorded, with increasing mean temperatures accompanied by an increase in the frequency of hot extremes. Experiments repeated in 2021 show a striking change in the bugs' temperature responses. In 2009, no eggs developed past the second nymphal stage at 33°C. In 2021, eggs developed into reproductive adults at 33°C. Upper thermal limits for maturation and survivorship have increased, along with a decrease in mortality risk with increasing age and temperature, and a decrease in the temperature sensitivity of mortality with increasing age. While we cannot exclude the possibility that other environmental factors occurring in concert could have affected our findings, the fact that all observed trait changes are in the direction of greater heat tolerance suggests that consistent exposure to extreme heat stress may at least be partially responsible for these changes. Harlequin bugs belong to the suborder Heteroptera, which contains a number of economically important pests, biological control agents and disease carriers. Their differential success in withstanding warming compared to beneficial holometabolous insects such as pollinators may exacerbate the decline of beneficial insects due to other causes (e.g. pollution and pesticides) with potentially serious consequences on both biodiversity and ecosystem functioning.
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Affiliation(s)
- Andre Ardelan
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Anne Tsai
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Sophia Will
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Rosa McGuire
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
| | - Priyanga Amarasekare
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, USA
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Murani E, Gilbert H, Rauw WM. Editorial: Genotype-by-environment interaction in farm animals: from measuring to understanding. Front Genet 2023; 14:1267334. [PMID: 37621708 PMCID: PMC10445942 DOI: 10.3389/fgene.2023.1267334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Affiliation(s)
- Eduard Murani
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Hélène Gilbert
- GenPhySE, INRAE, INP, Université de Toulouse, Castanet-Tolosan, France
| | - Wendy M. Rauw
- Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
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Lin H, Chen L, Li J. Multiple Introductions and Distinct Genetic Groups of Canada Goldenrod ( Solidago canadensis) in China Revealed by Genomic Single-Nucleotide Polymorphisms. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091734. [PMID: 37176791 PMCID: PMC10180931 DOI: 10.3390/plants12091734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 05/15/2023]
Abstract
Despite numerous studies reported in the context of ecology, the introduction history of the infamous invasive plant Canada goldenrod (Solidago canadensis L.) remains elusive. In the present study, we explored the sources and the number of introduction events of this species from its native areas into China. Using the genotyping-by-sequencing approach, we identified 34,035 selectively neutral single-nucleotide polymorphism (SNP) markers to infer the evolutionary trajectories of 77 S. canadensis individuals. Both the principal component analysis and the ADMIXTURE analysis revealed two genetic groups that are sympatric to each other in China and suggested the absence of genetic admixtures. The phylogenetic analysis indicated three feasible introduction routes and multiple introduction events of Canada goldenrod into China. Specifically, the one from the USA directly into China, the other from the USA into China through Japan, and the third from the USA into China through Europe. Based on the site frequency spectrum of these identified SNPs, we inferred strong bottleneck events for both genetic groups, and that the multiple introductions did not rescue the decline of genetic diversity. To conclude, multiple introduction events, genetic bottlenecks, and potential human-mediated spread characterize the introduction history of Canada goldenrod in China. The present study harnesses the power of SNP data in deciphering the evolutionary trajectory of invasive plants and paves the way for future studies concerning the invasion mechanism of Canada goldenrod.
