1
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Royle JW, Hurwood D, Sadowski P, Dudley KJ. Non-CG DNA methylation marks the transition from pupa to adult in Helicoverpa armigera. INSECT MOLECULAR BIOLOGY 2024; 33:493-502. [PMID: 38668923 DOI: 10.1111/imb.12917] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/10/2024] [Indexed: 08/20/2024]
Abstract
DNA methylation in insects is generally low in abundance, and its role is not well understood. It is often localised in protein coding regions and associated with the expression of 'housekeeping' genes. Few studies have explored DNA methylation dynamics during lifecycle stage transitions in holometabolous (metamorphosing) insects. Using targeted mass spectrometry, we have found a significant difference in global DNA methylation levels between larvae, pupae and adults of Helicoverpa armigera (Lepidoptera: Noctuidae) Hübner, a polyphagous pest of agricultural importance. Whole-genome bisulfite sequencing confirmed these observations and pointed to non-CG context being the primary explanation for the difference observed between pupa and adult. Non-CG methylation was enriched in genes specific to various signalling pathways (Hippo signalling, Hedgehog signalling and mitogen-activated protein kinase (MAPK) signalling) and ATP-dependent chromatin remodelling. Understanding the function of this epigenetic mark could be a target in future studies focusing on integrated pest management.
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Affiliation(s)
- Jack W Royle
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - David Hurwood
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Pawel Sadowski
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Kevin J Dudley
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
- Central Analytical Research Facility, Queensland University of Technology, Brisbane, Queensland, Australia
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2
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Geens B, Goossens S, Li J, Van de Peer Y, Vanden Broeck J. Untangling the gordian knot: The intertwining interactions between developmental hormone signaling and epigenetic mechanisms in insects. Mol Cell Endocrinol 2024; 585:112178. [PMID: 38342134 DOI: 10.1016/j.mce.2024.112178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/30/2024] [Accepted: 02/04/2024] [Indexed: 02/13/2024]
Abstract
Hormones control developmental and physiological processes, often by regulating the expression of multiple genes simultaneously or sequentially. Crosstalk between hormones and epigenetics is pivotal to dynamically coordinate this process. Hormonal signals can guide the addition and removal of epigenetic marks, steering gene expression. Conversely, DNA methylation, histone modifications and non-coding RNAs can modulate regional chromatin structure and accessibility and regulate the expression of numerous (hormone-related) genes. Here, we provide a review of the interplay between the classical insect hormones, ecdysteroids and juvenile hormones, and epigenetics. We summarize the mode-of-action and roles of these hormones in post-embryonic development, and provide a general overview of epigenetic mechanisms. We then highlight recent advances on the interactions between these hormonal pathways and epigenetics, and their involvement in development. Furthermore, we give an overview of several 'omics techniques employed in the field. Finally, we discuss which questions remain unanswered and possible avenues for future research.
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Affiliation(s)
- Bart Geens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Stijn Goossens
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
| | - Jia Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; VIB Center for Plant Systems Biology, VIB, Ghent, Belgium.
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59 box 2465, B-3000 Leuven, Belgium.
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3
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Zhang J, Liu M, Wen L, Hua Y, Zhang R, Li S, Zafar J, Pang R, Xu H, Xu X, Jin F. MiR-2b-3p Downregulated PxTrypsin-9 Expression in the Larval Midgut to Decrease Cry1Ac Susceptibility of the Diamondback Moth, Plutella xylostella (L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:2263-2276. [PMID: 38235648 DOI: 10.1021/acs.jafc.3c07678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Crystal (Cry) toxins, produced by Bacillus thuringiensis, are widely used as effective biological pesticides in agricultural production. However, insects always quickly evolve adaptations against Cry toxins within a few generations. In this study, we focused on the Cry1Ac protoxin activated by protease. Our results identified PxTrypsin-9 as a trypsin gene that plays a key role in Cry1Ac virulence in Plutella xylostella larvae. In addition, P. xylostella miR-2b-3p, a member of the micoRNA-2 (miR-2) family, was significantly upregulated by Cry1Ac protoxin and targeted to PxTrypsin-9 downregulated its expression. The mRNA level of PxTrypsin-9, regulated by miR-2b-3p, revealed an increased tolerance of P. xylostella larvae to Cry1Ac at the post-transcriptional level. Considering that miR-2b and trypsin genes are widely distributed in various pest species, our study provides the basis for further investigation of the roles of miRNAs in the regulation of the resistance to Cry1Ac and other insecticides.
