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Ye X, Xiong S, Teng Z, Yang Y, Wang J, Yu K, Wu H, Mei Y, Yan Z, Cheng S, Yin C, Wang F, Yao H, Fang Q, Song Q, Werren JH, Ye G, Li F. Amino acid synthesis loss in parasitoid wasps and other hymenopterans. eLife 2020; 9:e59795. [PMID: 33074103 PMCID: PMC7593089 DOI: 10.7554/elife.59795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/17/2020] [Indexed: 11/17/2022] Open
Abstract
Insects utilize diverse food resources which can affect the evolution of their genomic repertoire, including leading to gene losses in different nutrient pathways. Here, we investigate gene loss in amino acid synthesis pathways, with special attention to hymenopterans and parasitoid wasps. Using comparative genomics, we find that synthesis capability for tryptophan, phenylalanine, tyrosine, and histidine was lost in holometabolous insects prior to hymenopteran divergence, while valine, leucine, and isoleucine were lost in the common ancestor of Hymenoptera. Subsequently, multiple loss events of lysine synthesis occurred independently in the Parasitoida and Aculeata. Experiments in the parasitoid Cotesia chilonis confirm that it has lost the ability to synthesize eight amino acids. Our findings provide insights into amino acid synthesis evolution, and specifically can be used to inform the design of parasitoid artificial diets for pest control.
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Affiliation(s)
- Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
- Department of Biology, University of RochesterRochesterUnited States
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Ziwen Teng
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yi Yang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Kaili Yu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Huizi Wu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Yang Mei
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Sammy Cheng
- Department of Biology, University of RochesterRochesterUnited States
| | - Chuanlin Yin
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Fang Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Hongwei Yao
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of MissouriColumbiaUnited States
| | - John H Werren
- Department of Biology, University of RochesterRochesterUnited States
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
| | - Fei Li
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang UniversityHangzhouChina
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High-Quality Assemblies for Three Invasive Social Wasps from the Vespula Genus. G3-GENES GENOMES GENETICS 2020; 10:3479-3488. [PMID: 32859687 PMCID: PMC7534447 DOI: 10.1534/g3.120.401579] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Social wasps of the genus Vespula have spread to nearly all landmasses worldwide and have become significant pests in their introduced ranges, affecting economies and biodiversity. Comprehensive genome assemblies and annotations for these species are required to develop the next generation of control strategies and monitor existing chemical control. We sequenced and annotated the genomes of the common wasp (Vespula vulgaris), German wasp (Vespula germanica), and the western yellowjacket (Vespula pensylvanica). Our chromosome-level Vespula assemblies each contain 176–179 Mb of total sequence assembled into 25 scaffolds, with 10–200 unanchored scaffolds, and 16,566–18,948 genes. We annotated gene sets relevant to the applied management of invasive wasp populations, including genes associated with spermatogenesis and development, pesticide resistance, olfactory receptors, immunity and venom. These genomes provide evidence for active DNA methylation in Vespidae and tandem duplications of venom genes. Our genomic resources will contribute to the development of next-generation control strategies, and monitoring potential resistance to chemical control.