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Affiliation(s)
- Hanyang Lin
- School of Advanced Study, Taizhou University, Taizhou 318000, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China
| | - Luxi Chen
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China
| | - Junmin Li
- School of Advanced Study, Taizhou University, Taizhou 318000, China
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, School of Life Sciences, Taizhou University, Taizhou 318000, China
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Wang R, Wu B, Jian J, Tang Y, Zhang T, Song Z, Zhang W, Qiong L. How to survive in the world's third poplar: Insights from the genome of the highest altitude woody plant, Hippophae tibetana (Elaeagnaceae). FRONTIERS IN PLANT SCIENCE 2022; 13:1051587. [PMID: 36589082 PMCID: PMC9797102 DOI: 10.3389/fpls.2022.1051587] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Hippophae tibetana (Tibetan sea-buckthorn) is one of the highest distributed woody plants in the world (3,000-5,200 meters a.s.l.). It is characterized by adaptation to extreme environment and important economic values. Here, we combined PacBio Hifi platform and Hi-C technology to assemble a 1,452.75 Mb genome encoding 33,367 genes with a Contig N50 of 74.31 Mb, and inferred its sexual chromosome. Two Hippophae-specific whole-genome duplication events (18.7-21.2 million years ago, Ma; 28.6-32.4 Ma) and long terminal repeats retroelements (LTR-RTs) amplifications were detected. Comparing with related species at lower altitude, Ziziphus jujuba (<1, 700 meters a.s.l.), H. tibetana had some significantly rapid evolving genes involved in adaptation to high altitude habitats. However, comparing with Hippophae rhamnoides (<3, 700 meters a.s.l.), no rapid evolving genes were found except microtubule and microtubule-based process genes, H. tibetana has a larger genome, with extra 2, 503 genes (7.5%) and extra 680.46 Mb transposable elements (TEs) (46.84%). These results suggest that the changes in the copy number and regulatory pattern of genes play a more important role for H. tibetana adapting to more extreme and variable environments at higher altitude by more TEs and more genes increasing genome variability and expression plasticity. This suggestion was supported by two findings: nitrogen-fixing genes of H. tibetana having more copies, and intact TEs being significantly closer genes than fragmentary TEs. This study provided new insights into the evolution of alpine plants.
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Affiliation(s)
- Ruoqiu Wang
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Bin Wu
- BGI-Shenzhen, Shenzhen, China
| | | | - Yiwei Tang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Ticao Zhang
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhiping Song
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - Wenju Zhang
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai, China
| | - La Qiong
- Tibet University-Fudan University Joint Laboratory for Biodiversity and Global Change, School of Life Sciences, Fudan University, Shanghai, China
- Research Center for Ecology, College of Science, Tibet University, Lhasa, China
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WiFi Related Radiofrequency Electromagnetic Fields Promote Transposable Element Dysregulation and Genomic Instability in Drosophila melanogaster. Cells 2022; 11:cells11244036. [PMID: 36552798 PMCID: PMC9776602 DOI: 10.3390/cells11244036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
Exposure to artificial radio frequency electromagnetic fields (RF-EMFs) has greatly increased in recent years, thus promoting a growing scientific and social interest in deepening the biological impact of EMFs on living organisms. The current legislation governing the exposure to RF-EMFs is based exclusively on their thermal effects, without considering the possible non-thermal adverse health effects from long term exposure to EMFs. In this study we investigated the biological non-thermal effects of low-level indoor exposure to RF-EMFs produced by WiFi wireless technologies, using Drosophila melanogaster as the model system. Flies were exposed to 2.4 GHz radiofrequency in a Transverse Electromagnetic (TEM) cell device to ensure homogenous controlled fields. Signals were continuously monitored during the experiments and regulated at non thermal levels. The results of this study demonstrate that WiFi electromagnetic radiation causes extensive heterochromatin decondensation and thus a general loss of transposable elements epigenetic silencing in both germinal and neural tissues. Moreover, our findings provide evidence that WiFi related radiofrequency electromagnetic fields can induce reactive oxygen species (ROS) accumulation, genomic instability, and behavioural abnormalities. Finally, we demonstrate that WiFi radiation can synergize with RasV12 to drive tumor progression and invasion. All together, these data indicate that radiofrequency radiation emitted from WiFi devices could exert genotoxic effects in Drosophila and set the stage to further explore the biological effects of WiFi electromagnetic radiation on living organisms.