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Affiliation(s)
- Jie Zhang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Mingyou Liu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Liang Wen
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Yanyan Hua
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Ruonan Zhang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - ShuZhong Li
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Junaid Zafar
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Rui Pang
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Hanhong Xu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Xiaoxia Xu
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
| | - Fengliang Jin
- National Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou 510642, China
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4
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Somers DJ, Kushner DB, McKinnis AR, Mehmedovic D, Flame RS, Arnold TM. Epigenetic weapons in plant-herbivore interactions: Sulforaphane disrupts histone deacetylases, gene expression, and larval development in Spodoptera exigua while the specialist feeder Trichoplusia ni is largely resistant to these effects. PLoS One 2023; 18:e0293075. [PMID: 37856454 PMCID: PMC10586618 DOI: 10.1371/journal.pone.0293075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
Cruciferous plants produce sulforaphane (SFN), an inhibitor of nuclear histone deacetylases (HDACs). In humans and other mammals, the consumption of SFN alters enzyme activities, DNA-histone binding, and gene expression within minutes. However, the ability of SFN to act as an HDAC inhibitor in nature, disrupting the epigenetic machinery of insects feeding on these plants, has not been explored. Here, we demonstrate that SFN consumed in the diet inhibits the activity of HDAC enzymes and slows the development of the generalist grazer Spodoptera exigua, in a dose-dependent fashion. After consuming SFN for seven days, the activities of HDAC enzymes in S. exigua were reduced by 50%. Similarly, larval mass was reduced by 50% and pupation was delayed by 2-5 days, with no additional mortality. Similar results were obtained when SFN was applied topically to eggs. RNA-seq analyses confirm that SFN altered the expression of thousands of genes in S. exigua. Genes associated with energy conversion pathways were significantly downregulated while those encoding for ribosomal proteins were dramatically upregulated in response to the consumption of SFN. In contrast, the co-evolved specialist feeder Trichoplusia ni was not negatively impacted by SFN, whether it was consumed in their diet at natural concentrations or applied topically to eggs. The activities of HDAC enzymes were not inhibited and development was not disrupted. In fact, SFN exposure sometimes accelerated T. ni development. RNA-seq analyses revealed that the consumption of SFN alters gene expression in T. ni in similar ways, but to a lesser degree, compared to S. exigua. This apparent resistance of T. ni can be overwhelmed by unnaturally high levels of SFN or by exposure to more powerful pharmaceutical HDAC inhibitors. These results demonstrate that dietary SFN interferes with the epigenetic machinery of insects, supporting the hypothesis that plant-derived HDAC inhibitors serve as "epigenetic weapons" against herbivores.
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Affiliation(s)
- Dana J. Somers
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - David B. Kushner
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Alexandria R. McKinnis
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Dzejlana Mehmedovic
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Rachel S. Flame
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
| | - Thomas M. Arnold
- Department of Biology, Program in Biochemistry and Molecular Biology, Dickinson College, Carlisle, PA United States of America
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5
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Rahman SR, Lozier JD. Genome-wide DNA methylation patterns in bumble bee (Bombus vosnesenskii) populations from spatial-environmental range extremes. Sci Rep 2023; 13:14901. [PMID: 37689750 PMCID: PMC10492822 DOI: 10.1038/s41598-023-41896-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
Unraveling molecular mechanisms of adaptation to complex environments is crucial to understanding tolerance of abiotic pressures and responses to climatic change. Epigenetic variation is increasingly recognized as a mechanism that can facilitate rapid responses to changing environmental cues. To investigate variation in genetic and epigenetic diversity at spatial and thermal extremes, we use whole genome and methylome sequencing to generate a high-resolution map of DNA methylation in the bumble bee Bombus vosnesenskii. We sample two populations representing spatial and environmental range extremes (a warm southern low-elevation site and a cold northern high-elevation site) previously shown to exhibit differences in thermal tolerance and determine positions in the genome that are consistently and variably methylated across samples. Bisulfite sequencing reveals methylation characteristics similar to other arthropods, with low global CpG methylation but high methylation concentrated in gene bodies and in genome regions with low nucleotide diversity. Differentially methylated sites (n = 2066) were largely hypomethylated in the northern high-elevation population but not related to local sequence differentiation. The concentration of methylated and differentially methylated sites in exons and putative promoter regions suggests a possible role in gene regulation, and this high-resolution analysis of intraspecific epigenetic variation in wild Bombus suggests that the function of methylation in niche adaptation would be worth further investigation.