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53
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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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54
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Xu G, Yi Y, Lyu H, Gong C, Feng Q, Song Q, Peng X, Liu L, Zheng S. DNA methylation suppresses chitin degradation and promotes the wing development by inhibiting Bmara-mediated chitinase expression in the silkworm, Bombyx mori. Epigenetics Chromatin 2020; 13:34. [PMID: 32887667 PMCID: PMC7472703 DOI: 10.1186/s13072-020-00356-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 08/26/2020] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND DNA methylation, as an essential epigenetic modification found in mammals and plants, has been implicated to play an important role in insect reproduction. However, the functional role and the regulatory mechanism of DNA methylation during insect organ or tissue development are far from being clear. RESULTS Here, we found that DNA methylation inhibitor (5-aza-dC) treatment in newly molted pupae decreased the chitin content of pupal wing discs and adult wings and resulted in wing deformity of Bombyx mori. Transcriptome analysis revealed that the up-regulation of chitinase 10 (BmCHT10) gene might be related to the decrease of chitin content induced by 5-aza-dC treatment. Further, the luciferase activity assays demonstrated that DNA methylation suppressed the promoter activity of BmCHT10 by down-regulating the transcription factor, homeobox protein araucan (Bmara). Electrophoretic mobility shift assay, DNA pull-down and chromatin immunoprecipitation demonstrated that Bmara directly bound to the BmCHT10 promoter. Therefore, DNA methylation is involved in keeping the structural integrity of the silkworm wings from unwanted chitin degradation, as a consequence, it promotes the wing development of B. mori. CONCLUSIONS This study reveals that DNA methylation plays an important role in the wing development of B. mori. Our results support that the indirect transcriptional repression of a chitin degradation-related gene BmCHT10 by DNA methylation is necessary to keep the proper wing development in B. mori.
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Affiliation(s)
- Guanfeng Xu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yangqin Yi
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Hao Lyu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chengcheng Gong
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qili Feng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO, 65211, USA
| | - Xuezhen Peng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Lin Liu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Sichun Zheng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China. .,Guangzhou Key Laboratory of Insect Development Regulation and Applied Research, Institute of Insect Science and Technology, School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
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55
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Nagel M, Qiu B, Brandenborg LE, Larsen RS, Ning D, Boomsma JJ, Zhang G. The gene expression network regulating queen brain remodeling after insemination and its parallel use in ants with reproductive workers. SCIENCE ADVANCES 2020; 6:6/38/eaaz5772. [PMID: 32938672 PMCID: PMC7494347 DOI: 10.1126/sciadv.aaz5772] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 07/27/2020] [Indexed: 05/16/2023]
Abstract
Caste differentiation happens early in development to produce gynes as future colony germlines and workers as present colony soma. However, gynes need insemination to become functional queens, a transition that initiates reproductive role differentiation relative to unmated gynes. Here, we analyze the anatomy and transcriptomes of brains during this differentiation process within the reproductive caste of Monomorium pharaonis Insemination terminated brain growth, whereas unmated control gynes continued to increase brain volume. Transcriptomes revealed a specific gene regulatory network (GRN) mediating both brain anatomy changes and behavioral modifications. This reproductive role differentiation GRN hardly overlapped with the gyne-worker caste differentiation GRN, but appears to be also used by distantly related ants where workers became germline individuals after the queen caste was entirely or partially lost. The genes corazonin and neuroparsin A in the anterior neurosecretory cells were overexpressed in individuals with reduced or nonreproductive roles across all four ant species investigated.
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Affiliation(s)
- Manuel Nagel
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Bitao Qiu
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Centre for Social Evolution, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Lisa Eigil Brandenborg
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Rasmus Stenbak Larsen
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Dongdong Ning
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Jacobus Jan Boomsma
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Centre for Social Evolution, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518083, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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56
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Marshall H, Jones ARC, Lonsdale ZN, Mallon EB. Bumblebee Workers Show Differences in Allele-Specific DNA Methylation and Allele-Specific Expression. Genome Biol Evol 2020; 12:1471-1481. [PMID: 32597949 PMCID: PMC7502211 DOI: 10.1093/gbe/evaa132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/14/2022] Open
Abstract
Allele-specific expression is when one allele of a gene shows higher levels of expression compared with the other allele, in a diploid organism. Recent work has identified allele-specific expression in a number of Hymenopteran species. However, the molecular mechanism which drives this allelic expression bias remains unknown. In mammals, DNA methylation is often associated with genes which show allele-specific expression. DNA methylation systems have been described in species of Hymenoptera, providing a candidate mechanism. Using previously generated RNA-Seq and whole-genome bisulfite sequencing from reproductive and sterile bumblebee (Bombus terrestris) workers, we have identified genome-wide allele-specific expression and allele-specific DNA methylation. The majority of genes displaying allele-specific expression are common between reproductive and sterile workers and the proportion of allele-specific expression bias generally varies between genetically distinct colonies. We have also identified genome-wide allele-specific DNA methylation patterns in both reproductive and sterile workers, with reproductive workers showing significantly more genes with allele-specific methylation. Finally, there is no significant overlap between genes showing allele-specific expression and allele-specific methylation. These results indicate that cis-acting DNA methylation does not directly drive genome-wide allele-specific expression in this species.