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12
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Berger J, Legendre F, Zelosko KM, Harrison MC, Grandcolas P, Bornberg-Bauer E, Fouks B. Eusocial Transition in Blattodea: Transposable Elements and Shifts of Gene Expression. Genes (Basel) 2022; 13:1948. [PMID: 36360186 PMCID: PMC9689775 DOI: 10.3390/genes13111948] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2023] Open
Abstract
(1) Unravelling the molecular basis underlying major evolutionary transitions can shed light on how complex phenotypes arise. The evolution of eusociality, a major evolutionary transition, has been demonstrated to be accompanied by enhanced gene regulation. Numerous pieces of evidence suggest the major impact of transposon insertion on gene regulation and its role in adaptive evolution. Transposons have been shown to be play a role in gene duplication involved in the eusocial transition in termites. However, evidence of the molecular basis underlying the eusocial transition in Blattodea remains scarce. Could transposons have facilitated the eusocial transition in termites through shifts of gene expression? (2) Using available cockroach and termite genomes and transcriptomes, we investigated if transposons insert more frequently in genes with differential expression in queens and workers and if those genes could be linked to specific functions essential for eusocial transition. (3) The insertion rate of transposons differs among differentially expressed genes and displays opposite trends between termites and cockroaches. The functions of termite transposon-rich queen- and worker-biased genes are related to reproduction and ageing and behaviour and gene expression, respectively. (4) Our study provides further evidence on the role of transposons in the evolution of eusociality, potentially through shifts in gene expression.
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Affiliation(s)
- Juliette Berger
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Frédéric Legendre
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Kevin-Markus Zelosko
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
| | - Mark C. Harrison
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
| | - Philippe Grandcolas
- Institut de Systématique, Évolution, Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, CP50, 57 rue Cuvier, 75005 Paris, France
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Bertrand Fouks
- Institute for Evolution and Biodiversity, Molecular Evolution and Bioinformatics, Westfälische Wilhelms-Universität, Hüfferstrasse 1, 48149 Münster, Germany
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13
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Planidin NP, de Carvalho CF, Feder JL, Gompert Z, Nosil P. Epigenetics and reproductive isolation: a commentary on Westram et al., 2022. J Evol Biol 2022; 35:1188-1194. [PMID: 36063158 PMCID: PMC9541925 DOI: 10.1111/jeb.14033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 05/24/2022] [Indexed: 12/23/2022]
Affiliation(s)
| | | | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | | | - Patrik Nosil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
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14
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Ma B, Li Z, Lv Y, E Z, Fang J, Ren C, Luo P, Hu C. Analysis of Complete Mitochondrial Genome of Bohadschia argus (Jaeger, 1833) (Aspidochirotida, Holothuriidae). Animals (Basel) 2022; 12:ani12111437. [PMID: 35681901 PMCID: PMC9179316 DOI: 10.3390/ani12111437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/26/2022] [Accepted: 05/31/2022] [Indexed: 12/04/2022] Open
Abstract
Bohadschia argu is a kind of sea cucumber with high economic value; it is the only undisputed species in the genus Bohadschia. In this study, the complete mitochondrial genome (mitogenome) of B. argus was acquired through high-throughput sequencing. The mitochondrial genome of B. argus was 15,656 bp in total length and contained a putative control region (CR) and 37 typical genes of animal mitochondrial genomes, including 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rrnS and rrnL) and 22 transfer RNA genes (tRNA). The sizes of the PCGs ranged from 168 bp to 1833 bp, and all PCGs except nad6 were encoded on the heavy chain (H). Both rrnS and rrnL were also encoded on the H chain. Twenty-two tRNA genes had positive AT skew and GC skew. All tRNAs had a typical cloverleaf secondary structure except for trnI, in which an arm of dihydrouridine was missing. B. argus shared the same gene arrangement order (the echinoderm ground pattern) as other species in Aspidochirotida. Phylogenetic analysis clearly revealed that B. argus belongs as a member of the Holothuriidae, and it is closely related to members of Actinopyga and Holothuria.
