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Fishman B, Tauber E. Epigenetics and seasonal timing in animals: a concise review. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:565-574. [PMID: 37695537 PMCID: PMC11226475 DOI: 10.1007/s00359-023-01673-3] [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: 05/07/2023] [Revised: 08/27/2023] [Accepted: 09/01/2023] [Indexed: 09/12/2023]
Abstract
Seasonal adaptation in animals is a complex process that involves genetic, epigenetic, and environmental factors. The present review explores recent studies on epigenetic mechanisms implicated in seasonal adaptation in animals. The review is divided into three main sections, each focusing on a different epigenetic mechanism: DNA methylation, histone modifications, and non-coding RNA. Additionally, the review delves into the current understanding of how these epigenetic factors contribute to the regulation of circadian and seasonal cycles. Understanding these molecular mechanisms provides the first step in deciphering the complex interplay between genetics, epigenetics, and the environment in driving seasonal adaptation in animals. By exploring these mechanisms, a better understanding of how animals adapt to changing environmental conditions can be achieved.
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Affiliation(s)
- Bettina Fishman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eran Tauber
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel.
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2
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Bogan SN, Yi SV. Potential Role of DNA Methylation as a Driver of Plastic Responses to the Environment Across Cells, Organisms, and Populations. Genome Biol Evol 2024; 16:evae022. [PMID: 38324384 PMCID: PMC10899001 DOI: 10.1093/gbe/evae022] [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: 07/13/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024] Open
Abstract
There is great interest in exploring epigenetic modifications as drivers of adaptive organismal responses to environmental change. Extending this hypothesis to populations, epigenetically driven plasticity could influence phenotypic changes across environments. The canonical model posits that epigenetic modifications alter gene regulation and subsequently impact phenotypes. We first discuss origins of epigenetic variation in nature, which may arise from genetic variation, spontaneous epimutations, epigenetic drift, or variation in epigenetic capacitors. We then review and synthesize literature addressing three facets of the aforementioned model: (i) causal effects of epigenetic modifications on phenotypic plasticity at the organismal level, (ii) divergence of epigenetic patterns in natural populations distributed across environmental gradients, and (iii) the relationship between environmentally induced epigenetic changes and gene expression at the molecular level. We focus on DNA methylation, the most extensively studied epigenetic modification. We find support for environmentally associated epigenetic structure in populations and selection on stable epigenetic variants, and that inhibition of epigenetic enzymes frequently bears causal effects on plasticity. However, there are pervasive confounding issues in the literature. Effects of chromatin-modifying enzymes on phenotype may be independent of epigenetic marks, alternatively resulting from functions and protein interactions extrinsic of epigenetics. Associations between environmentally induced changes in DNA methylation and expression are strong in plants and mammals but notably absent in invertebrates and nonmammalian vertebrates. Given these challenges, we describe emerging approaches to better investigate how epigenetic modifications affect gene regulation, phenotypic plasticity, and divergence among populations.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, USA
| | - Soojin V Yi
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
- Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
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3
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Yu X, Yu K, Chen B, Liao Z, Liang J, Qin Z, Gao X. Metabolic and immune costs balance during natural acclimation of corals in fluctuating environments. MARINE ENVIRONMENTAL RESEARCH 2024; 193:106284. [PMID: 38048660 DOI: 10.1016/j.marenvres.2023.106284] [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: 09/22/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/06/2023]
Abstract
Epigenetic modifications based on DNA methylation can rapidly improve the potential of corals to adapt to environmental pressures by increasing their phenotypic plasticity, a factor important for scleractinian corals to adapt to future global warming. However, the extent to which corals develop similar adaptive mechanisms and their specific adaptation processes remain unclear. Here, to reveal the regulatory mechanism by which DNA methylation improves thermal tolerance in Pocillopora damicornis under fluctuating environments, we analyzed genome-wide DNA methylation signatures in P. damicornis and compared the differences in the methylation and transcriptional responses of P. damicornis from fluctuating and stable environments using whole-genome bisulfite sequencing and nanopore-based RNA sequencingtranscriptome sequencing. We discovered low methylation levels in P. damicornis (average methylation 4.14%), with CpG accounting for 74.88%, CHH for 13.27%, and CHG for 11.85% of this methylation. However, methylation levels did not change between coral samples from the fluctuating and stable environments. The varied methylation levels in different regions of the gene revealed that the overall methylation level of the gene body was relatively high and showed a bimodal methylation pattern. Methylation occurs primarily in exons rather than introns within the gene body In P. damicornis, there was only a weak correlation between methylation and transcriptional changes at the individual gene level, and the methylation and gene expression levels generally exhibited a bell-shaped relationship, which we speculate may be due to the specificity of cnidarian species. Correlation analysis between methylation levels and the transcriptome revealed that the highest proportion of the top 20 enriched KEGG pathways was related to immunity. Additionally, P. damicornis collected from a high-temperature pool had a lower metabolic rate than those collected from a low-temperature pool. We hypothesize that the dynamic balance of energy-expenditure costs between immunity and metabolism is an important strategy for increasing P. damicornis tolerance. The fluctuating environment of high-temperature pools may increase the heat tolerance in corals by increasing their immunity and thus lowering their metabolism.
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Affiliation(s)
- Xiaopeng Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Kefu Yu
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China; Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China.
| | - Biao Chen
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhiheng Liao
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Jiayuan Liang
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Zhenjun Qin
- Guangxi Laboratory on the Study of Coral Reefs in the South China Sea, Coral Reef Research Center of China, School of Marine Sciences, Guangxi University, Nanning, China
| | - Xu Gao
- Guangxi University of Chinese Medicine, Nanning, Guangxi, China
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4
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Jia K, Duan J, Cheng G, Li H, Li S, Hu M. DNA Methylation is Involved in Sex Determination in Spinach. Biochem Genet 2023:10.1007/s10528-023-10524-4. [PMID: 37950843 DOI: 10.1007/s10528-023-10524-4] [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: 10/09/2022] [Accepted: 09/07/2023] [Indexed: 11/13/2023]
Abstract
DNA methylation plays a critical role in the modulation of gene expression. The role of DNA methylation in sex determination was investigated in spinach. The differentiated cytosine CpG methylation profiles of CCGG motifs were assessed with methylation sensitivity amplification polymorphism (MSAP) in spinach. Among 442 DNA fragments from four plants, 134 methylated fragments were found. Relative proportions of methylation sites were 28.8% in male plants and 31.8% in female plants. At the same time, cytosine methylation levels were higher in females than in males in CCGG motifs of genomes in the spinach. These findings suggest that methylation of CG islands is involved in sex determination and differentiation in spinach.
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Affiliation(s)
- Keli Jia
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Jiaming Duan
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | | | - Heng Li
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China
| | - Shufen Li
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China.
| | - Miao Hu
- School of Medical Laboratory, Sanquan College of Xinxiang Medical University, Xinxiang, China.
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5
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Okwaro LA, Korb J. Epigenetic regulation and division of labor in social insects. CURRENT OPINION IN INSECT SCIENCE 2023; 58:101051. [PMID: 37164259 DOI: 10.1016/j.cois.2023.101051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
Analogous to multicellular organisms, social insect colonies are characterized by division of labor with queens and workers reflecting germline and soma, respectively. In multicellular organisms, such division is achieved through epigenetic factors regulating cell differentiation during development. Analogously, epigenetic regulation is postulated to regulate caste differences in social insects. We summarize recent findings about the role of epigenetics in social insects, focusing on DNA methylation and histone modifications. We specifically address (i) queen versus worker caste differentiation, (ii) queen versus worker caste differences, and (iii) division of labor among workers. Our review provides an overview of an exciting and controversially discussed field in developmental and molecular biology. It shows that our current understanding about the role of epigenetics in regulating division of labor in social insects is still fragmentary but that refined methods with well-replicated samples and targeted questions offer promising insights into this emerging field of socio-epigenomics.
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Affiliation(s)
- Louis A Okwaro
- University of Freiburg, Evolutionary Biology and Ecology D-79104 Freiburg, Germany
| | - Judith Korb
- University of Freiburg, Evolutionary Biology and Ecology D-79104 Freiburg, Germany.
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6
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Bogan SN, Strader ME, Hofmann GE. Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity. BMC Biol 2023; 21:149. [PMID: 37365578 DOI: 10.1186/s12915-023-01645-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 06/07/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Epigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally induced changes in DNA methylation exhibit little-to-no association with differential gene expression in metazoans at a transcriptome-wide level. It remains unexplored whether associations between environmentally induced differential methylation and expression are contingent upon other epigenomic processes such as chromatin accessibility. We quantified methylation and gene expression in larvae of the purple sea urchin Strongylocentrotus purpuratus exposed to different ecologically relevant conditions during gametogenesis (maternal conditioning) and modeled changes in gene expression and splicing resulting from maternal conditioning as functions of differential methylation, incorporating covariates for genomic features and chromatin accessibility. We detected significant interactions between differential methylation, chromatin accessibility, and genic feature type associated with differential expression and splicing. RESULTS Differential gene body methylation had significantly stronger effects on expression among genes with poorly accessible transcriptional start sites while baseline transcript abundance influenced the direction of this effect. Transcriptional responses to maternal conditioning were 4-13 × more likely when accounting for interactions between methylation and chromatin accessibility, demonstrating that the relationship between differential methylation and gene regulation is partially explained by chromatin state. CONCLUSIONS DNA methylation likely possesses multiple associations with gene regulation during transgenerational plasticity in S. purpuratus and potentially other metazoans, but its effects are dependent on chromatin accessibility and underlying genic features.
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Affiliation(s)
- Samuel N Bogan
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA.
| | - Marie E Strader
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
- Department of Biology, Texas A&M University, College Station, USA
| | - Gretchen E Hofmann
- Department of Ecology, Evolution and Marine Biology, University of California Santa Barbara, Santa Barbara, USA
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7
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Marshall H, Nicholas MT, van Zweden JS, Wäckers F, Ross L, Wenseleers T, Mallon EB. DNA methylation is associated with codon degeneracy in a species of bumblebee. Heredity (Edinb) 2023; 130:188-195. [PMID: 36658299 PMCID: PMC10076500 DOI: 10.1038/s41437-023-00591-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Social insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.
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Affiliation(s)
- H Marshall
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK.
| | - M T Nicholas
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK
| | - J S van Zweden
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - F Wäckers
- Biobest Belgium N.V., Westerlo, Belgium
- The Lancaster Environmental Centre, University of Lancaster, Lancaster, UK
| | - L Ross
- The Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - T Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - E B Mallon
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK.