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Affiliation(s)
- Hollie Marshall
- Department of Genetics and Genome Biology, University of Leicester, United Kingdom
| | - Alun R C Jones
- Department of Genetics and Genome Biology, University of Leicester, United Kingdom
| | - Zoë N Lonsdale
- Department of Genetics and Genome Biology, University of Leicester, United Kingdom
| | - Eamonn B Mallon
- Department of Genetics and Genome Biology, University of Leicester, United Kingdom
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57
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Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R. Social reprogramming in ants induces longevity-associated glia remodeling. SCIENCE ADVANCES 2020; 6:eaba9869. [PMID: 32875108 PMCID: PMC7438095 DOI: 10.1126/sciadv.aba9869] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 07/09/2020] [Indexed: 05/16/2023]
Abstract
In social insects, workers and queens arise from the same genome but display profound differences in behavior and longevity. In Harpegnathos saltator ants, adult workers can transition to a queen-like state called gamergate, which results in reprogramming of social behavior and life-span extension. Using single-cell RNA sequencing, we compared the distribution of neuronal and glial populations before and after the social transition. We found that the conversion of workers into gamergates resulted in the expansion of neuroprotective ensheathing glia. Brain injury assays revealed that activation of the damage response gene Mmp1 was weaker in old workers, where the relative frequency of ensheathing glia also declined. On the other hand, long-lived gamergates retained a larger fraction of ensheathing glia and the ability to mount a strong Mmp1 response to brain injury into old age. We also observed molecular and cellular changes suggestive of age-associated decline in ensheathing glia in Drosophila.
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Affiliation(s)
- Lihong Sheng
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Emily J. Shields
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Janko Gospocic
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karl M. Glastad
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Puttachai Ratchasanmuang
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Shelley L. Berger
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Arjun Raj
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Shawn Little
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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58
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Kapheim KM, Jones BM, Søvik E, Stolle E, Waterhouse RM, Bloch G, Ben-Shahar Y. Brain microRNAs among social and solitary bees. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200517. [PMID: 32874647 PMCID: PMC7428247 DOI: 10.1098/rsos.200517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.
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Affiliation(s)
- Karen M. Kapheim
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
- Author for correspondence: Karen M. Kapheim e-mail:
| | - Beryl M. Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Eirik Søvik
- Department of Science and Mathematics, Volda University College, 6100 Volda, Norway
| | - Eckart Stolle
- Centre of Molecular Biodiversity Research, Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Guy Bloch
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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Hou L, Wang X, Yang P, Li B, Lin Z, Kang L, Wang X. DNA methyltransferase 3 participates in behavioral phase change in the migratory locust. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2020; 121:103374. [PMID: 32283278 DOI: 10.1016/j.ibmb.2020.103374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 03/06/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
DNA methylation plays important roles in the behavioral plasticity of animals. The migratory locust, Locusta migratoria, displays striking density-dependent phenotypic plasticity that can reversely transit between solitarious and gregarious phases. However, the role and the mechanism through which DNA methylation is involved in locust phase change remain unknown. Here, we investigated the expression levels of three DNA methyltransferase genes and their roles in the regulation of locust phase changes. All three Dnmt genes, namely, Dnmt1, Dnmt2 and Dnmt3 showed high expression levels in the brains of gregarious locusts. By contrast, only Dnmt3 transcript rapidly responded to population density changes, decreasing during the isolation of gregarious locusts and steadily increasing upon the crowding of solitarious locusts. Dnmt3 knockdown significantly reduced the phase-related locomotor activity, rather than the attraction index, in gregarious and crowded solitarious locusts. Transcriptome analysis showed that Dnmt3 knockdown upregulated the genes related to metabolism and transporting activity and downregulated those associated with oxidative stress response. The expression level of the phase-core transcriptional factor, hormone receptor HR3, was significantly suppressed in the brain after Dnmt3 knockdown. Moreover, there was significant overlap in the differentially expressed genes between Dnmt3 RNAi and HR3 RNAi data sets, suggesting HR3 may act as key transcriptional factor mediating Dnmt3-controlled gene expression profiles in locust brains. These findings suggest that Dnmt3 transcription is involved in locust behavioral transition, implying the possible roles of DNA methylation in phase-related phenotypic plasticity in locusts.