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Affiliation(s)
- Bo Ma
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuobo Li
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ying Lv
- Guangxi Key Laboratory of Beibu Gulf Marine Biodiversity Conservation, Beibu Gulf University, Qinzhou 535011, China;
| | - Zixuan E
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianxiang Fang
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunhua Ren
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
| | - Peng Luo
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
- Correspondence: ; Tel.: +86-18520090836
| | - Chaoqun Hu
- CAS Key Laboratory of Tropical Marine Bioresources and Ecology (LMB), South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; (B.M.); (Z.L.); (Z.E.); (J.F.); (C.R.); (C.H.)
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou 510301, China
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15
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Wyngaard GA, Skern-Mauritzen R, Malde K, Prendergast R, Peruzzi S. The salmon louse genome may be much larger than sequencing suggests. Sci Rep 2022; 12:6616. [PMID: 35459797 PMCID: PMC9033869 DOI: 10.1038/s41598-022-10585-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/08/2022] [Indexed: 12/30/2022] Open
Abstract
The genome size of organisms impacts their evolution and biology and is often assumed to be characteristic of a species. Here we present the first published estimates of genome size of the ecologically and economically important ectoparasite, Lepeophtheirus salmonis (Copepoda, Caligidae). Four independent L. salmonis genome assemblies of the North Atlantic subspecies Lepeophtheirus salmonis salmonis, including two chromosome level assemblies, yield assemblies ranging from 665 to 790 Mbps. These genome assemblies are congruent in their findings, and appear very complete with Benchmarking Universal Single-Copy Orthologs analyses finding > 92% of expected genes and transcriptome datasets routinely mapping > 90% of reads. However, two cytometric techniques, flow cytometry and Feulgen image analysis densitometry, yield measurements of 1.3-1.6 Gb in the haploid genome. Interestingly, earlier cytometric measurements reported genome sizes of 939 and 567 Mbps in L. salmonis salmonis samples from Bay of Fundy and Norway, respectively. Available data thus suggest that the genome sizes of salmon lice are variable. Current understanding of eukaryotic genome dynamics suggests that the most likely explanation for such variability involves repetitive DNA, which for L. salmonis makes up ≈ 60% of the genome assemblies.
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Affiliation(s)
- Grace A Wyngaard
- Department of Biology, James Madison University, Harrisonburg, VA, USA
| | | | - Ketil Malde
- Institute of Marine Research, Bergen, Norway
- Department of Informatics, University of Bergen, Bergen, Norway
| | | | - Stefano Peruzzi
- Department of Arctic Marine Biology, UiT-the Arctic University of Norway, Tromsø, Norway.
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16
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Colonna Romano N, Fanti L. Transposable Elements: Major Players in Shaping Genomic and Evolutionary Patterns. Cells 2022; 11:cells11061048. [PMID: 35326499 PMCID: PMC8947103 DOI: 10.3390/cells11061048] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Transposable elements (TEs) are ubiquitous genetic elements, able to jump from one location of the genome to another, in all organisms. For this reason, on the one hand, TEs can induce deleterious mutations, causing dysfunction, disease and even lethality in individuals. On the other hand, TEs can increase genetic variability, making populations better equipped to respond adaptively to environmental change. To counteract the deleterious effects of TEs, organisms have evolved strategies to avoid their activation. However, their mobilization does occur. Usually, TEs are maintained silent through several mechanisms, but they can be reactivated during certain developmental windows. Moreover, TEs can become de-repressed because of drastic changes in the external environment. Here, we describe the ‘double life’ of TEs, being both ‘parasites’ and ‘symbionts’ of the genome. We also argue that the transposition of TEs contributes to two important evolutionary processes: the temporal dynamic of evolution and the induction of genetic variability. Finally, we discuss how the interplay between two TE-dependent phenomena, insertional mutagenesis and epigenetic plasticity, plays a role in the process of evolution.