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Affiliation(s)
| | - Jeffrey D Lozier
- Department of Biological Sciences, The University of Alabama, Tuscaloosa, AL, USA
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6
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Boman J, Zhu Y, Höök L, Vila R, Talavera G, Backström N. Environmental stress during larval development induces DNA methylation shifts in the migratory painted lady butterfly (Vanessa cardui). Mol Ecol 2023. [PMID: 37088782 DOI: 10.1111/mec.16957] [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: 01/24/2023] [Revised: 03/22/2023] [Accepted: 04/12/2023] [Indexed: 04/25/2023]
Abstract
Seasonal environmental fluctuations provide formidable challenges for living organisms, especially small ectotherms such as butterflies. A common strategy to cope with harsh environments is to enter diapause, but some species avoid unsuitable conditions by migrating. Despite a growing understanding of migration in the life cycles of some butterfly species, it remains unknown how individuals register and store environmental cues to determine whether and where to migrate. Here, we explored how competition and host plant availability during larval development affect patterns of DNA methylation in the migratory painted lady (Vanessa cardui) butterfly. We identify a set of potentially functional methylome shifts associated with differences in the environment, indicating that DNA methylation is involved in the response to different conditions during larval development. By analysing the transcriptome for the same samples used for methylation profiling, we also uncovered a non-monotonic relationship between gene body methylation and gene expression. Our results provide a starting point for understanding the interplay between DNA methylation and gene expression in butterflies in general and how differences in environmental conditions during development can trigger unique epigenetic marks that might be important for behavioural decisions in the adult stage.
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Affiliation(s)
- Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Yishu Zhu
- Animal Ecology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Lars Höök
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-Univ. Pompeu Fabra), Barcelona, Spain
| | - Gerard Talavera
- Institut Botànic de Barcelona (IBB), CSIC-Ajuntament de Barcelona, Barcelona, Spain
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Uppsala, Sweden
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7
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Zhao Y, Hu J, Wu J, Li Z. ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis. Front Genet 2023; 14:1108104. [PMID: 36911387 PMCID: PMC9996634 DOI: 10.3389/fgene.2023.1108104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
Introduction: While it has been suggested that histone modifications can facilitate animal responses to rapidly changing environments, few studies have profiled whole-genome histone modification patterns in invasive species, leaving the regulatory landscape of histone modifications in invasive species unclear. Methods: Here, we screen genome-wide patterns of two important histone modifications, trimethylated Histone H3 Lysine 4 (H3K4me3) and trimethylated Histone H3 Lysine 27 (H3K27me3), in adult thorax muscles of a notorious invasive pest, the Oriental fruit fly Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), using Chromatin Immunoprecipitation with high-throughput sequencing (ChIP-seq). Results: We identified promoters featured by the occupancy of H3K4me3, H3K27me3 or bivalent histone modifications that were respectively annotated with unique genes key to muscle development and structure maintenance. In addition, we found H3K27me3 occupied the entire body of genes, where the average enrichment was almost constant. Transcriptomic analysis indicated that H3K4me3 is associated with active gene transcription, and H3K27me3 is mostly associated with transcriptional repression. Importantly, we identified genes and putative motifs modified by distinct histone modification patterns that may possibly regulate flight activity. Discussion: These findings provide the first evidence of histone modification signature in B. dorsalis, and will be useful for future studies of epigenetic signature in other invasive insect species.