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8
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Silliman K, Spencer LH, White SJ, Roberts SB. Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate. Genome Biol Evol 2023; 15:evad013. [PMID: 36740242 PMCID: PMC10468963 DOI: 10.1093/gbe/evad013] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.
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Affiliation(s)
- Katherine Silliman
- South Carolina Department of Natural Resources, Marine Resources Research
Institute, Charleston, South Carolina
| | - Laura H Spencer
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Samuel J White
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
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9
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Arsala D, Wu X, Yi SV, Lynch JA. Dnmt1a is essential for gene body methylation and the regulation of the zygotic genome in a wasp. PLoS Genet 2022; 18:e1010181. [PMID: 35522715 PMCID: PMC9075658 DOI: 10.1371/journal.pgen.1010181] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 04/01/2022] [Indexed: 11/19/2022] Open
Abstract
Gene body methylation (GBM) is an ancestral mode of DNA methylation whose role in development has been obscured by the more prominent roles of promoter and CpG island methylation. The wasp Nasonia vitripennis has little promoter and CpG island methylation, yet retains strong GBM, making it an excellent model for elucidating the roles of GBM. Here we show that N. vitripennis DNA methyltransferase 1a (Nv-Dnmt1a) knockdown leads to failures in cellularization and gastrulation of the embryo. Both of these disrupted events are hallmarks of the maternal-zygotic transition (MZT) in insects. Analysis of the embryonic transcriptome and methylome revealed strong reduction of GBM and widespread disruption of gene expression during embryogenesis after Nv-Dnmt1a knockdown. Strikingly, there was a strong correlation between loss of GBM and reduced gene expression in thousands of methylated loci, consistent with the hypothesis that GBM directly facilitates high levels of transcription. We propose that lower expression levels of methylated genes due to reduced GBM is the crucial direct effect of Nv-Dnmt1 knockdown. Subsequently, the disruption of methylated genes leads to downstream dysregulation of the MZT, culminating in developmental failure at gastrulation.
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Affiliation(s)
- Deanna Arsala
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Ecology & Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Xin Wu
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Soojin V. Yi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, Santa Barbara, California, United States of America
| | - Jeremy A. Lynch
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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10
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Wang J, Zhang W, Hou W, Zhao E, Li X. Molecular Characterization, Tumor Microenvironment Association, and Drug Susceptibility of DNA Methylation-Driven Genes in Renal Cell Carcinoma. Front Cell Dev Biol 2022; 10:837919. [PMID: 35386197 PMCID: PMC8978676 DOI: 10.3389/fcell.2022.837919] [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: 12/17/2021] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Accumulating evidence suggests that DNA methylation has essential roles in the development of renal cell carcinoma (RCC). Aberrant DNA methylation acts as a vital role in RCC progression through regulating the gene expression, yet little is known about the role of methylation and its association with prognosis in RCC. The purpose of this study is to explore the DNA methylation-driven genes for establishing prognostic-related molecular clusters and providing a basis for survival prediction. In this study, 5,198 differentially expressed genes (DEGs) and 270 DNA methylation-driven genes were selected to obtain 146 differentially expressed DNA methylation-driven genes (DEMDGs). Two clusters were distinguished by consensus clustering using 146 DEMDGs. We further evaluated the immune status of two clusters and selected 106 DEGs in cluster 1. Cluster-based immune status analysis and functional enrichment analysis of 106 DEGs provide new insights for the development of RCC. To predict the prognosis of patients with RCC, a prognostic model based on eight DEMDGs was constructed. The patients were divided into high-risk groups and low-risk groups based on their risk scores. The predictive nomogram and the web-based survival rate calculator (http://127.0.0.1:3496) were built to validate the predictive accuracy of the prognostic model. Gene set enrichment analysis was performed to annotate the signaling pathways in which the genes are enriched. The correlation of the risk score with clinical features, immune status, and drug susceptibility was also evaluated. These results suggested that the prognostic model might be a promising prognostic tool for RCC and might facilitate the management of patients with RCC.
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Affiliation(s)
- Jinpeng Wang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wei Zhang
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenbin Hou
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Enyang Zhao
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xuedong Li
- Department of Urology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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11
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Transcriptome Sequencing Highlights the Regulatory Role of DNA Methylation in Immune-Related Genes’ Expression of Chinese Oak Silkworm, Antheraea pernyi. INSECTS 2022; 13:insects13030296. [PMID: 35323594 PMCID: PMC8951095 DOI: 10.3390/insects13030296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 12/12/2022]
Abstract
Simple Summary Antheraea pernyi is an important lepidopteran that has been used as a model insect for various physiological systems. DNA methylation has recently been discovered to control a variety of physiological processes in animals throughout their lives. We investigated the effect of DNA methylation on the innate immune system of A. pernyi and found that DNA methylation inhibition modifies gene expression, especially in immune-related genes. Finally, our data suggest that DNA methylation may regulate gene expression in insects, and microbial infection likely induces DNA methylation of the host genome. Abstract Antheraea pernyi is an important lepidopteran used as a model insect species to investigate immune responses, development, and metabolism modulation. DNA methylation has recently been found to control various physiological processes throughout the life of animals; however, DNA methylation and its effect on the physiology of insects have been poorly investigated so far. In the present study, to better understand DNA methylation and its biological role in the immune system, we analyzed transcriptome profiles of A. pernyi pupae following DNA methylation inhibitor injection and Gram-positive bacteria stimulation. We then compared the profiles with a control group. We identified a total of 55,131 unigenes from the RNA sequence data. A comparison of unigene expression profiles showed that a total of 680 were up-regulated and 631 unigenes were down-regulated in the DNA-methylation-inhibition-bacteria-infected group compared to the control group (only bacteria-injected pupae), respectively. Here, we focused on the immune-related differentially expressed genes (DEGs) and screened 10 genes that contribute to immune responses with an up-regulation trend, suggesting that microbial pathogens evade host immunity by increasing DNA methylation of the host genome. Furthermore, several other unigenes related to other pathways were also changed, as shown in the KEGG analysis. Taken together, our data revealed that DNA methylation seems to play a crucial biological role in the regulation of gene expression in insects, and that infection may enhance the host genome DNA methylation by a yet-unknown mechanism.
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12
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Zhang X, Jacobs D. OUP accepted manuscript. Genome Biol Evol 2022; 14:6519162. [PMID: 35104341 PMCID: PMC8857923 DOI: 10.1093/gbe/evab284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2021] [Indexed: 11/14/2022] Open
Abstract
DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.
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Affiliation(s)
- Xinhui Zhang
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
| | - David Jacobs
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Corresponding author: E-mail:
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13
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Waiker P, de Abreu FCP, Luna-Lucena D, Freitas FCP, Simões ZLP, Rueppell O. Recombination mapping of the Brazilian stingless bee Frieseomelitta varia confirms high recombination rates in social hymenoptera. BMC Genomics 2021; 22:673. [PMID: 34536998 PMCID: PMC8449902 DOI: 10.1186/s12864-021-07987-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 09/04/2021] [Indexed: 11/26/2022] Open
Abstract
Background Meiotic recombination is a fundamental genetic process that shuffles allele combinations and promotes accurate segregation of chromosomes. Analyses of the ubiquitous variation of recombination rates within and across species suggest that recombination is evolving adaptively. All studied insects with advanced eusociality have shown exceptionally high recombination rates, which may represent a prominent case of adaptive evolution of recombination. However, our understanding of the relationship between social evolution and recombination rates is incomplete, partly due to lacking empirical data. Here, we present a linkage map of the monandrous, advanced eusocial Brazilian stingless bee, Frieseomelitta varia, providing the first recombination analysis in the diverse Meliponini (Hymenoptera, Apidae). Results Our linkage map includes 1417 markers in 19 linkage groups. This map spans approximately 2580 centimorgans, and comparisons to the physical genome assembly indicate that it covers more than 75 % of the 275 Megabasepairs (Mbp) F. varia genome. Thus, our study results in a genome-wide recombination rate estimate of 9.3–12.5 centimorgan per Mbp. This value is higher than estimates from nonsocial insects and comparable to other highly social species, although it does not support our prediction that monandry and strong queen-worker caste divergence of F. varia lead to even higher recombination rates than other advanced eusocial species. Conclusions Our study expands the association between elevated recombination and sociality in the order Hymenoptera and strengthens the support for the hypothesis that advanced social evolution in hymenopteran insects invariably selects for high genomic recombination rates. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07987-3.
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Affiliation(s)
- Prashant Waiker
- Biology Department, University of North Carolina at Greensboro, 321 McIver St, Greensboro, NC, 27412, USA.
| | - Fabiano Carlos Pinto de Abreu
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, SP, Ribeirão Preto, Brazil
| | - Danielle Luna-Lucena
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Flávia Cristina Paula Freitas
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.,Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, Alfenas, MG, Brazil
| | - Zilá Luz Paulino Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, SP, Ribeirão Preto, Brazil
| | - Olav Rueppell
- Biology Department, University of North Carolina at Greensboro, 321 McIver St, Greensboro, NC, 27412, USA.,Department of Biological Sciences, University of Alberta, AB, T6G 2E9, Edmonton, Canada
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14
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Entrambasaguas L, Ruocco M, Verhoeven KJF, Procaccini G, Marín-Guirao L. Gene body DNA methylation in seagrasses: inter- and intraspecific differences and interaction with transcriptome plasticity under heat stress. Sci Rep 2021; 11:14343. [PMID: 34253765 PMCID: PMC8275578 DOI: 10.1038/s41598-021-93606-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 06/28/2021] [Indexed: 02/06/2023] Open
Abstract
The role of DNA methylation and its interaction with gene expression and transcriptome plasticity is poorly understood, and current insight comes mainly from studies in very few model plant species. Here, we study gene body DNA methylation (gbM) and gene expression patterns in ecotypes from contrasting thermal environments of two marine plants with contrasting life history strategies in order to explore the potential role epigenetic mechanisms could play in gene plasticity and responsiveness to heat stress. In silico transcriptome analysis of CpGO/E ratios suggested that the bulk of Posidonia oceanica and Cymodocea nodosa genes possess high levels of intragenic methylation. We also observed a correlation between gbM and gene expression flexibility: genes with low DNA methylation tend to show flexible gene expression and plasticity under changing conditions. Furthermore, the empirical determination of global DNA methylation (5-mC) showed patterns of intra and inter-specific divergence that suggests a link between methylation level and the plants' latitude of origin and life history. Although we cannot discern whether gbM regulates gene expression or vice versa, or if other molecular mechanisms play a role in facilitating transcriptome responsiveness, our findings point to the existence of a relationship between gene responsiveness and gbM patterns in marine plants.