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17
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What Have We Learned in 30 Years of Investigations on Bari Transposons? Cells 2022; 11:cells11030583. [PMID: 35159391 PMCID: PMC8834629 DOI: 10.3390/cells11030583] [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: 01/12/2022] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/17/2022] Open
Abstract
Transposable elements (TEs) have been historically depicted as detrimental genetic entities that selfishly aim at perpetuating themselves, invading genomes, and destroying genes. Scientists often co-opt "special" TEs to develop new and powerful genetic tools, that will hopefully aid in changing the future of the human being. However, many TEs are gentle, rarely unleash themselves to harm the genome, and bashfully contribute to generating diversity and novelty in the genomes they have colonized, yet they offer the opportunity to develop new molecular tools. In this review we summarize 30 years of research focused on the Bari transposons. Bari is a "normal" transposon family that has colonized the genomes of several Drosophila species and introduced genomic novelties in the melanogaster species. We discuss how these results have contributed to advance the field of TE research and what future studies can still add to the current knowledge.
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18
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Methylation patterns of Tf2 retrotransposons linked to rapid adaptive stress response in the brown planthopper (Nilaparvata lugens). Genomics 2021; 113:4214-4226. [PMID: 34774681 DOI: 10.1016/j.ygeno.2021.11.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/12/2021] [Accepted: 11/07/2021] [Indexed: 11/23/2022]
Abstract
Transposable elements (TEs) exhibit vast diversity across insect orders and are one of the major factors driving insect evolution and speciation. Presence of TEs can be both beneficial and deleterious to their host. While it is well-established that TEs impact life-history traits, adaptations and survivability of insects under hostile environments, the influence of the ecological niche on TE-landscape remains unclear. Here, we analysed the dynamics of Tf2 retrotransposons in the brown planthopper (BPH), under environmental fluctuations. BPH, a major pest of rice, is found in almost all rice-growing ecosystems. We believe genome plasticity, attributed to TEs, has allowed BPH to adapt and colonise novel ecological niches. Our study revealed bimodal age-distribution for Tf2 elements in BPH, indicating the occurrence of two major transpositional events in its evolutionary history and their contribution in shaping BPH genome. While TEs can provide genome flexibility and facilitate adaptations, they impose massive load on the genome. Hence, we investigated the involvement of methylation in modulating transposition in BPH. We performed comparative analyses of the methylation patterns of Tf2 elements in BPH feeding on resistant- and susceptible-rice varieties, and also under pesticide stress, across different life-stages. Results confirmed that methylation, particularly in non-CG context, is involved in TE regulation and dynamics under stress. Furthermore, we observed differential methylation for BPH adults and nymphs, emphasising the importance of screening juvenile life-stages in understanding adaptive-stress-responses in insects. Collectively, this study enhances our understanding of the role of transposons in influencing the evolutionary trajectory and survival strategies of BPH across generations.
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19
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Lemmen KD, Verhoeven KJF, Declerck SAJ. Experimental evidence of rapid heritable adaptation in the absence of initial standing genetic variation. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kimberley D. Lemmen
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland
| | - Koen J. F. Verhoeven
- Department of Terrestrial Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
| | - Steven A. J. Declerck
- Department of Aquatic Ecology Netherlands Institute of Ecology (NIOO‐KNAW) Wageningen The Netherlands
- Department of Biology Laboratory of Aquatic Ecology, Evolution and Conservation KULeuven Leuven Belgium
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20
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Zhang L, Zhang ZR, Zheng YQ, Zhang LJ, Wang MY, Wang XT, Yuan ML. Genome-wide gene expression profiles of the pea aphid (Acyrthosiphon pisum) under cold temperatures provide insights into body color variation. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2021; 108:e21797. [PMID: 34272770 DOI: 10.1002/arch.21797] [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: 03/20/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 06/13/2023]
Abstract
Cold temperatures are one of the factors influencing color polymorphisms in Acyrthosiphon pisum, resulting in a change from a red to greenish color. Here we characterized gene expression profiles of A. pisum under different low temperatures (1°C, 4°C, 8°C, and 14°C) and durations (3, 6, 12, and 24 h). The number of differentially expressed genes (DEGs) increased as temperatures decreased and time increased, but only a small number of significant DEGs were identified. Genes involved in pigment metabolism were downregulated. An interaction network analysis for 506 common DEGs in comparisons among aphids exposed to 1°C for four durations indicated that a cytochrome P450 gene (CYP, LOC112935894) significantly downregulated may interact with a carotenoid metabolism gene (LOC100574964), similar to other genes encoding CYP, lycopene dehydrogenase and fatty acid synthase. We proposed that the body color shift in A. pisum responding to low temperatures may be regulated by CYPs.