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Affiliation(s)
- Yan Zhao
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, 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, China
| | - Jiajiao Wu
- Technology Center of Guangzhou Customs, Guangzhou, China
| | - Zhihong Li
- Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Ministry of Agriculture and Rural Affairs, College of Plant Protection, China Agricultural University, Beijing, China
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8
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Liu L, Li Z, Luo X, Zhang X, Chou SH, Wang J, He J. Which Is Stronger? A Continuing Battle Between Cry Toxins and Insects. Front Microbiol 2021; 12:665101. [PMID: 34140940 PMCID: PMC8203666 DOI: 10.3389/fmicb.2021.665101] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/20/2021] [Indexed: 12/20/2022] Open
Abstract
In this article, we review the latest works on the insecticidal mechanisms of Bacillus thuringiensis Cry toxins and the resistance mechanisms of insects against Cry toxins. Currently, there are two models of insecticidal mechanisms for Cry toxins, namely, the sequential binding model and the signaling pathway model. In the sequential binding model, Cry toxins are activated to bind to their cognate receptors in the mid-intestinal epithelial cell membrane, such as the glycophosphatidylinositol (GPI)-anchored aminopeptidases-N (APNs), alkaline phosphatases (ALPs), cadherins, and ABC transporters, to form pores that elicit cell lysis, while in the signaling pathway model, the activated Cry toxins first bind to the cadherin receptor, triggering an extensive cell signaling cascade to induce cell apoptosis. However, these two models cannot seem to fully describe the complexity of the insecticidal process of Cry toxins, and new models are required. Regarding the resistance mechanism against Cry toxins, the main method insects employed is to reduce the effective binding of Cry toxins to their cognate cell membrane receptors by gene mutations, or to reduce the expression levels of the corresponding receptors by trans-regulation. Moreover, the epigenetic mechanisms, host intestinal microbiota, and detoxification enzymes also play significant roles in the insects' resistance against Cry toxins. Today, high-throughput sequencing technologies like transcriptomics, proteomics, and metagenomics are powerful weapons for studying the insecticidal mechanisms of Cry toxins and the resistance mechanisms of insects. We believe that this review shall shed some light on the interactions between Cry toxins and insects, which can further facilitate the development and utilization of Cry toxins.
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Affiliation(s)
- Lu Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhou Li
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xing Luo
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xia Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China.,Department of Molecular Biology, Qingdao Vland Biotech Inc., Qingdao, China
| | - Shan-Ho Chou
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jieping Wang
- Agricultural Bioresources Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Jin He
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
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9
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Boman J, Mugal CF, Backström N. The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes. Genome Biol Evol 2021; 13:evab064. [PMID: 33760095 PMCID: PMC8175052 DOI: 10.1093/gbe/evab064] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/28/2022] Open
Abstract
Recombination reshuffles the alleles of a population through crossover and gene conversion. These mechanisms have considerable consequences on the evolution and maintenance of genetic diversity. Crossover, for example, can increase genetic diversity by breaking the linkage between selected and nearby neutral variants. Bias in favor of G or C alleles during gene conversion may instead promote the fixation of one allele over the other, thus decreasing diversity. Mutation bias from G or C to A and T opposes GC-biased gene conversion (gBGC). Less recognized is that these two processes may-when balanced-promote genetic diversity. Here, we investigate how gBGC and mutation bias shape genetic diversity patterns in wood white butterflies (Leptidea sp.). This constitutes the first in-depth investigation of gBGC in butterflies. Using 60 resequenced genomes from six populations of three species, we find substantial variation in the strength of gBGC across lineages. When modeling the balance of gBGC and mutation bias and comparing analytical results with empirical data, we reject gBGC as the main determinant of genetic diversity in these butterfly species. As alternatives, we consider linked selection and GC content. We find evidence that high values of both reduce diversity. We also show that the joint effects of gBGC and mutation bias can give rise to a diversity pattern which resembles the signature of linked selection. Consequently, gBGC should be considered when interpreting the effects of linked selection on levels of genetic diversity.