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Affiliation(s)
- Laura Entrambasaguas
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Miriam Ruocco
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
| | - Koen J F Verhoeven
- Terrestrial Ecology Department, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Gabriele Procaccini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy.
| | - Lazaro Marín-Guirao
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121, Napoli, Italy
- Seagrass Ecology Group, Oceanographic Center of Murcia, Spanish Institute of Oceanography, C/Varadero, 30740, San Pedro del Pinatar, Spain
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15
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Oldroyd BP, Yagound B. The role of epigenetics, particularly DNA methylation, in the evolution of caste in insect societies. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200115. [PMID: 33866805 PMCID: PMC8059649 DOI: 10.1098/rstb.2020.0115] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Eusocial insects can be defined as those that live in colonies and have distinct queens and workers. For most species, queens and workers arise from a common genome, and so caste-specific developmental trajectories must arise from epigenetic processes. In this review, we examine the epigenetic mechanisms that may be involved in the regulation of caste dimorphism. Early work on honeybees suggested that DNA methylation plays a causal role in the divergent development of queen and worker castes. This view has now been challenged by studies that did not find consistent associations between methylation and caste in honeybees and other species. Evidence for the involvement of methylation in modulating behaviour of adult workers is also inconsistent. Thus, the functional significance of DNA methylation in social insects remains equivocal. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Benjamin P. Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
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16
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Männer L, Schell T, Provataris P, Haase M, Greve C. Inference of DNA methylation patterns in molluscs. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200166. [PMID: 33813896 DOI: 10.1098/rstb.2020.0166] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mollusca are the second largest and arguably most diverse phylum of the animal kingdom. This is in sharp contrast to our very limited knowledge concerning epigenetic mechanisms including DNA methylation in this invertebrate group. Here, we inferred DNA methylation patterns by analysing the normalized dinucleotide CG content in protein-coding sequences and identified DNA methyltransferases (DNMT1 and 3) in published transcriptomes and genomes of 140 species across all eight classes of molluscs. Given the evolutionary age and morphological diversity of molluscs, we expected to find evidence for diverse methylation patterns. Our inferences suggest that molluscs possess substantial levels of DNA methylation in gene bodies as a rule. Yet, we found deviations from this general picture with regard to (i) the CpG observed/expected distributions indicating a reduction in DNA methylation in certain groups and (ii) the completeness of the DNMT toolkit. Reductions were evident in Caudofoveata, Solenogastres, Polyplacophora, Monoplacophora, as well as Scaphopoda. Heterobranchia and Oegopsida were remarkable as they lacked DNMT3, usually responsible for de novo methylation, yet showed signs of DNA methylation. Our survey may serve as guidance for direct empirical analyses of DNA methylation in molluscs. This article is part of the Theo Murphy meeting issue 'Molluscan genomics: broad insights and future directions for a neglected phylum'.
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Affiliation(s)
- Lisa Männer
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
| | - Tilman Schell
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany.,Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Martin Haase
- AG Vogelwarte, Zoological Institute and Museum, University of Greifswald, Soldmannstraße 23, 17489 Greifswald, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
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17
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105217. [PMID: 33276167 DOI: 10.1016/j.marenvres.2020.105217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/07/2020] [Accepted: 05/10/2020] [Indexed: 06/12/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122, NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China.
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18
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Lim YK, Cheung K, Dang X, Roberts SB, Wang X, Thiyagarajan V. DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis. MARINE ENVIRONMENTAL RESEARCH 2021; 163:105214. [PMID: 33221553 DOI: 10.1016/j.marenvres.2020.105214] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Unprecedented rate of increased CO2 level in the ocean and the subsequent changes in carbonate system including decreased pH, known as ocean acidification (OA), is predicted to disrupt not only the calcification process but also several other physiological and developmental processes in a variety of marine organisms, including edible oysters. Nonetheless, not all species are vulnerable to those OA threats, e.g. some species may be able to cope with OA stress using environmentally induced modifications on gene and protein expressions. For example, external environmental stressors including OA can influence the addition and removal of methyl groups through epigenetic modification (e.g. DNA methylation) process to turn gene expression "on or off" as part of a rapid adaptive mechanism to cope with OA. In this study, we tested the above hypothesis through testing the effect of OA, using decreased pH 7.4 as proxy, on DNA methylation pattern of an endemic and a commercially important estuary oyster species, Crassostrea hongkongensis at the time of larval habitat selection and metamorphosis. Larval growth rate did not differ between control pH 8.1 and treatment pH 7.4. The metamorphosis rate of the pediveliger larvae was higher at pH 7.4 than those in control pH 8.1, however over one-third of the larvae raised at pH 7.4 failed to attach on optimal substrate as defined by biofilm presence. During larval development, a total of 130 genes were differentially methylated across the two treatments. The differential methylation in the larval genes may have partially accounted for the higher metamorphosis success rate under decreased pH 7.4 but with poor substratum selection ability. Differentially methylated loci were concentrated in the exon regions and appear to be associated with cytoskeletal and signal transduction, oxidative stress, metabolic processes, and larval metamorphosis, which implies the high potential of C. hongkongensis larvae to acclimate and adapt through non-genetic ways to OA threats within a single generation.
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Affiliation(s)
- Yong-Kian Lim
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Khan Cheung
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Xin Dang
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of Washington, 1122 NE Boat Street, Seattle, WA, USA
| | - Xiaotong Wang
- School of Agriculture, Ludong University, Yantai, 264025, China
| | - Vengatesen Thiyagarajan
- The Swire Institute of Marine Science and School of Biological Sciences, University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China.
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19
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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20
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Distinct epigenomic and transcriptomic modifications associated with Wolbachia-mediated asexuality. PLoS Pathog 2020; 16:e1008397. [PMID: 32187233 PMCID: PMC7105135 DOI: 10.1371/journal.ppat.1008397] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/30/2020] [Accepted: 02/11/2020] [Indexed: 11/19/2022] Open
Abstract
Wolbachia are maternally transmitted intracellular bacteria that induce a range of pathogenic and fitness-altering effects on insect and nematode hosts. In parasitoid wasps of the genus Trichogramma, Wolbachia infection induces asexual production of females, thus increasing transmission of Wolbachia. It has been hypothesized that Wolbachia infection accompanies a modification of the host epigenome. However, to date, data on genome-wide epigenomic changes associated with Wolbachia are limited, and are often confounded by background genetic differences. Here, we took sexually reproducing Trichogramma free of Wolbachia and introgressed their genome into a Wolbachia-infected cytoplasm, converting them to Wolbachia-mediated asexuality. Wolbachia was then cured from replicates of these introgressed lines, allowing us to examine the genome-wide effects of wasps newly converted to asexual reproduction while controlling for genetic background. We thus identified gene expression and DNA methylation changes associated with Wolbachia-infection. We found no overlaps between differentially expressed genes and differentially methylated genes, indicating that Wolbachia-infection associated DNA methylation change does not directly modulate levels of gene expression. Furthermore, genes affected by these mechanisms exhibit distinct evolutionary histories. Genes differentially methylated due to the infection tended to be evolutionarily conserved. In contrast, differentially expressed genes were significantly more likely to be unique to the Trichogramma lineage, suggesting host-specific transcriptomic responses to infection. Nevertheless, we identified several novel aspects of Wolbachia-associated DNA methylation changes. Differentially methylated genes included those involved in oocyte development and chromosome segregation. Interestingly, Wolbachia-infection was associated with higher levels of DNA methylation. Additionally, Wolbachia infection reduced overall variability in gene expression, even after accounting for the effect of DNA methylation. We also identified specific cases where alternative exon usage was associated with DNA methylation changes due to Wolbachia infection. These results begin to reveal distinct genes and molecular pathways subject to Wolbachia induced epigenetic modification and/or host responses to Wolbachia-infection. Wolbachia is an extremely common endosymbiotic infection of arthropods and nematodes. One of the reasons why Wolbachia can so successfully infect diverse species is the bacterium’s ability to profoundly alter the reproductive behavior of its host. It has been proposed that Wolbachia may modify host’s epigenetic programs to alter its reproductive behavior. However, it has been difficult to study how epigenetic programs change with Wolbachia infection, due to the confounding effects of genetic backgrounds. Here, we studied host transcriptome and epigenome changes associated with Wolbachia infection in a homogenous genetic background, by carrying out an innovative introgression scheme. By doing so, we show, for the first time, high-resolution molecular consequences of intracellular infection and offer insights into epigenetic and transcriptomic regulation of invertebrates.
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21
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Rago A, Werren JH, Colbourne JK. Sex biased expression and co-expression networks in development, using the hymenopteran Nasonia vitripennis. PLoS Genet 2020; 16:e1008518. [PMID: 31986136 PMCID: PMC7004391 DOI: 10.1371/journal.pgen.1008518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 02/06/2020] [Accepted: 11/13/2019] [Indexed: 12/17/2022] Open
Abstract
Sexual dimorphism requires regulation of gene expression in developing organisms. These developmental differences are caused by differential expression of genes and isoforms. The effect of expressing a gene is also influenced by which other genes are simultaneously expressed (functional interactions). However, few studies have described how these processes change across development. We compare the dynamics of differential expression, isoform switching and functional interactions in the sexual development of the model parasitoid wasp Nasonia vitripennis, a system that permits genome wide analysis of sex bias from early embryos to adults. We find relatively little sex-bias in embryos and larvae at the gene level, but several sub-networks show sex-biased functional interactions in early developmental stages. These networks provide new candidates for hymenopteran sex determination, including histone modification. In contrast, sex-bias in pupae and adults is driven by the differential expression of genes. We observe sex-biased isoform switching consistently across development, but mostly in genes that are already differentially expressed. Finally, we discover that sex-biased networks are enriched by genes specific to the Nasonia clade, and that those genes possess the topological properties of key regulators. These findings suggest that regulators in sex-biased networks evolve more rapidly than regulators of other developmental networks.