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Affiliation(s)
- Li Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Department of Biology, The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Zhou-Rui Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Department of Biology, The Institute for Advanced Studies (IAS), Wuhan University, Wuhan, China
| | - Yong-Qiang Zheng
- Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Li-Jun Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Meng-Yao Wang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
- Developmental Biology, College of Life Sciences, Wuhan University, Wuhan, China
| | - Xiao-Tong Wang
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-ecosystems, Lanzhou University, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
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21
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Crespi E, Burnap R, Chen J, Das M, Gassman N, Rosa E, Simmons R, Wada H, Wang ZQ, Xiao J, Yang B, Yin J, Goldstone JV. Resolving the Rules of Robustness and Resilience in Biology Across Scales. Integr Comp Biol 2021; 61:2163-2179. [PMID: 34427654 DOI: 10.1093/icb/icab183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/23/2021] [Accepted: 08/20/2021] [Indexed: 12/29/2022] Open
Abstract
Why do some biological systems and communities persist while others fail? Robustness, a system's stability, and resilience, the ability to return to a stable state, are key concepts that span multiple disciplines within and outside the biological sciences. Discovering and applying common rules that govern the robustness and resilience of biological systems is a critical step toward creating solutions for species survival in the face of climate change, as well as the for the ever-increasing need for food, health, and energy for human populations. We propose that network theory provides a framework for universal scalable mathematical models to describe robustness and resilience and the relationship between them, and hypothesize that resilience at lower organization levels contribute to robust systems. Insightful models of biological systems can be generated by quantifying the mechanisms of redundancy, diversity, and connectivity of networks, from biochemical processes to ecosystems. These models provide pathways towards understanding how evolvability can both contribute to and result from robustness and resilience under dynamic conditions. We now have an abundance of data from model and non-model systems and the technological and computational advances for studying complex systems. Several conceptual and policy advances will allow the research community to elucidate the rules of robustness and resilience. Conceptually, a common language and data structure that can be applied across levels of biological organization needs to be developed. Policy advances such as cross-disciplinary funding mechanisms, access to affordable computational capacity, and the integration of network theory and computer science within the standard biological science curriculum will provide the needed research environments. This new understanding of biological systems will allow us to derive ever more useful forecasts of biological behaviors and revolutionize the engineering of biological systems that can survive changing environments or disease, navigate the deepest oceans, or sustain life throughout the solar system.
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Affiliation(s)
- Erica Crespi
- School of Biological Sciences, Washington State University
| | - Robert Burnap
- Microbiology and Molecular Genetics, Oklahoma State University
| | - Jing Chen
- Department of Biological Sciences, Virginia Polytechnic Institute and State University
| | - Moumita Das
- School of Physics and Astronomy, Rochester Institute of Technology
| | | | - Epaminondas Rosa
- Department of Physics and School of Biological Sciences, Illinois State University
| | | | - Haruka Wada
- Department of Biological Sciences, Auburn University
| | - Zhen Q Wang
- Department of Biological Sciences, University at Buffalo
| | - Jie Xiao
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine
| | - Bing Yang
- Division of Plant Sciences, University of Missouri
| | - John Yin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison
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22
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Liu RL, Yang YB, Lee BR, Liu G, Zhang WG, Chen XY, Song XJ, Kang JQ, Zhu ZH. The dispersal-related traits of an invasive plant Galinsoga quadriradiata correlate with elevation during range expansion into mountain ranges. AOB PLANTS 2021; 13:plab008. [PMID: 34194688 PMCID: PMC8237851 DOI: 10.1093/aobpla/plab008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Detecting shifts in trait values among populations of an invasive plant is important for assessing invasion risks and predicting future spread. Although a growing number of studies suggest that the dispersal propensity of invasive plants increases during range expansion, there has been relatively little attention paid to dispersal patterns along elevational gradients. In this study, we tested the differentiation of dispersal-related traits in an invasive plant, Galinsoga quadriradiata, across populations at different elevations in the Qinling and Bashan Mountains in central China. Seed mass-area ratio (MAR), an important seed dispersal-related trait, of 45 populations from along an elevational gradient was measured, and genetic variation of 23 populations was quantified using inter-simple sequence repeat (ISSR) markers. Individuals from four populations were then planted in a greenhouse to compare their performance under shared conditions. Changing patterns of seed dispersal-related traits and populations genetic diversity along elevation were tested using linear regression. Mass-area ratio of G. quadriradiata increased, while genetic diversity decreased with elevation in the field survey. In the greenhouse, populations of G. quadriradiata sourced from different elevations showed a difference response of MAR. These results suggest that although rapid evolution may contribute to the range expansion of G. quadriradiata in mountain ranges, dispersal-related traits will also likely be affected by phenotypic plasticity. This challenges the common argument that dispersal ability of invasive plants increases along dispersal routes. Furthermore, our results suggest that high-altitude populations would be more effective at seed dispersal once they continue to expand their range downslope on the other side. Our experiment provides novel evidence that the spread of these high-altitude populations may be more likely than previously theorized and that they should thus be cautiously monitored.
