Review
Biology
Pierre Baduel, Vincent Colot
Summary: DNA provides the basic framework for heritability, but heritable trait variation is not completely hard-coded into the DNA sequence. In plants, the epigenetic machinery controls transposable element activity, and DNA methylation underpins most known cases of inherited trait variants independent of DNA sequence changes.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Taku Sasaki, Kyudo Ro, Erwann Caillieux, Riku Manabe, Gregoire Bohl-Viallefond, Pierre Baduel, Vincent Colot, Tetsuji Kakutani, Leandro Quadrana
Summary: Research has shown that anti-silencing systems have rapidly diversified in eudicots, determining specificity through gaining and losing specific domains and target sequence motifs. At least 10 distinct VANC-induced anti-silencing systems have been identified in Arabidopsis. Anti-silencing of non-autonomous VANDALs is crucial to prevent the demise of cognate autonomous TEs and ensure their propagation.
Article
Cell Biology
Patricia Barbosa, Zelinda Schemczssen-Graeff, Andre Marques, Maelin da Silva, Giovani Marino Favero, Bernardo Passos Sobreiro, Mara Cristina de Almeida, Orlando Moreira-Filho, Duilio Mazzoni Zerbinato de Andrade Silva, Fabio Porto-Foresti, Fausto Foresti, Roberto Ferreira Artoni
Summary: Transcriptional activity and DNA structure regulation involve complex processes not fully understood, with evidence of epigenetic regulation related to B chromosomes and transposable elements in a fish species. Methylation is associated with gene silencing and heterochromatin, potentially silencing transposable elements in gene regulation.
Article
Biochemistry & Molecular Biology
Lisa Schneider, Yi-Ke Guo, David Birch, Peter Sarkies
Summary: Transposable elements (TEs) are widespread in eukaryotic genomes, with their diversity shaped by complex genetic and epigenetic mechanisms. Tracking TE evolution through network analysis can reveal previously unknown properties of TE evolution across species.
MOLECULAR SYSTEMS BIOLOGY
(2021)
Review
Cell Biology
Nunzia Colonna Romano, Laura Fanti
Summary: Transposable elements (TEs) are genetic elements that can move within the genome, causing both deleterious mutations and increasing genetic variability. Organisms have developed strategies to prevent their activation, but TEs can still be activated during certain developmental windows or in response to drastic changes in the environment. TEs have a dual role as both parasites and symbionts of the genome, contributing to the temporal dynamics of evolution and the induction of genetic variability. Insertional mutagenesis and epigenetic plasticity also play a role in the evolutionary process.
Article
Biochemistry & Molecular Biology
Mengyu Zhang, Weikang Sun, Xiaoxin You, Dongge Xu, Lingling Wang, Jingping Yang, Erguang Li, Susu He
Summary: This study analyzed publicly available datasets and found that EBV-associated gastric cancer (EBVaGC) has a repression of L1 transcription compared with EBV-negative gastric cancer (EBVnGC). Retrotransposition-associated young and full-length L1s (FL-L1s) were found to be the most repressed L1s in EBVaGC. Increased deposition of H3K9me3 on FL-L1s was observed, potentially attributed to increased TASOR expression and the interaction between viral DNA and the TASOR enhancer. This study uncovers a regulation mechanism of L1 expression by chromatin topology remodeling associated with viral-host genome interaction in EBVaGC.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biotechnology & Applied Microbiology
Maria I. Pozo, Benjamin J. Hunt, Gaby Van Kemenade, Jose M. Guerra-Sanz, Felix Waeckers, Eamonn B. Mallon, Hans Jacquemyn
Summary: Overall, the altered methylation patterns improved cooperation between workers without affecting abnormal worker dominance or caste determination. Treated colonies tended to develop faster with more workers at a given developmental stage, while control colonies had higher male production.
Article
Evolutionary Biology
Galen T. Martin, Danelle K. Seymour, Brandon S. Gaut
Summary: Methylated CHH (mCHH) islands are peaks of CHH methylation that occur primarily upstream to genes and are associated with 39% of genes. They tend to be more common in smaller genomes and are often found near genes with nearby transposable elements (TEs). Other genic properties, such as gene length, gene-body methylation (gbM), and gene expression level, are also predictors of the presence of mCHH islands. However, these islands are generally not conserved across evolutionary time.
GENOME BIOLOGY AND EVOLUTION
(2021)
Review
Plant Sciences
Stephanie P. Klein, Sarah N. Anderson
Summary: Transposable elements (TEs) are a significant component of plant genomes, and growing evidence suggests that they play a crucial role in driving phenotypic diversity and stress responses in plants. The lack of evolutionary conservation in TE families and locus insertions necessitates collaboration among TE experts across diverse species for utilizing TE variation in crop improvement.