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Affiliation(s)
- Alfredo Rago
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
| | - John H. Werren
- Department of Biology, University of Rochester, Rochester, NY, United States of America
| | - John K. Colbourne
- School of Biosciences, The University of Birmingham, Birmingham, United Kingdom
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22
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DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Mol Cell 2020; 77:310-323.e7. [DOI: 10.1016/j.molcel.2019.10.011] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 08/26/2019] [Accepted: 10/10/2019] [Indexed: 12/12/2022]
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23
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Huang H, Wu P, Zhang S, Shang Q, Yin H, Hou Q, Zhong J, Guo X. DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori. BMC Genomics 2019; 20:736. [PMID: 31615392 PMCID: PMC6792228 DOI: 10.1186/s12864-019-6146-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 09/29/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Bombyx mori nucleopolyhedrosis virus (BmNPV) is a major pathogen that threatens the sustainability of the sericultural industry. DNA methylation is a widespread gene regulation mode in epigenetics, which plays an important role in host immune response. Until now, little has been known about epigenetic regulation on virus diseases in insects. This study aims to explore the role of DNA methylation in BmNPV proliferation. RESULTS Inhibiting DNA methyltransferase (DNMT) activity of silkworm can suppress BmNPV replication. The integrated analysis of transcriptomes and DNA methylomes in silkworm midguts infected with or without BmNPV showed that both the expression pattern of transcriptome and DNA methylation pattern are changed significantly upon BmNPV infection. A total of 241 differentially methylated regions (DMRs) were observed in BmNPV infected midguts, among which, 126 DMRs were hyper-methylated and 115 DMRs were hypo-methylated. Significant differences in both mRNA transcript level and DNA methylated levels were found in 26 genes. BS-PCR validated the hypermethylation of BGIBMGA014008, a structural maintenance of chromosomes protein gene in the BmNPV-infected midgut. In addition, DNMT inhibition reduced the expression of inhibitor of apoptosis family genes, iap1 from BmNPV, Bmiap2, BmSurvivin1 and BmSurvivin2. CONCLUSION Our results indicate that DNA methylation plays positive roles in BmNPV proliferation and loss of DNMT activity could induce the apoptosis of infected cells to suppress BmNPV proliferation. Our results may provide a new idea and research direction for the molecular mechanism on insect-virus interaction.
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Affiliation(s)
- Haoling Huang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Ping Wu
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China. .,The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, China. .,Quality inspection center for sericultural products, Ministry of Agriculture and Rural Affairs, Zhenjiang, 212018, China.
| | - Shaolun Zhang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Qi Shang
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Haotong Yin
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Qirui Hou
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China.,The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, China.,Quality inspection center for sericultural products, Ministry of Agriculture and Rural Affairs, Zhenjiang, 212018, China
| | - Jinbo Zhong
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China
| | - Xijie Guo
- Sericultural Research Institute, Jiangsu University of Science and Technology, Zhenjiang, 212018, China. .,The Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212018, China.
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24
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Chen W, Dong Y, Lin L, Saqib HSA, Ma X, Xu X, Zhang L, Jing X, Peng L, Wang Y, Vasseur L, He W, You M. Implication for DNA methylation involved in the host transfer of diamondback moth, Plutella xylostella (L.). ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2019; 102:e21600. [PMID: 31328824 DOI: 10.1002/arch.21600] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA methylation exerts extensive impacts on gene expression of various living organisms exposed to environmental variation. However, little is known whether DNA methylation is involved in the host transfer of diamondback moth, Plutella xylostella (L.), a worldwide destructive pest of crucifers. In this study, we found that P. xylostella genome exhibited a relatively low level of DNA methylation on the basis of the CpG O/E prediction and experimental validation. A significant positive linear correlation was observed between the stage-specific expressions of PxDNMT1 and DNA methylation levels (5mC content). Particularly, high levels of DNA methylation and gene expression of PxDNMT1 were observed in eggs and mature females of P. xylostella. After host transfer of P. xylostella from Raphanus sativus to Arabidopsis thaliana, we identified some potential genomic loci that might have changed methylation levels. Using the method of fluorescence-labeled methylation-sensitive amplified polymorphism (F-MSAP), we also found the corresponding genes primarily involved in neural system and signaling. The expressions of six candidate genes were verified by qRT-PCR. One of the genes, Px009600, might be regulated by a DNA methylation-mediated mechanism in response to host transfer. Our study provides evidence for a functional system of DNA methylation in P. xylostella and its possible role in adaptation during host transfer. Further studies should examine methylation as responsive factors to different host plants and environmental cues in insect pests.
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Affiliation(s)
- Wei Chen
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuhong Dong
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianyun Lin
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hafiz Sohaib Ahmed Saqib
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaoli Ma
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuejiao Xu
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lingling Zhang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaodong Jing
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lu Peng
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yue Wang
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liette Vasseur
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Biological Sciences, Brock University, St. Catharines, Ontario, Canada
| | - Weiyi He
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Minsheng You
- State Key Laboratory for Ecological Pest Control of Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, China
- International Joint Research Laboratory of Ecological Pest Control, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China
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25
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Xiu Y, Shao C, Zhu Y, Li Y, Gan T, Xu W, Piferrer F, Chen S. Differences in DNA Methylation Between Disease-Resistant and Disease-Susceptible Chinese Tongue Sole ( Cynoglossus semilaevis) Families. Front Genet 2019; 10:847. [PMID: 31572451 PMCID: PMC6753864 DOI: 10.3389/fgene.2019.00847] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 08/14/2019] [Indexed: 12/12/2022] Open
Abstract
DNA methylation, the most widely studied and most well-understood epigenetic modification, has been reported to play crucial roles in diverse processes. Although it has been found that DNA methylation can modulate the expression of immune-related genes in teleosts, a systemic analysis of epigenetic regulation on teleost immunity has rarely been performed. In this research, we employed whole-genome bisulfite sequencing to investigate the genome-wide DNA methylation profiles in select disease-resistant Cynoglossus semilaevis (DR-CS, family 14L006) and disease-susceptible C. semilaevis (DS-CS, family 14L104) against Vibrio harveyi infection. The results showed that following selective breeding, DR-CS had higher DNA methylation levels and different DNA methylation patterns, with 3,311 differentially methylated regions and 6,456 differentially methylated genes. Combining these data with the corresponding transcriptome data, we identified several immune-related genes that exhibited differential expression levels that were modulated by DNA methylation. Specifically, DNA methylation of tumor necrosis factor–like and lipopolysaccharide-binding protein-like was significantly correlated with their expression and significantly contributed to the disease resistance of the selected C. semilaevis family. In conclusion, we suggest that artificial selection for disease resistance in Chinese tongue sole causes changes in DNA methylation levels in important immune-related genes and that these epigenetic changes are potentially involved in multiple immune responses in Chinese tongue sole.
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Affiliation(s)
- Yunji Xiu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Ying Zhu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yangzhen Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Tian Gan
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wenteng Xu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Francesc Piferrer
- Institut de Ciències del Mar (ICM), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Songlin Chen
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture; Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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26
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Huh I, Wu X, Park T, Yi SV. Detecting differential DNA methylation from sequencing of bisulfite converted DNA of diverse species. Brief Bioinform 2019; 20:33-46. [PMID: 28981571 PMCID: PMC6357555 DOI: 10.1093/bib/bbx077] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Indexed: 12/26/2022] Open
Abstract
DNA methylation is one of the most extensively studied epigenetic modifications of genomic DNA. In recent years, sequencing of bisulfite-converted DNA, particularly via next-generation sequencing technologies, has become a widely popular method to study DNA methylation. This method can be readily applied to a variety of species, dramatically expanding the scope of DNA methylation studies beyond the traditionally studied human and mouse systems. In parallel to the increasing wealth of genomic methylation profiles, many statistical tools have been developed to detect differentially methylated loci (DMLs) or differentially methylated regions (DMRs) between biological conditions. We discuss and summarize several key properties of currently available tools to detect DMLs and DMRs from sequencing of bisulfite-converted DNA. However, the majority of the statistical tools developed for DML/DMR analyses have been validated using only mammalian data sets, and less priority has been placed on the analyses of invertebrate or plant DNA methylation data. We demonstrate that genomic methylation profiles of non-mammalian species are often highly distinct from those of mammalian species using examples of honey bees and humans. We then discuss how such differences in data properties may affect statistical analyses. Based on these differences, we provide three specific recommendations to improve the power and accuracy of DML and DMR analyses of invertebrate data when using currently available statistical tools. These considerations should facilitate systematic and robust analyses of DNA methylation from diverse species, thus advancing our understanding of DNA methylation.
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Affiliation(s)
- Iksoo Huh
- School of Biological Sciences, Georgia Institute of Technology
| | - Xin Wu
- School of Biological Sciences, Georgia Institute of Technology
| | - Taesung Park
- Department of Statistics, Seoul National University
| | - Soojin V Yi
- School of Biological Sciences, Georgia Institute of Technology
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27
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Liu S, Aageaard A, Bechsgaard J, Bilde T. DNA Methylation Patterns in the Social Spider, Stegodyphus dumicola. Genes (Basel) 2019; 10:E137. [PMID: 30759892 PMCID: PMC6409797 DOI: 10.3390/genes10020137] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/25/2019] [Accepted: 01/25/2019] [Indexed: 12/18/2022] Open
Abstract
Variation in DNA methylation patterns among genes, individuals, and populations appears to be highly variable among taxa, but our understanding of the functional significance of this variation is still incomplete. We here present the first whole genome bisulfite sequencing of a chelicerate species, the social spider Stegodyphus dumicola. We show that DNA methylation occurs mainly in CpG context and is concentrated in genes. This is a pattern also documented in other invertebrates. We present RNA sequence data to investigate the role of DNA methylation in gene regulation and show that, within individuals, methylated genes are more expressed than genes that are not methylated and that methylated genes are more stably expressed across individuals than unmethylated genes. Although no causal association is shown, this lends support for the implication of DNA CpG methylation in regulating gene expression in invertebrates. Differential DNA methylation between populations showed a small but significant correlation with differential gene expression. This is consistent with a possible role of DNA methylation in local adaptation. Based on indirect inference of the presence and pattern of DNA methylation in chelicerate species whose genomes have been sequenced, we performed a comparative phylogenetic analysis. We found strong evidence for exon DNA methylation in the horseshoe crab Limulus polyphemus and in all spider and scorpion species, while most Parasitiformes and Acariformes species seem to have lost DNA methylation.
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Affiliation(s)
- Shenglin Liu
- Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark.