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Affiliation(s)
- Rui-Ling Liu
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Ying-Bo Yang
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Benjamin R Lee
- School for Environment and Sustainability, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gang Liu
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
- National Engineering Laboratory for Resource Development of Endangered Crude Drugs in Northwest China, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Wen-Gang Zhang
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Xiao-Yan Chen
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Xing-Jiang Song
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Ju-Qing Kang
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
| | - Zhi-Hong Zhu
- College of Life Sciences, Shaanxi Normal University, 710119 Xi’an, People’s Republic of China
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23
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Baduel P, Colot V. The epiallelic potential of transposable elements and its evolutionary significance in plants. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200123. [PMID: 33866816 PMCID: PMC8059525 DOI: 10.1098/rstb.2020.0123] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA provides the fundamental framework for heritability, yet heritable trait variation need not be completely ‘hard-wired’ into the DNA sequence. In plants, the epigenetic machinery that controls transposable element (TE) activity, and which includes DNA methylation, underpins most known cases of inherited trait variants that are independent of DNA sequence changes. Here, we review our current knowledge of the extent, mechanisms and potential adaptive contribution of epiallelic variation at TE-containing alleles in this group of species. For the purpose of this review, we focus mainly on DNA methylation, as it provides an easily quantifiable readout of such variation. The picture that emerges is complex. On the one hand, pronounced differences in DNA methylation at TE sequences can either occur spontaneously or be induced experimentally en masse across the genome through genetic means. Many of these epivariants are stably inherited over multiple sexual generations, thus leading to transgenerational epigenetic inheritance. Functional consequences can be significant, yet they are typically of limited magnitude and although the same epivariants can be found in nature, the factors involved in their generation in this setting remain to be determined. On the other hand, moderate DNA methylation variation at TE-containing alleles can be reproducibly induced by the environment, again usually with mild effects, and most of this variation tends to be lost across generations. Based on these considerations, we argue that TE-containing alleles, rather than their inherited epiallelic variants, are the main targets of natural selection. Thus, we propose that the adaptive contribution of TE-associated epivariation, whether stable or not, lies predominantly in its capacity to modulate TE mobilization in response to the environment, hence providing hard-wired opportunities for the flexible exploration of the phenotypic space. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’
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Affiliation(s)
- Pierre Baduel
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005 Paris, France
| | - Vincent Colot
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM), Ecole Normale Supérieure, PSL Research University, 75005 Paris, France
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Transposable Elements and Teleost Migratory Behaviour. Int J Mol Sci 2021; 22:ijms22020602. [PMID: 33435333 PMCID: PMC7827017 DOI: 10.3390/ijms22020602] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transposable elements (TEs) represent a considerable fraction of eukaryotic genomes, thereby contributing to genome size, chromosomal rearrangements, and to the generation of new coding genes or regulatory elements. An increasing number of works have reported a link between the genomic abundance of TEs and the adaptation to specific environmental conditions. Diadromy represents a fascinating feature of fish, protagonists of migratory routes between marine and freshwater for reproduction. In this work, we investigated the genomes of 24 fish species, including 15 teleosts with a migratory behaviour. The expected higher relative abundance of DNA transposons in ray-finned fish compared with the other fish groups was not confirmed by the analysis of the dataset considered. The relative contribution of different TE types in migratory ray-finned species did not show clear differences between oceanodromous and potamodromous fish. On the contrary, a remarkable relationship between migratory behaviour and the quantitative difference reported for short interspersed nuclear (retro)elements (SINEs) emerged from the comparison between anadromous and catadromous species, independently from their phylogenetic position. This aspect is likely due to the substantial environmental changes faced by diadromous species during their migratory routes.