CURRENT OPINION IN PLANT BIOLOGY
(2022)
Article
Biology
Thibaut Renard, Baptiste Martinet, Natalia De Souza Araujo, Serge Aron
Summary: Epigenetic alterations are a primary hallmark of aging, and this study found that such changes occur not only in mammals but also play a crucial role in insects. By using a hypomethylating agent, the researchers extended the average lifespan of bumblebees and induced differential methylation of genes associated with aging. Additionally, they discovered that the overexpression of the longevity gene sirt1 was positively correlated with lifespan.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Taku Sasaki, Kae Kato, Aoi Hosaka, Yu Fu, Atsushi Toyoda, Asao Fujiyama, Yoshiaki Tarutani, Tetsuji Kakutani
Summary: Transposable elements (TEs) are silenced through epigenetic mechanisms in eukaryotes, but Arabidopsis TEs called VANDALs counteract this silencing through sequence-specific anti-silencing proteins, VANCs. These VANC proteins bind to noncoding regions of specific VANDAL copies and induce loss of silent chromatin marks. However, RNA-directed DNA methylation (RdDM) can efficiently silence these TEs, suggesting that escape from RdDM drives the rapid evolution and diversification of sequence-specific anti-silencing systems.
Review
Plant Sciences
Matin Miryeganeh
Summary: Plants adapt to climate change by altering their DNA, and mangroves are promising models for studying this due to their natural exposure to environmental changes.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Klara Konecna, Pavla Polanska Sovakova, Karin Antekova, Jiri Fajkus, Miloslava Fojtova
Summary: The study found that exposure to the hypomethylation drug zebularine resulted in shorter telomeres in Arabidopsis plants, with progressive changes across generations, high inter-individual variability, and diverse responses among different ecotypes. Shortening of telomeres corresponded to the transcriptional activation of transposable elements (TEs), indicating a correlated response to zebularine treatment. Changes in telomere lengths and TE transcript levels were not always associated with cytosine hypomethylation, suggesting an independent regulatory mechanism.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Jaehoon Lee, Seunga Lee, Kyunghyuk Park, Sang-Yoon Shin, Jennifer M. Frost, Ping-Hung Hsieh, Chanseok Shin, Robert L. Fischer, Tzung-Fu Hsieh, Yeonhee Choi
Summary: Through profiling DNA methylation at five stages of Arabidopsis embryogenesis, we found that the gradual increase in mCHH coincides with the expansion of small RNA expression and the spreading of mCHH to nearby sites. We also identified distinct methylation dynamics in different groups of mCHH targets, which are associated with the length, location, and cytosine frequency of transposons.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Renata Orlowska, Katarzyna A. Pachota, Wioletta M. Dynkowska, Agnieszka Niedziela, Piotr T. Bednarek
Summary: Transposable elements (TEs) in plant genomes may be activated under stress, leading to DNA sequence variation. In vitro plant regeneration can induce changes in DNA methylation levels, affecting the activation of TEs and DNA sequence variation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Ecology
Jillian Schat, Yi-Ming Weng, Roman Yu Dudko, David H. Kavanaugh, Lan Luo, Sean D. Schoville
Summary: Limited evidence of ecological selection on functional traits was found. Instead, reproductive and genetic divergence evolved among isolated populations in both species complexes, suggesting niche conservatism may be a common outcome in alpine species diversification.
JOURNAL OF BIOGEOGRAPHY
(2022)
Article
Biochemistry & Molecular Biology
Benjamin Pelissie, Yolanda H. Chen, Zachary P. Cohen, Michael S. Crossley, David J. Hawthorne, Victor Izzo, Sean D. Schoville
Summary: Insecticide resistance and rapid pest evolution pose threats to food security and sustainable agricultural practices. This study investigates the evolutionary mechanisms of the Colorado potato beetle (CPB) in rapidly adapting to insecticides. The researchers found evidence for three models of rapid evolution: selection on novel mutations, regulatory evolution, and selection on standing genetic variation. Understanding these mechanisms is crucial for effective pest management and maintaining the efficacy and sustainability of control techniques.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Ecology
Emily M. Beasley, Natalia Aristizabal, Erika M. Bueno, Easton R. White
Summary: The structure of the landscape has an influence on the spread of coffee leaf rust, with clustering of coffee farms being the main driver of transmission. Deforestation is a secondary driver, with outbreaks spreading more rapidly when deforested areas are evenly dispersed throughout the landscape. Considering landscape structure is essential in managing the spread of crop diseases, and increasing spacing between coffee farms and reducing forest fragmentation can benefit biodiversity conservation and reduce the economic impacts of coffee leaf rust.
Editorial Material
Genetics & Heredity
Eveline M. Ibeagha-Awemu, Helene Kiefer, Stephanie McKay, George E. Liu
FRONTIERS IN GENETICS
(2022)
Article
Evolutionary Biology
Zachary P. Cohen, Yolanda H. Chen, Russell Groves, Sean D. Schoville
Summary: Pesticide resistance in the Colorado potato beetle illustrates rapid evolution in response to environmental change. Studying two highly resistant populations in the United States, researchers found differences in demography, recombination, and selection. They identified specific genes associated with insecticide resistance that underwent independent, rapid evolution in geographically distinct populations.