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28
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Aliaga B, Bulla I, Mouahid G, Duval D, Grunau C. Universality of the DNA methylation codes in Eucaryotes. Sci Rep 2019; 9:173. [PMID: 30655579 PMCID: PMC6336885 DOI: 10.1038/s41598-018-37407-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 10/24/2018] [Indexed: 12/26/2022] Open
Abstract
Genetics and epigenetics are tightly linked heritable information classes. Question arises if epigenetics provides just a set of environment dependent instructions, or whether it is integral part of an inheritance system. We argued that in the latter case the epigenetic code should share the universality quality of the genetic code. We focused on DNA methylation. Since availability of DNA methylation data is biased towards model organisms we developed a method that uses kernel density estimations of CpG observed/expected ratios to infer DNA methylation types in any genome. We show here that our method allows for robust prediction of mosaic and full gene body methylation with a PPV of 1 and 0.87, respectively. We used this prediction to complement experimental data, and applied hierarchical clustering to identify methylation types in ~150 eucaryotic species covering different body plans, reproduction types and living conditions. Our analysis indicates that there are only four gene body methylation types. These types do not follow phylogeny (i.e. phylogenetically distant clades can have identical methylation types) but they are consistent within clades. We conclude that the gene body DNA methylation codes have universality similar to the universality of the genetic code and should consequently be considered as part of the inheritance system.
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Affiliation(s)
- Benoît Aliaga
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - Ingo Bulla
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
- Institute for Mathematics and Informatics, University of Greifswald, Greifswald, Germany
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Gabriel Mouahid
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - David Duval
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France
| | - Christoph Grunau
- University Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, University Montpellier, F-66860, Perpignan, France.
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29
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Provataris P, Meusemann K, Niehuis O, Grath S, Misof B. Signatures of DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola. Genome Biol Evol 2018; 10:1185-1197. [PMID: 29697817 PMCID: PMC5915941 DOI: 10.1093/gbe/evy066] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/17/2018] [Indexed: 12/20/2022] Open
Abstract
It has been experimentally shown that DNA methylation is involved in the regulation of gene expression and the silencing of transposable element activity in eukaryotes. The variable levels of DNA methylation among different insect species indicate an evolutionarily flexible role of DNA methylation in insects, which due to a lack of comparative data is not yet well-substantiated. Here, we use computational methods to trace signatures of DNA methylation across insects by analyzing transcriptomic and genomic sequence data from all currently recognized insect orders. We conclude that: 1) a functional methylation system relying exclusively on DNA methyltransferase 1 is widespread across insects. 2) DNA methylation has potentially been lost or extremely reduced in species belonging to springtails (Collembola), flies and relatives (Diptera), and twisted-winged parasites (Strepsiptera). 3) Holometabolous insects display signs of reduced DNA methylation levels in protein-coding sequences compared with hemimetabolous insects. 4) Evolutionarily conserved insect genes associated with housekeeping functions tend to display signs of heavier DNA methylation in comparison to the genomic/transcriptomic background. With this comparative study, we provide the much needed basis for experimental and detailed comparative analyses required to gain a deeper understanding on the evolution and function of DNA methylation in insects.
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Affiliation(s)
- Panagiotis Provataris
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
| | - Karen Meusemann
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Freiburg (Brsg.), Germany
- Australian National Insect Collection, CSIRO National Research Collections Australia, Acton, Australian Capital Territory, Australia
| | - Oliver Niehuis
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
- Evolutionary Biology and Ecology, Institute of Biology I (Zoology), Albert Ludwig University Freiburg, Freiburg (Brsg.), Germany
| | - Sonja Grath
- Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg, Germany
- Corresponding authors: E-mails: ;
| | - Bernhard Misof
- Center for Molecular Biodiversity Research, Zoological Research Museum Alexander Koenig, Bonn, Germany
- Corresponding authors: E-mails: ;
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30
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Pegoraro M, Marshall H, Lonsdale ZN, Mallon EB. Do social insects support Haig's kin theory for the evolution of genomic imprinting? Epigenetics 2018; 12:725-742. [PMID: 28703654 PMCID: PMC5739101 DOI: 10.1080/15592294.2017.1348445] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Although numerous imprinted genes have been described in several lineages, the phenomenon of genomic imprinting presents a peculiar evolutionary problem. Several hypotheses have been proposed to explain gene imprinting, the most supported being Haig's kinship theory. This theory explains the observed pattern of imprinting and the resulting phenotypes as a competition for resources between related individuals, but despite its relevance it has not been independently tested. Haig's theory predicts that gene imprinting should be present in eusocial insects in many social scenarios. These lineages are therefore ideal for testing both the theory's predictions and the mechanism of gene imprinting. Here we review the behavioral evidence of genomic imprinting in eusocial insects, the evidence of a mechanism for genomic imprinting and finally we evaluate recent results showing parent of origin allele specific expression in honeybees in the light of Haig's theory.
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Affiliation(s)
- Mirko Pegoraro
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Hollie Marshall
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Zoë N Lonsdale
- a Department of Genetics and Genome Biology , University of Leicester , UK
| | - Eamonn B Mallon
- a Department of Genetics and Genome Biology , University of Leicester , UK
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31
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Trijau M, Asselman J, Armant O, Adam-Guillermin C, De Schamphelaere KAC, Alonzo F. Transgenerational DNA Methylation Changes in Daphnia magna Exposed to Chronic γ Irradiation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:4331-4339. [PMID: 29486114 DOI: 10.1021/acs.est.7b05695] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Our aim was to investigate epigenetic changes in Daphnia magna after a 25-day chronic external γ irradiation (generation F0 exposed to 6.5 μGy·h-1 or 41.3 mGy·h-1) and their potential inheritance by subsequent recovering generations, namely, F2 (exposed as germline cells in F1 embryos) and F3 (the first truly unexposed generation). Effects on survival, growth, and reproduction were observed and DNA was extracted for whole-genome bisulfite sequencing in all generations. Results showed effects on reproduction in F0 but no effect in the subsequent generations F1, F2, and F3. In contrast, we observed significant methylation changes at specific CpG positions in every generation independent of dose rate, with a majority of hypomethylation. Some of these changes were shared between dose rates and between generations. Associated gene functions included gene families and genes that were previously shown to play roles during exposure to ionizing radiation. Common methylation changes detected between generations F2 and F3 clearly showed that epigenetic modifications can be transmitted to unexposed generations, most likely through the germline, with potential implications for environmental risk.
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Affiliation(s)
- Marie Trijau
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
| | - Jana Asselman
- Laboratory for Environmental Toxicology and Aquatic Ecology , Ghent University , Ghent 9000 , Belgium
| | - Olivier Armant
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
| | - Christelle Adam-Guillermin
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
| | | | - Frédéric Alonzo
- Institut de Radioprotection et de Sûreté Nucléaire , PSE-ENV, SRTE, LECO, Cadarache, Saint-Paul-lèz-Durance 13115 , France
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32
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Bulla I, Aliaga B, Lacal V, Bulla J, Grunau C, Chaparro C. Notos - a galaxy tool to analyze CpN observed expected ratios for inferring DNA methylation types. BMC Bioinformatics 2018; 19:105. [PMID: 29587630 PMCID: PMC5870242 DOI: 10.1186/s12859-018-2115-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 03/13/2018] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND DNA methylation patterns store epigenetic information in the vast majority of eukaryotic species. The relatively high costs and technical challenges associated with the detection of DNA methylation however have created a bias in the number of methylation studies towards model organisms. Consequently, it remains challenging to infer kingdom-wide general rules about the functions and evolutionary conservation of DNA methylation. Methylated cytosine is often found in specific CpN dinucleotides, and the frequency distributions of, for instance, CpG observed/expected (CpG o/e) ratios have been used to infer DNA methylation types based on higher mutability of methylated CpG. RESULTS Predominantly model-based approaches essentially founded on mixtures of Gaussian distributions are currently used to investigate questions related to the number and position of modes of CpG o/e ratios. These approaches require the selection of an appropriate criterion for determining the best model and will fail if empirical distributions are complex or even merely moderately skewed. We use a kernel density estimation (KDE) based technique for robust and precise characterization of complex CpN o/e distributions without a priori assumptions about the underlying distributions. CONCLUSIONS We show that KDE delivers robust descriptions of CpN o/e distributions. For straightforward processing, we have developed a Galaxy tool, called Notos and available at the ToolShed, that calculates these ratios of input FASTA files and fits a density to their empirical distribution. Based on the estimated density the number and shape of modes of the distribution is determined, providing a rational for the prediction of the number and the types of different methylation classes. Notos is written in R and Perl.
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Affiliation(s)
- Ingo Bulla
- Institut für Mathematik und Informatik, Universität Greifswald, Walther-Rathenau-Str. 47, Greifswald, 17487 Germany
- Theoretical Biology and Biophysics, Group T-6, Los Alamos National Laboratory, New Mexico, Los Alamos USA
| | - Benoît Aliaga
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, 58 Avenue Paul Alduy, Perpignan, 66860 France
| | - Virginia Lacal
- Department of Mathematics, University of Bergen, P.O. Box 7803, Bergen, 5020 Norway
| | - Jan Bulla
- Department of Mathematics, University of Bergen, P.O. Box 7803, Bergen, 5020 Norway
| | - Christoph Grunau
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, 58 Avenue Paul Alduy, Perpignan, 66860 France
| | - Cristian Chaparro
- Univ. Perpignan Via Domitia, IHPE UMR 5244, CNRS, IFREMER, Univ. Montpellier, 58 Avenue Paul Alduy, Perpignan, 66860 France
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33
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Rapid regulatory evolution of a nonrecombining autosome linked to divergent behavioral phenotypes. Proc Natl Acad Sci U S A 2018; 115:2794-2799. [PMID: 29483264 PMCID: PMC5856536 DOI: 10.1073/pnas.1717721115] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In the white-throated sparrow (Zonotrichia albicollis), the second chromosome bears a striking resemblance to sex chromosomes. First, within each breeding pair of birds, one bird is homozygous for the standard arrangement of the chromosome (ZAL2/ZAL2) and its mate is heterozygous for a different version (ZAL2/ZAL2m). Second, recombination is profoundly suppressed between the two versions, leading to genetic differentiation between them. Third, the ZAL2m version is linked with phenotypic traits, such as bright plumage, high aggression, and low parental behavior, which are usually associated with males. These similarities to sex chromosomes suggest that the evolutionary mechanisms that shape sex chromosomes, in particular genetic degeneration of the heterogametic version due to the suppression of recombination, are likely important in this system as well. Here, we investigated patterns of protein sequence evolution and gene expression evolution between the ZAL2 and ZAL2m chromosomes by whole-genome sequencing and transcriptome analyses. Patterns of protein evolution exhibited only weak signals of genetic degeneration, and few genes harbored signatures of positive selection. We found substantial evidence of transcriptome evolution, such as significant expression divergence between ZAL2 and ZAL2m alleles and signatures of dosage compensation for highly expressed genes. These results suggest that, early in the evolution of heteromorphic chromosomes, gene expression divergence and dosage compensation can prevail before large-scale genetic degeneration. Our results show further that suppression of recombination between heteromorphic chromosomes can lead to the evolution of alternative (sex-like) behavioral phenotypes before substantial genetic degeneration.