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Affiliation(s)
- Jesper Boman
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Sweden
| | - Carina F Mugal
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Sweden
| | - Niclas Backström
- Evolutionary Biology Program, Department of Ecology and Genetics (IEG), Uppsala University, Sweden
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10
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Vogt G. Epigenetic variation in animal populations: Sources, extent, phenotypic implications, and ecological and evolutionary relevance. J Biosci 2021. [DOI: 10.1007/s12038-021-00138-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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11
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Coninx E, Chew YC, Yang X, Guo W, Coolkens A, Baatout S, Moons L, Verslegers M, Quintens R. Hippocampal and cortical tissue-specific epigenetic clocks indicate an increased epigenetic age in a mouse model for Alzheimer's disease. Aging (Albany NY) 2020; 12:20817-20834. [PMID: 33082299 PMCID: PMC7655172 DOI: 10.18632/aging.104056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 04/17/2023]
Abstract
Epigenetic clocks are based on age-associated changes in DNA methylation of CpG-sites, which can accurately measure chronological age in different species. Recently, several studies have indicated that the difference between chronological and epigenetic age, defined as the age acceleration, could reflect biological age indicating functional decline and age-associated diseases. In humans, an epigenetic clock associated Alzheimer's disease (AD) pathology with an acceleration of the epigenetic age. In this study, we developed and validated two mouse brain region-specific epigenetic clocks from the C57BL/6J hippocampus and cerebral cortex. Both clocks, which could successfully estimate chronological age, were further validated in a widely used mouse model for AD, the triple transgenic AD (3xTg-AD) mouse. We observed an epigenetic age acceleration indicating an increased biological age for the 3xTg-AD mice compared to non-pathological C57BL/6J mice, which was more pronounced in the cortex as compared to the hippocampus. Genomic region enrichment analysis revealed that age-dependent CpGs were enriched in genes related to developmental, aging-related, neuronal and neurodegenerative functions. Due to the limited access of human brain tissues, these epigenetic clocks specific for mouse cortex and hippocampus might be important in further unravelling the role of epigenetic mechanisms underlying AD pathology or brain aging in general.
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Affiliation(s)
- Emma Coninx
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Yap Ching Chew
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Xiaojing Yang
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Wei Guo
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Amelie Coolkens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Roel Quintens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
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12
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Li B, Hu P, Zhu LB, You LL, Cao HH, Wang J, Zhang SZ, Liu MH, Toufeeq S, Huang SJ, Xu JP. DNA Methylation Is Correlated with Gene Expression during Diapause Termination of Early Embryonic Development in the Silkworm ( Bombyx mori). Int J Mol Sci 2020; 21:E671. [PMID: 31968548 PMCID: PMC7013401 DOI: 10.3390/ijms21020671] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
DNA modification is a naturally occurring DNA modification in prokaryotic and eukaryotic organisms and is involved in several biological processes. Although genome-wide methylation has been studied in many insects, the understanding of global and genomic DNA methylation during insect early embryonic development, is lacking especially for insect diapause. In this study, we analyzed the relationship between DNA methylomes and transcriptomes in diapause-destined eggs compared to diapause-terminated eggs in the silkworm, Bombyx mori (B. mori). The results revealed that methylation was sparse in this species, as previously reported. Moreover, methylation levels in diapause-terminated eggs (HCl-treated) were 0.05% higher than in non-treated eggs, mainly due to the contribution of CG methylation sites. Methylation tends to occur in the coding sequences and promoter regions, especially at transcription initiation sites and short interspersed elements. Additionally, 364 methylome- and transcriptome-associated genes were identified, which showed significant differences in methylation and expression levels in diapause-destined eggs when compared with diapause-terminated eggs, and 74% of methylome and transcriptome associated genes showed both hypermethylation and elevated expression. Most importantly, Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses showed that methylation may be positively associated with Bombyx mori embryonic development, by regulating cell differentiation, metabolism, apoptosis pathways and phosphorylation. Through analyzing the G2/M phase-specific E3 ubiquitin-protein ligase (G2E3), we speculate that methylation may affect embryo diapause by regulating the cell cycle in Bombyx mori. These findings will help unravel potential linkages between DNA methylation and gene expression during early insect embryonic development and insect diapause.