EVOLUTIONARY APPLICATIONS
(2022)
Article
Zoology
Zachary P. Cohen, Olivier Francois, Sean D. Schoville
Summary: This study uses museum samples and modern sampling data to analyze the evolution of population genetic diversity and structure in the Colorado potato beetle (CPB). The results show that CPB rapidly expanded in the 19th century, leading to a reduction in diversity and limited genetic structure. The study also identifies genomic regions under selection in resistant field populations in Wisconsin and New York.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2022)
Article
Agronomy
Erika M. Bueno, Casey L. McIlhenny, Yolanda H. Chen
Summary: The article discusses the adaptability of agricultural insect pests to stressors and the potential role of cross-protection mechanisms. By studying single and multiple stressors, the importance of cross-protection in insect pests is revealed, and mechanisms such as epigenetic modifications that facilitate cross-protection are proposed.
PEST MANAGEMENT SCIENCE
(2023)
Review
Agriculture, Dairy & Animal Science
Hafedh Ben Zaabza, Curtis P. Van Tassell, Jeremie Vandenplas, Paul VanRaden, Zengting Liu, Herwin Eding, Stephanie McKay, Katrine Haugaard, Martin H. Lidauer, Esa A. Mantysaari, Ismo Stranden
Summary: This paper provides an overview of different methods and computational approaches for calculating reliability, from the animal model era to the single-step genomic model era. It also discusses the challenges faced in reliability computation and presents efficient and accurate algorithms developed recently for large-scale genomic evaluations.
JOURNAL OF DAIRY SCIENCE
(2023)
Article
Biology
Yolanda H. Chen, Zachary P. Cohen, Erika M. Bueno, Blair M. Christensen, Sean Schoville
Summary: Despite extensive research, efforts to manage insecticide resistance have been unsuccessful. The Colorado potato beetle, which has rapidly evolved resistance to over 50 insecticides, challenges models of resistance evolution from rare mutations. Recent research suggests that polygenic resistance from standing genetic diversity explains the genomic patterns of insecticide resistance evolution, but rapid gene regulatory evolution indicates that other mechanisms may also contribute. This study explores the hypothesis that sublethal stress from insecticide exposure could induce heritable epigenetic modifications, and discusses the range of experimental approaches needed to fully understand insecticide resistance evolution in this super pest.
CURRENT OPINION IN INSECT SCIENCE
(2023)
Article
Agronomy
Zachary Cohen, John Bamberg, Sean Schoville, Russel Groves, Benjamin Bradford
Summary: The study examines the performance of Colorado potato beetles on different populations of wild potatoes and finds that beetles are more attracted to populations where they have been observed in the wild. This observation can be helpful in predicting the beetles' preferences in field conditions.
AMERICAN JOURNAL OF POTATO RESEARCH
(2023)
Article
Multidisciplinary Sciences
Kalle Tunstrom, Alyssa Woronik, Joseph J. Hanly, Pasi Rastas, Anton Chichvarkhin, Andrew D. Warren, Akito Y. Kawahara, Sean D. Schoville, Vincent Ficarrotta, Adam H. Porter, Ward B. Watt, Arnaud Martin, Christopher W. Wheat
Summary: Understanding the evolutionary origins and maintenance of alternative life history strategies is a major goal in evolutionary research. The study focused on the polymorphic Alba ALHS in Colias butterflies and aimed to determine its origins and evolutionary persistence. By using comparative genome-wide association study and population genomic analyses, the researchers found that Alba evolved once at the base of the genus and has been maintained via introgression and balancing selection. CRISPR-Cas9 mutagenesis was used to verify a putative cis-regulatory region of Alba, which likely acts as a modular enhancer for its induction.
Article
Evolutionary Biology
Sean D. Schoville, Zachery Farrand, David H. Kavanaugh, Benton Veire, Yi-Ming Weng
Summary: The oscillating glacial-interglacial climate has driven rapid distributional and demographic shifts in alpine species, leading to lineage diversification. By exploring the genetic pathways induced during environmental stress responses, this study found evidence of adaptive evolution in the alpine ground beetle Nebria vandykei. Additionally, phylogenetic analyses suggest that admixture or rapid diversification underlies the evolution of N. vandykei.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY
(2023)
Article
Entomology
Kristian Brevik, Sean D. Schoville, Anna Muszewska, Benjamin Pelissie, Zachary Cohen, Victor Izzo, Yolanda H. Chen
Summary: The Colorado potato beetle, a highly adaptable agricultural insect herbivore, is shown to have variations in transposable element abundance and diversity among different populations. This reflects the evolutionary history and adaptation mechanisms of this species. The presence of transposable elements does not seem to be affected by geographical location or host plant, nor does it relate to insecticide resistance.
ENVIRONMENTAL ENTOMOLOGY
(2023)
Article
Entomology
Elisabeth A. Hodgdon, Rebecca H. Hallett, James D. Heal, Chase A. Stratton, Christine A. Hoepting, Yolanda H. Chen
Summary: In field plots, the study tested the effect of three-component stereospecific, lower-cost racemic, and single-component pheromone blends on swede midge mating disruption. It was found that the three-component stereospecific blend showed promise in reducing male catches, indicating its potential as a pheromone blend for swede midge mating disruption.
CANADIAN ENTOMOLOGIST
(2022)