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Hemimetabolous genomes reveal molecular basis of termite eusociality. Nat Ecol Evol 2018; 2:557-566. [PMID: 29403074 PMCID: PMC6482461 DOI: 10.1038/s41559-017-0459-1] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/19/2017] [Indexed: 11/25/2022]
Abstract
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects. Dramatic adaptive changes in genes underlying the production and perception of pheromones confirm the importance of chemical communication in the termites. These are accompanied by major changes in gene regulation and the molecular evolution of caste determination. Many of these results parallel molecular mechanisms of eusocial evolution in Hymenoptera. However, the specific solutions are remarkably different, thus revealing a striking case of convergence in one of the major evolutionary transitions in biological complexity.
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35
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Takuno S, Seymour DK, Gaut BS. The Evolutionary Dynamics of Orthologs That Shift in Gene Body Methylation between Arabidopsis Species. Mol Biol Evol 2017; 34:1479-1491. [PMID: 28333248 DOI: 10.1093/molbev/msx099] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation labels a specific subset of genes in plant genomes. Recent work has shown that this gene-body methylation (gbM) is a conserved feature of orthologs, because highly methylated genes in one species tend to be highly methylated in another. In this study, we examined the exceptions to that rule by identifying genes that differ in gbM status between two plant species-Arabidopsis thaliana and Arabidopsis lyrata. Using Capsella grandiflora as an outgroup, we polarized the loss and gain of gbM for orthologs in the Arabidopsis lineage. Our survey identified a few hundred genes that differed between ingroup species, out of ∼9,000 orthologs. The estimated rate of gbM gain was ∼2 × 10-9 per gene per year for both ingroup taxa and was similar to the loss rate in A. lyrata. In contrast, A. thaliana had a ∼3-fold higher estimated rate of gbM loss per gene, consistent with a recent diminishment of genome size. As in previous studies, we found that body-methylated genes were expressed broadly across tissues and were also longer than other genic sets. Genes that differed in gbM status exhibited higher variance in expression between species than genes that were body-methylated in both species. Moreover, the gain of gbM in one lineage tended to be associated with an increase of expression in that lineage. The genes that varied in gbM status between species varied more significantly in length between species than other sets of genes; we hypothesize that length is a key feature in the transition between body-methylated and nonmethylated genes.
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Affiliation(s)
- Shohei Takuno
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Kanagawa, Japan
| | - Danelle K Seymour
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA
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36
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Song K, Li L, Zhang G. The association between DNA methylation and exon expression in the Pacific oyster Crassostrea gigas. PLoS One 2017; 12:e0185224. [PMID: 28945769 PMCID: PMC5612690 DOI: 10.1371/journal.pone.0185224] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 09/09/2017] [Indexed: 12/13/2022] Open
Abstract
Background DNA methylation is one of the most important epigenetic modifications of eukaryotic genomes and is believed to play integral roles in diverse biological processes. Although DNA methylation has been well studied in mammals, data are limited in invertebrates, particularly Mollusca. The Pacific oyster Crassostrea gigas is an emerging genetic model for functional analysis of DNA methylation in Mollusca. Recent studies have shown that there is a positive association between methylation status and gene expression in C. gigas; however, whether this association exists at the exon level remains to be determined. Results In this study, we characterized the genome-wide methylation pattern across two different tissues of C. gigas and found that methylated genes are expressed in more tissues and development stages than unmethylated genes. Furthermore, we found that different types of exons had different methylation levels, with the lowest methylation levels in the first exons, followed by the last exons, and the internal exons. We found that the exons included in the gene transcript contained significantly higher DNA methylation levels than skipped exons. We observed that the DNA methylation levels increased slowly after the start sites and end sites of exons seperately, and then decreased quickly towards the middle sites of exons. We also found that methylated exons were significantly longer than unmethylated exons. Conclusion This study constitutes the first genome-wide analysis to show an association between exon-level DNA methylation and mRNA expression in the oyster. Our findings suggest that exon-level DNA methylation may play a role in the construction of alternative splicing by positively influencing exon inclusion during transcription.
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Affiliation(s)
- Kai Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- * E-mail: (LL); (GZ)
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- * E-mail: (LL); (GZ)
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Radhakrishnan S, Literman R, Mizoguchi B, Valenzuela N. MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination. Epigenetics Chromatin 2017; 10:28. [PMID: 28533820 PMCID: PMC5438563 DOI: 10.1186/s13072-017-0136-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 05/12/2017] [Indexed: 12/15/2022] Open
Abstract
Background DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis. Results Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation. Conclusions Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Robert Literman
- Ecology and Evolutionary Biology Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Beatriz Mizoguchi
- Interdepartmental Genetics and Genomics Program, Iowa State University, Ames, IA 50011 USA.,Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, 251 Bessey Hall, Ames, IA 50011 USA
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38
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Shaham R, Ben-Shlomo R, Motro U, Keasar T. Genome methylation patterns across castes and generations in a parasitoid wasp. Ecol Evol 2016; 6:7943-7953. [PMID: 27878068 PMCID: PMC5108247 DOI: 10.1002/ece3.2395] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/13/2016] [Accepted: 08/01/2016] [Indexed: 01/01/2023] Open
Abstract
Environmental influences shape phenotypes within and across generations, often through DNA methylations that modify gene expression. Methylations were proposed to mediate caste and task allocation in some eusocial insects, but how an insect's environment affects DNA methylation in its offspring is yet unknown. We characterized parental effects on methylation profiles in the polyembryonic parasitoid wasp Copidosoma koehleri, as well as methylation patterns associated with its simple caste system. We used methylation‐sensitive amplified fragment length polymorphism (MS‐AFLP) to compare methylation patterns, among (1) reproductive and soldier larvae; and (2) offspring (larvae, pupae, and adults) of wasps that were reared at either high or low larval density and mated in the four possible combinations. Methylation frequencies were similar across castes, but the profiles of methylated fragments differed significantly. Parental rearing density did not affect methylation frequencies in the offspring at any developmental stage. Principal coordinate analysis indicated no significant differences in methylation profiles among the four crossbreeding groups and the three developmental stages. Nevertheless, a clustering analysis, performed on a subset of the fragments, revealed similar methylation patterns in larvae, pupae, and adults in two of the four parental crosses. Nine fragments were methylated at two cytosine sites in all larvae, and five others were methylated at two sites in all adults. Thus, DNA methylations correlate with within‐generation phenotypic plasticity due to caste. However, their association with developmental stage and with transgenerational epigenetic effects is not clearly supported.
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Affiliation(s)
- Roei Shaham
- Evolutionary and Environmental Biology University of Haifa Haifa Israel
| | - Rachel Ben-Shlomo
- Biology and the Environment University of Haifa - Oranim Tivon Israel
| | - Uzi Motro
- Evolution, Ecology and Behavior The Hebrew University of Jerusalem Jerusalem Israel
| | - Tamar Keasar
- Biology and the Environment University of Haifa - Oranim Tivon Israel
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39
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Kim D, Thairu MW, Hansen AK. Novel Insights into Insect-Microbe Interactions-Role of Epigenomics and Small RNAs. FRONTIERS IN PLANT SCIENCE 2016; 7:1164. [PMID: 27540386 PMCID: PMC4972996 DOI: 10.3389/fpls.2016.01164] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/20/2016] [Indexed: 05/23/2023]
Abstract
It has become increasingly clear that microbes form close associations with the vast majority of animal species, especially insects. In fact, an array of diverse microbes is known to form shared metabolic pathways with their insect hosts. A growing area of research in insect-microbe interactions, notably for hemipteran insects and their mutualistic symbionts, is to elucidate the regulation of this inter-domain metabolism. This review examines two new emerging mechanisms of gene regulation and their importance in host-microbe interactions. Specifically, we highlight how the incipient areas of research on regulatory "dark matter" such as epigenomics and small RNAs, can play a pivotal role in the evolution of both insect and microbe gene regulation. We then propose specific models of how these dynamic forms of gene regulation can influence insect-symbiont-plant interactions. Future studies in this area of research will give us a systematic understanding of how these symbiotic microbes and animals reciprocally respond to and regulate their shared metabolic processes.
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40
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Abstract
Gene body methylation (gbM) is an ancestral and widespread feature in Eukarya, yet its adaptive value and evolutionary implications remain unresolved. The occurrence of gbM within protein-coding sequences is particularly puzzling, because methylation causes cytosine hypermutability and hence is likely to produce deleterious amino acid substitutions. We investigate this enigma using an evolutionarily basal group of Metazoa, the stony corals (order Scleractinia, class Anthozoa, phylum Cnidaria). We show that patterns of coral gbM are similar to other invertebrate species, predicting wide and active transcription and slower sequence evolution. We also find a strong correlation between gbM and codon bias, resulting from systematic replacement of CpG bearing codons. We conclude that gbM has strong effects on codon evolution and speculate that this may influence establishment of optimal codons.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas
| | - Line K Bay
- Australian Institute of Marine Science, Townsville, QLD, Australia ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD, Australia
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41
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Robinson KL, Tohidi-Esfahani D, Ponton F, Simpson SJ, Sword GA, Lo N. Alternative migratory locust phenotypes are associated with differences in the expression of genes encoding the methylation machinery. INSECT MOLECULAR BIOLOGY 2016; 25:105-115. [PMID: 26612460 DOI: 10.1111/imb.12203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite the importance of locust density-dependent polyphenism as a model system for understanding phenotypic plasticity, there is still much to be learnt about its underlying molecular control. Here we describe the first investigation into the expression of genes encoding the DNA methylation machinery in the migratory locust (Locusta migratoria). We show that the alternative solitarious and gregarious phenotypic states induced by different locust rearing densities are associated with significant differences in the expression of the target genes DNA methyltransferase 1, DNA methyltransferase 2 and methyl-CpG-binding domain protein 2/3. This variation was most pronounced in the embryos of solitarious vs. gregarious mothers. We mapped the embryonic methylation profiles of several intragenic regions and a Long Interspersed Nuclear Element (LINE), each of which is known to be differentially expressed between alternative locust phenotypes or has been directly implicated in phase change. LmI and three genes, adenyl cyclase-associated binding protein 2, choline kinase alpha-like and henna, were methylated. Our results set the stage for future studies investigating the specific role of DNA methylation in the maternal transfer of migratory locust phase polyphenism.