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Affiliation(s)
- Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei 230061, Anhui, China;
| | - Pei Hu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Lin-Bao Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Ling-Ling You
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Hui-Hua Cao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Shang-Zhi Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Ming-Hui Liu
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei 230061, Anhui, China;
| | - Shahzad Toufeeq
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Shou-Jun Huang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
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13
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Arnemann JA, Roxburgh S, Walsh T, Guedes J, Gordon K, Smagghe G, Tay WT. Multiple incursion pathways for Helicoverpa armigera in Brazil show its genetic diversity spreading in a connected world. Sci Rep 2019; 9:19380. [PMID: 31852963 PMCID: PMC6920452 DOI: 10.1038/s41598-019-55919-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/29/2019] [Indexed: 02/06/2023] Open
Abstract
The Old World cotton bollworm Helicoverpa armigera was first detected in Brazil with subsequent reports from Paraguay, Argentina, Bolivia, and Uruguay. This pattern suggests that the H. armigera spread across the South American continent following incursions into northern/central Brazil, however, this hypothesis has not been tested. Here we compare northern and central Brazilian H. armigera mtDNA COI haplotypes with those from southern Brazil, Uruguay, Argentina, and Paraguay. We infer spatial genetic and gene flow patterns of this dispersive pest in the agricultural landscape of South America. We show that the spatial distribution of H. armigera mtDNA haplotypes and its inferred gene flow patterns in the southwestern region of South America exhibited signatures inconsistent with a single incursion hypothesis. Simulations on spatial distribution patterns show that the detection of rare and/or the absence of dominant mtDNA haplotypes in southern H. armigera populations are inconsistent with genetic signatures observed in northern and central Brazil. Incursions of H. armigera into the New World are therefore likely to have involved independent events in northern/central Brazil, and southern Brazil/Uruguay-Argentina-Paraguay. This study demonstrates the significant biosecurity challenges facing the South American continent, and highlights alternate pathways for introductions of alien species into the New World.
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Affiliation(s)
- Jonas Andre Arnemann
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia.
- Department of Crop Protection, Universidade Federal de Santa Maria, Santa Maria, Brazil.
- Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium.
| | - Stephen Roxburgh
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia
| | - Tom Walsh
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia
| | - Jerson Guedes
- Department of Crop Protection, Universidade Federal de Santa Maria, Santa Maria, Brazil
| | - Karl Gordon
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia
| | - Guy Smagghe
- Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wee Tek Tay
- CSIRO, Black Mountain Laboratories, Clunies Ross Street, ACT 2601, Canberra, Australia
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14
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Baradaran E, Moharramipour S, Asgari S, Mehrabadi M. Induction of DNA methyltransferase genes in Helicoverpa armigera following injection of pathogenic bacteria modulates expression of antimicrobial peptides and affects bacterial proliferation. JOURNAL OF INSECT PHYSIOLOGY 2019; 118:103939. [PMID: 31493391 DOI: 10.1016/j.jinsphys.2019.103939] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/02/2019] [Accepted: 09/03/2019] [Indexed: 06/10/2023]
Abstract
Following pathogen attack in a host, widespread changes are induced in the host's gene expression, in particular those involved in the immune system, growth and survival. Epigenetic mechanisms have been suggested to be involved in the regulation of these changes through a number of mechanisms. DNA methylation is one of the important epigenetic processes that is carried out by DNA (cytosine-5) methyltransferase (DNMT) and alters expression of target genes. Here, we identified two putative sequences of DNMT (i.e. DNMT1 and DNMT2) from the transcriptome dataset of Helicoverpa armigera that showed high similarity to the homologous sequences in Bombyx mori. Domain architectures of DNMT1 and DNMT2 exhibit the unique pattern of DNMTs that highlights conserved function of these genes in different insects. To see if these genes play any role in bacterial infection, we challenged the fifth instar larvae of H. armigera by injecting Bacillus thuringiensis and Serratia marcescens cells into the hemolymph. Transcript levels of the DNMTs were analyzed by RT-qPCR. The results showed that the expression levels of DNMT1 and DNMT2 increased in the bacteria-injected larvae. Injection of the heat-killed bacteria also induced the expression of the DNMTs, but lower than that of the live bacteria. To determine whether these genes function during bacterial infection, we injected the inhibitor of DNMTs, 5-azacytidine (5-AZA), into the larvae and 24 h later, the bacterial cells were also injected into the larvae. Bacterial replication and larval mortality were analyzed in the treated and control insects. We found that 5-AZA reduced bacterial replication and also mortality of the bacterial-injected larvae regardless of the pathogenic bacterial species. Interestingly, the expression levels of antimicrobial peptides (AMPs) were also modulated following 5-AZA treatment. In conclusion, we showed that upregulation of the DNMTs in H. armigera following bacterial infections modulates AMPs and thereby affects the insect-bacteria interactions.