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Androsiuk P, Chwedorzewska KJ, Dulska J, Milarska S, Giełwanowska I. Retrotransposon-based genetic diversity of Deschampsia antarctica Desv. from King George Island (Maritime Antarctic). Ecol Evol 2021; 11:648-663. [PMID: 33437458 PMCID: PMC7790655 DOI: 10.1002/ece3.7095] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Deschampsia antarctica Desv. can be found in diverse Antarctic habitats which may vary considerably in terms of environmental conditions and soil properties. As a result, the species is characterized by wide ecotypic variation in terms of both morphological and anatomical traits. The species is a unique example of an organism that can successfully colonize inhospitable regions due to its phenomenal ability to adapt to both the local mosaic of microhabitats and to general climatic fluctuations. For this reason, D. antarctica has been widely investigated in studies analyzing morphophysiological and biochemical responses to various abiotic stresses (frost, drought, salinity, increased UV radiation). However, there is little evidence to indicate whether the observed polymorphism is accompanied by the corresponding genetic variation. In the present study, retrotransposon-based iPBS markers were used to trace the genetic variation of D. antarctica collected in nine sites of the Arctowski oasis on King George Island (Western Antarctic). The genotyping of 165 individuals from nine populations with seven iPBS primers revealed 125 amplification products, 15 of which (12%) were polymorphic, with an average of 5.6% polymorphic fragments per population. Only one of the polymorphic fragments, observed in population 6, was represented as a private band. The analyzed specimens were characterized by low genetic diversity (uHe = 0.021, I = 0.030) and high population differentiation (F ST = 0.4874). An analysis of Fu's F S statistics and mismatch distribution in most populations (excluding population 2, 6 and 9) revealed demographic/spatial expansion, whereas significant traces of reduction in effective population size were found in three populations (1, 3 and 5). The iPBS markers revealed genetic polymorphism of D. antarctica, which could be attributed to the mobilization of random transposable elements, unique features of reproductive biology, and/or geographic location of the examined populations.
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Affiliation(s)
- Piotr Androsiuk
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
| | | | - Justyna Dulska
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
| | - Sylwia Milarska
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
| | - Irena Giełwanowska
- Department of Plant Physiology, Genetics and BiotechnologyFaculty of Biology and BiotechnologyUniversity of Warmia and Mazury in OlsztynOlsztynPoland
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Affiliation(s)
- Anthony Herrel
- Département Adaptations du Vivant UMR 7179 CNRS/MNHN Paris Cedex 5 France
| | - Dominique Joly
- Laboratoire Evolution, Génomes, Comportement, Ecologie UMR9191 CNRS/IRD/Université Paris-Saclay Gif-sur-Yvette France
| | - Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB) UMR5174, CNRSUniversité Fédérale de ToulouseIRD Toulouse Cedex 9 France
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