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Affiliation(s)
- K L Robinson
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
| | - D Tohidi-Esfahani
- ANU College of Medicine, Biology and Environment, Australian National University, Canberra, ACT, Australia
| | - F Ponton
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, NSW, Australia
- Department of Biological Sciences, Macquarie University, North Ryde NSW, Australia
| | - S J Simpson
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
- Charles Perkins Centre, The University of Sydney, NSW, Australia
| | - G A Sword
- Department of Entomology, Texas A&M University, College Station, TX, USA
| | - N Lo
- School of Biological Sciences, The University of Sydney, Sydney, NSW, Australia
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42
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Dimond JL, Roberts SB. Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change. Mol Ecol 2016; 25:1895-904. [DOI: 10.1111/mec.13414] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/26/2015] [Accepted: 10/01/2015] [Indexed: 12/27/2022]
Affiliation(s)
- James L. Dimond
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
| | - Steven B. Roberts
- School of Aquatic and Fishery Sciences; University of Washington; 1122 Boat Street Seattle WA 98105 USA
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43
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Metzger DCH, Schulte PM. Epigenomics in marine fishes. Mar Genomics 2016; 30:43-54. [PMID: 26833273 DOI: 10.1016/j.margen.2016.01.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/31/2022]
Abstract
Epigenetic mechanisms are an underappreciated and often ignored component of an organism's response to environmental change and may underlie many types of phenotypic plasticity. Recent technological advances in methods for detecting epigenetic marks at a whole-genome scale have launched new opportunities for studying epigenomics in ecologically relevant non-model systems. The study of ecological epigenomics holds great promise to better understand the linkages between genotype, phenotype, and the environment and to explore mechanisms of phenotypic plasticity. The many attributes of marine fish species, including their high diversity, variable life histories, high fecundity, impressive plasticity, and economic value provide unique opportunities for studying epigenetic mechanisms in an environmental context. To provide a primer on epigenomic research for fish biologists, we start by describing fundamental aspects of epigenetics, focusing on the most widely studied and most well understood of the epigenetic marks: DNA methylation. We then describe the techniques that have been used to investigate DNA methylation in marine fishes to date and highlight some new techniques that hold great promise for future studies. Epigenomic research in marine fishes is in its early stages, so we first briefly discuss what has been learned about the establishment, maintenance, and function of DNA methylation in fishes from studies in zebrafish and then summarize the studies demonstrating the pervasive effects of the environment on the epigenomes of marine fishes. We conclude by highlighting the potential for ongoing research on the epigenomics of marine fishes to reveal critical aspects of the interaction between organisms and their environments.
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Affiliation(s)
- David C H Metzger
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| | - Patricia M Schulte
- Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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44
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Keller TE, Han P, Yi SV. Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate-Vertebrate Boundary. Mol Biol Evol 2015; 33:1019-28. [PMID: 26715626 PMCID: PMC4776710 DOI: 10.1093/molbev/msv345] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genomes of invertebrates and vertebrates exhibit highly divergent patterns of DNA methylation. Invertebrate genomes tend to be sparsely methylated, and DNA methylation is mostly targeted to a subset of transcription units (gene bodies). In a drastic contrast, vertebrate genomes are generally globally and heavily methylated, punctuated by the limited local hypo-methylation of putative regulatory regions such as promoters. These genomic differences also translate into functional differences in DNA methylation and gene regulation. Although promoter DNA methylation is an important regulatory component of vertebrate gene expression, its role in invertebrate gene regulation has been little explored. Instead, gene body DNA methylation is associated with expression of invertebrate genes. However, the evolutionary steps leading to the differentiation of invertebrate and vertebrate genomic DNA methylation remain unresolved. Here we analyzed experimentally determined DNA methylation maps of several species across the invertebrate–vertebrate boundary, to elucidate how vertebrate gene methylation has evolved. We show that, in contrast to the prevailing idea, a substantial number of promoters in an invertebrate basal chordate Ciona intestinalis are methylated. Moreover, gene expression data indicate significant, epigenomic context-dependent associations between promoter methylation and expression in C. intestinalis. However, there is no evidence that promoter methylation in invertebrate chordate has been evolutionarily maintained across the invertebrate–vertebrate boundary. Rather, body-methylated invertebrate genes preferentially obtain hypo-methylated promoters among vertebrates. Conversely, promoter methylation is preferentially found in lineage- and tissue-specific vertebrate genes. These results provide important insights into the evolutionary origin of epigenetic regulation of vertebrate gene expression.
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Affiliation(s)
| | | | - Soojin V Yi
- School of Biology, Georgia Institute of Technology
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45
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Pegoraro M, Bafna A, Davies NJ, Shuker DM, Tauber E. DNA methylation changes induced by long and short photoperiods in Nasonia. Genome Res 2015; 26:203-10. [PMID: 26672019 PMCID: PMC4728373 DOI: 10.1101/gr.196204.115] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 12/14/2015] [Indexed: 02/07/2023]
Abstract
Many organisms monitor the annual change in day length and use this information for the timing of their seasonal response. However, the molecular mechanisms underlying photoperiodic timing are largely unknown. The wasp Nasonia vitripennis is an emerging model organism that exhibits a strong photoperiodic response: Short autumnal days experienced by females lead to the induction of developmental arrest (diapause) in their progeny, allowing winter survival of the larvae. How female Nasonia control the developmental trajectory of their offspring is unclear. Here, we took advantage of the recent discovery that DNA methylation is pervasive in Nasonia and tested its role in photoperiodism. We used reduced representation bisulfite sequencing (RRBS) to profile DNA methylation in adult female wasps subjected to different photoperiods and identified substantial differential methylation at the single base level. We also show that knocking down DNA methyltransferase 1a (Dnmt1a), Dnmt3, or blocking DNA methylation pharmacologically, largely disrupts the photoperiodic diapause response of the wasps. To our knowledge, this is the first example for a role of DNA methylation in insect photoperiodic timing.
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Affiliation(s)
- Mirko Pegoraro
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Akanksha Bafna
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Nathaniel J Davies
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - David M Shuker
- School of Biology, University of St Andrews, St Andrews KY16 9TH, United Kingdom
| | - Eran Tauber
- Department of Genetics, University of Leicester, Leicester LE1 7RH, United Kingdom
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46
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Davies NJ, Tauber E. WaspAtlas: a Nasonia vitripennis gene database and analysis platform. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2015; 2015:bav103. [PMID: 26452372 PMCID: PMC4599445 DOI: 10.1093/database/bav103] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Accepted: 09/18/2015] [Indexed: 12/27/2022]
Abstract
Nasonia vitripennis is a parasitoid wasp which is becoming an important model organism for parasitism, epigenetics, evolutionary and developmental genetics. WaspAtlas is a new gene database in which we have compiled annotation data from all available N. vitripennis releases along with a wealth of transcriptomic data, methylation data and original analyses and annotations to form a comprehensive resource to aid the study of Nasonia. WaspAtlas allows users to explore gene structure and function, to compare expression data across sexes, tissues, developmental stages and conditions, and to explore published data relating to gene(s) of interest. WaspAtlas is easy to navigate and the database is easily searchable through the web interface. Detailed illustrations are provided for splice variants, protein domain predictions and the results of analyses. The website also functions as an analysis platform analysis for Nasonia, providing a set of tools designed to perform common analyses including GO term overrepresentation and RNAi off-target prediction. WaspAtlas will act as a hub for published data relating to Nasonia genes, and will be continually updated with new data to reflect the state of Nasonia-omics research. Database URL: http://waspatlas.com
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Affiliation(s)
- Nathaniel J Davies
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
| | - Eran Tauber
- Department of Genetics, University of Leicester, University Road, Leicester LE1 7RH, UK
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47
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Abstract
Parent-specific gene expression (PSGE) is little known outside of mammals and plants. PSGE occurs when the expression level of a gene depends on whether an allele was inherited from the mother or the father. Kin selection theory predicts that there should be extensive PSGE in social insects because social insect parents can gain inclusive fitness benefits by silencing parental alleles in female offspring. We searched for evidence of PSGE in honey bees using transcriptomes from reciprocal crosses between European and Africanized strains. We found 46 transcripts with significant parent-of-origin effects on gene expression, many of which overexpressed the maternal allele. Interestingly, we also found a large proportion of genes showing a bias toward maternal alleles in only one of the reciprocal crosses. These results indicate that PSGE may occur in social insects. The nonreciprocal effects could be largely driven by hybrid incompatibility between these strains. Future work will help to determine if these are indeed parent-of-origin effects that can modulate inclusive fitness benefits.
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48
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Galbraith DA, Yang X, Niño EL, Yi S, Grozinger C. Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera). PLoS Pathog 2015; 11:e1004713. [PMID: 25811620 PMCID: PMC4374888 DOI: 10.1371/journal.ppat.1004713] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/28/2015] [Indexed: 01/07/2023] Open
Abstract
Populations of honey bees are declining throughout the world, with US beekeepers losing 30% of their colonies each winter. Though multiple factors are driving these colony losses, it is increasingly clear that viruses play a major role. However, information about the molecular mechanisms mediating antiviral immunity in honey bees is surprisingly limited. Here, we examined the transcriptional and epigenetic (DNA methylation) responses to viral infection in honey bee workers. One-day old worker honey bees were fed solutions containing Israeli Acute Paralysis Virus (IAPV), a virus which causes muscle paralysis and death and has previously been associated with colony loss. Uninfected control and infected, symptomatic bees were collected within 20-24 hours after infection. Worker fat bodies, the primary tissue involved in metabolism, detoxification and immune responses, were collected for analysis. We performed transcriptome- and bisulfite-sequencing of the worker fat bodies to identify genome-wide gene expression and DNA methylation patterns associated with viral infection. There were 753 differentially expressed genes (FDR<0.05) in infected versus control bees, including several genes involved in epigenetic and antiviral pathways. DNA methylation status of 156 genes (FDR<0.1) changed significantly as a result of the infection, including those involved in antiviral responses in humans. There was no significant overlap between the significantly differentially expressed and significantly differentially methylated genes, and indeed, the genomic characteristics of these sets of genes were quite distinct. Our results indicate that honey bees have two distinct molecular pathways, mediated by transcription and methylation, that modulate protein levels and/or function in response to viral infections.