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Affiliation(s)
- Ehsan Baradaran
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Saeid Moharramipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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15
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Gegner J, Baudach A, Mukherjee K, Halitschke R, Vogel H, Vilcinskas A. Epigenetic Mechanisms Are Involved in Sex-Specific Trans-Generational Immune Priming in the Lepidopteran Model Host Manduca sexta. Front Physiol 2019; 10:137. [PMID: 30886585 PMCID: PMC6410660 DOI: 10.3389/fphys.2019.00137] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/06/2019] [Indexed: 12/13/2022] Open
Abstract
Parents invest in their offspring by transmitting acquired resistance against pathogens that only the parents have encountered, a phenomenon known as trans-generational immune priming (TGIP). Examples of TGIP are widespread in the animal kingdom. Female vertebrates achieve TGIP by passing antibodies to their offspring, but the mechanisms of sex-specific TGIP in invertebrates are unclear despite increasing evidence suggesting that both male-specific and female-specific TGIP occurs in insects. We used the tobacco hornworm (Manduca sexta) to investigate sex-specific TGIP in insects because it is a model host for the analysis of insect immunity and the complete genome sequence is available. We found that feeding larvae with non-pathogenic Escherichia coli or the entomopathogen Serratia entomophila triggered immune responses in the infected host associated with shifts in both DNA methylation and histone acetylation. Maternal TGIP was mediated by the translocation of bacterial structures from the gut lumen to the eggs, resulting in the microbe-specific transcriptional reprogramming of genes encoding immunity-related effector molecules and enzymes involved in the regulation of histone acetylation as well as DNA methylation in larvae of the F1 generation. The third-instar F1 larvae displayed sex-specific differences in the expression profiles of immunity-related genes and DNA methylation. We observed crosstalk between histone acetylation and DNA methylation, which mediated sex-specific immune responses in the F1 generation derived from parents exposed to a bacterial challenge. Multiple routes for TGIP seem to exist in M. sexta and – partially sex-specific – effects in the offspring depend on the microbial exposure history of their parents. Crucially, the entomopathogen S. entomophila appears to be capable of interfering with TGIP in the host.
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Affiliation(s)
- Jasmin Gegner
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany
| | - Arne Baudach
- Institute for Insect Biotechnology, Faculty of Agricultural Sciences, Nutritional Sciences, and Environmental Management, Justus-Liebig University of Giessen, Giessen, Germany
| | - Krishnendu Mukherjee
- Institute for Insect Biotechnology, Faculty of Agricultural Sciences, Nutritional Sciences, and Environmental Management, Justus-Liebig University of Giessen, Giessen, Germany
| | - Rayko Halitschke
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany.,Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Heiko Vogel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Andreas Vilcinskas
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Giessen, Germany.,Institute for Insect Biotechnology, Faculty of Agricultural Sciences, Nutritional Sciences, and Environmental Management, Justus-Liebig University of Giessen, Giessen, Germany
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