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Affiliation(s)
- David A. Galbraith
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Xingyu Yang
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Elina Lastro Niño
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Soojin Yi
- School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Christina Grozinger
- Department of Entomology, Center for Pollinator Research, Pennsylvania State University, University Park, Pennsylvania, United States of America
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49
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Dixon GB, Bay LK, Matz MV. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014; 15:1109. [PMID: 25511458 PMCID: PMC4378018 DOI: 10.1186/1471-2164-15-1109] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 12/10/2014] [Indexed: 11/24/2022] Open
Abstract
Background In invertebrates, genes belonging to dynamically regulated functional categories appear to be less methylated than “housekeeping” genes, suggesting that DNA methylation may modulate gene expression plasticity. To date, however, experimental evidence to support this hypothesis across different natural habitats has been lacking. Results Gene expression profiles were generated from 30 pairs of genetically identical fragments of coral Acropora millepora reciprocally transplanted between distinct natural habitats for 3 months. Gene expression was analyzed in the context of normalized CpG content, a well-established signature of historical germline DNA methylation. Genes with weak methylation signatures were more likely to demonstrate differential expression based on both transplant environment and population of origin than genes with strong methylation signatures. Moreover, the magnitude of expression differences due to environment and population were greater for genes with weak methylation signatures. Conclusions Our results support a connection between differential germline methylation and gene expression flexibility across environments and populations. Studies of phylogenetically basal invertebrates such as corals will further elucidate the fundamental functional aspects of gene body methylation in Metazoa. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1109) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Groves B Dixon
- Institute for Cell and Molecular Biology, University of Texas Austin, Austin, USA.
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50
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Chipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST, Schröder R, Torres-Oliva M, Znassi N, Jiang H, Almeida FC, Alonso CR, Apostolou Z, Aqrawi P, Arthur W, Barna JCJ, Blankenburg KP, Brites D, Capella-Gutiérrez S, Coyle M, Dearden PK, Du Pasquier L, Duncan EJ, Ebert D, Eibner C, Erikson G, Evans PD, Extavour CG, Francisco L, Gabaldón T, Gillis WJ, Goodwin-Horn EA, Green JE, Griffiths-Jones S, Grimmelikhuijzen CJP, Gubbala S, Guigó R, Han Y, Hauser F, Havlak P, Hayden L, Helbing S, Holder M, Hui JHL, Hunn JP, Hunnekuhl VS, Jackson L, Javaid M, Jhangiani SN, Jiggins FM, Jones TE, Kaiser TS, Kalra D, Kenny NJ, Korchina V, Kovar CL, Kraus FB, Lapraz F, Lee SL, Lv J, Mandapat C, Manning G, Mariotti M, Mata R, Mathew T, Neumann T, Newsham I, Ngo DN, Ninova M, Okwuonu G, Ongeri F, Palmer WJ, Patil S, Patraquim P, Pham C, Pu LL, Putman NH, Rabouille C, Ramos OM, Rhodes AC, Robertson HE, Robertson HM, Ronshaugen M, Rozas J, Saada N, Sánchez-Gracia A, Scherer SE, Schurko AM, Siggens KW, Simmons D, Stief A, Stolle E, Telford MJ, Tessmar-Raible K, Thornton R, van der Zee M, von Haeseler A, Williams JM, Willis JH, Wu Y, Zou X, Lawson D, Muzny DM, Worley KC, Gibbs RA, Akam M, Richards S. The first myriapod genome sequence reveals conservative arthropod gene content and genome organisation in the centipede Strigamia maritima. PLoS Biol 2014; 12:e1002005. [PMID: 25423365 PMCID: PMC4244043 DOI: 10.1371/journal.pbio.1002005] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 10/15/2014] [Indexed: 12/14/2022] Open
Abstract
Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda is the only arthropod class not represented by a sequenced genome. We present an analysis of the genome of the centipede Strigamia maritima. It retains a compact genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many orthologues of genes conserved from the bilaterian ancestor that have been lost in insects. Our analysis locates many genes in conserved macro-synteny contexts, and many small-scale examples of gene clustering. We describe several examples where S. maritima shows different solutions from insects to similar problems. The insect olfactory receptor gene family is absent from S. maritima, and olfaction in air is likely effected by expansion of other receptor gene families. For some genes S. maritima has evolved paralogues to generate coding sequence diversity, where insects use alternate splicing. This is most striking for the Dscam gene, which in Drosophila generates more than 100,000 alternate splice forms, but in S. maritima is encoded by over 100 paralogues. We see an intriguing linkage between the absence of any known photosensory proteins in a blind organism and the additional absence of canonical circadian clock genes. The phylogenetic position of myriapods allows us to identify where in arthropod phylogeny several particular molecular mechanisms and traits emerged. For example, we conclude that juvenile hormone signalling evolved with the emergence of the exoskeleton in the arthropods and that RR-1 containing cuticle proteins evolved in the lineage leading to Mandibulata. We also identify when various gene expansions and losses occurred. The genome of S. maritima offers us a unique glimpse into the ancestral arthropod genome, while also displaying many adaptations to its specific life history. Arthropods are the most abundant animals on earth. Among them, insects clearly dominate on land, whereas crustaceans hold the title for the most diverse invertebrates in the oceans. Much is known about the biology of these groups, not least because of genomic studies of the fruit fly Drosophila, the water flea Daphnia, and other species used in research. Here we report the first genome sequence from a species belonging to a lineage that has previously received very little attention—the myriapods. Myriapods were among the first arthropods to invade the land over 400 million years ago, and survive today as the herbivorous millipedes and venomous centipedes, one of which—Strigamia maritima—we have sequenced here. We find that the genome of this centipede retains more characteristics of the presumed arthropod ancestor than other sequenced insect genomes. The genome provides access to many aspects of myriapod biology that have not been studied before, suggesting, for example, that they have diversified receptors for smell that are quite different from those used by insects. In addition, it shows specific consequences of the largely subterranean life of this particular species, which seems to have lost the genes for all known light-sensing molecules, even though it still avoids light.
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Affiliation(s)
- Ariel D. Chipman
- The Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, Israel
| | - David E. K. Ferrier
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Carlo Brena
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Jiaxin Qu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daniel S. T. Hughes
- EMBL - European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Reinhard Schröder
- Institut für Biowissenschaften, Universität Rostock, Abt. Genetik, Rostock, Germany
| | | | - Nadia Znassi
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Huaiyang Jiang
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Francisca C. Almeida
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET), Universidad Nacional de Tucumán, Facultad de Ciencias Naturales e Instituto Miguel Lillo, San Miguel de Tucumán, Argentina
| | - Claudio R. Alonso
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Zivkos Apostolou
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute of Molecular Biology & Biotechnology, Foundation for Research & Technology - Hellas, Heraklion, Crete, Greece
| | - Peshtewani Aqrawi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wallace Arthur
- Department of Zoology, National University of Ireland, Galway, Ireland
| | | | - Kerstin P. Blankenburg
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daniela Brites
- Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | | | - Marcus Coyle
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Peter K. Dearden
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Louis Du Pasquier
- Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - Elizabeth J. Duncan
- Gravida and Genetics Otago, Biochemistry Department, University of Otago, Dunedin, New Zealand
| | - Dieter Ebert
- Evolutionsbiologie, Zoologisches Institut, Universität Basel, Basel, Switzerland
| | - Cornelius Eibner
- Department of Zoology, National University of Ireland, Galway, Ireland
| | - Galina Erikson
- Razavi Newman Center for Bioinformatics, Salk Institute, La Jolla, California, United States of America
- Scripps Translational Science Institute, La Jolla, California, United States of America
| | | | - Cassandra G. Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Liezl Francisco
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Toni Gabaldón
- Centre for Genomic Regulation, Barcelona, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - William J. Gillis
- Department of Biochemistry and Cell Biology, Center for Developmental Genetics, Stony Brook University, Stony Brook, New York, United States of America
| | | | - Jack E. Green
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Sam Griffiths-Jones
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Sai Gubbala
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Roderic Guigó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Genomic Regulation, Barcelona, Spain
| | - Yi Han
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Frank Hauser
- Center for Functional and Comparative Insect Genomics, University of Copenhagen, Copenhagen, Denmark
| | - Paul Havlak
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America
| | - Luke Hayden
- Department of Zoology, National University of Ireland, Galway, Ireland
| | - Sophie Helbing
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Michael Holder
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jerome H. L. Hui
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Julia P. Hunn
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Vera S. Hunnekuhl
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - LaRonda Jackson
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mehwish Javaid
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shalini N. Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Tamsin E. Jones
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Tobias S. Kaiser
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Divya Kalra
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nathan J. Kenny
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, China
| | - Viktoriya Korchina
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Christie L. Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - F. Bernhard Kraus
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
- Department of Laboratory Medicine, University Hospital Halle (Saale), Halle (Saale), Germany
| | - François Lapraz
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Sandra L. Lee
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jie Lv
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America
| | - Christigale Mandapat
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Gerard Manning
- Razavi Newman Center for Bioinformatics, Salk Institute, La Jolla, California, United States of America
| | - Marco Mariotti
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Genomic Regulation, Barcelona, Spain
| | - Robert Mata
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tittu Mathew
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Tobias Neumann
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
| | - Irene Newsham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Dinh N. Ngo
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Geoffrey Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fiona Ongeri
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - William J. Palmer
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Shobha Patil
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro Patraquim
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Christopher Pham
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ling-Ling Pu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Nicholas H. Putman
- Department of Ecology and Evolutionary Biology, Rice University, Houston, Texas, United States of America
| | - Catherine Rabouille
- Hubrecht Institute for Developmental Biology and Stem Cell Research, Utrecht, The Netherlands
| | - Olivia Mendivil Ramos
- The Scottish Oceans Institute, Gatty Marine Laboratory, University of St Andrews, St Andrews, Fife, United Kingdom
| | - Adelaide C. Rhodes
- Harte Research Institute, Texas A&M University Corpus Christi, Corpus Christi, Texas, United States of America
| | - Helen E. Robertson
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Hugh M. Robertson
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Matthew Ronshaugen
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Julio Rozas
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Nehad Saada
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Alejandro Sánchez-Gracia
- Departament de Genètica and Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Barcelona, Spain
| | - Steven E. Scherer
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Andrew M. Schurko
- Department of Biology, Hendrix College, Conway, Arkansas, United States of America
| | - Kenneth W. Siggens
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - DeNard Simmons
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anna Stief
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
- Institute for Biochemistry and Biology, University Potsdam, Potsdam-Golm, Germany
| | - Eckart Stolle
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
| | - Maximilian J. Telford
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Kristin Tessmar-Raible
- Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
- Research Platform “Marine Rhythms of Life”, Vienna, Austria
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | | | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - James M. Williams
- Department of Biology, Hendrix College, Conway, Arkansas, United States of America
| | - Judith H. Willis
- Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America
| | - Yuanqing Wu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiaoyan Zou
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daniel Lawson
- EMBL - European Bioinformatics Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Donna M. Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kim C. Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Michael Akam
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Stephen Richards
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- * E-mail:
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