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Affiliation(s)
- Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuesong Wang
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengcheng Yang
- Beijing Institutes of Life Science, Chinese Academy of Science, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China
| | - Beibei Li
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhe Lin
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China; Beijing Institutes of Life Science, Chinese Academy of Science, 1 Beichen West Road, Chaoyang District, Beijing, 100101, China.
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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60
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Developmental plasticity shapes social traits and selection in a facultatively eusocial bee. Proc Natl Acad Sci U S A 2020; 117:13615-13625. [PMID: 32471944 PMCID: PMC7306772 DOI: 10.1073/pnas.2000344117] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Developmental processes are an important source of phenotypic variation, but the extent to which this variation contributes to evolutionary change is unknown. We used integrative genomic analyses to explore the relationship between developmental and social plasticity in a bee species that can adopt either a social or solitary lifestyle. We find genes regulating this social flexibility also regulate development, and positive selection on these genes is influenced by their function during development. This suggests that developmental plasticity may influence the evolution of sociality. Our additional finding of genetic variants linked to differences in social behavior sheds light on how phenotypic variation derived from development may become encoded into the genome, and thus contribute to evolutionary change. Developmental plasticity generates phenotypic variation, but how it contributes to evolutionary change is unclear. Phenotypes of individuals in caste-based (eusocial) societies are particularly sensitive to developmental processes, and the evolutionary origins of eusociality may be rooted in developmental plasticity of ancestral forms. We used an integrative genomics approach to evaluate the relationships among developmental plasticity, molecular evolution, and social behavior in a bee species (Megalopta genalis) that expresses flexible sociality, and thus provides a window into the factors that may have been important at the evolutionary origins of eusociality. We find that differences in social behavior are derived from genes that also regulate sex differentiation and metamorphosis. Positive selection on social traits is influenced by the function of these genes in development. We further identify evidence that social polyphenisms may become encoded in the genome via genetic changes in regulatory regions, specifically in transcription factor binding sites. Taken together, our results provide evidence that developmental plasticity provides the substrate for evolutionary novelty and shapes the selective landscape for molecular evolution in a major evolutionary innovation: Eusociality.
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Omar MA, Li M, Liu F, He K, Qasim M, Xiao H, Jiang M, Li F. The Roles of DNA Methyltransferases 1 (DNMT1) in Regulating Sexual Dimorphism in the Cotton Mealybug, Phenacoccus solenopsis. INSECTS 2020; 11:insects11020121. [PMID: 32059417 PMCID: PMC7074402 DOI: 10.3390/insects11020121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/08/2020] [Accepted: 02/10/2020] [Indexed: 01/04/2023]
Abstract
The cotton mealybug, Phenacoccus solenopsis, is an invasive pest that can cause massive damage to many host plants of agricultural importance. P. solenopsis is highly polyphagous, and shows extreme sexual dimorphism between males and females. The functions of DNA methyltransferase (DNMT) enzymes in the cotton mealybug have not been well studied. Here, we carried out an investigation of DNMTs in cotton mealybug to study their roles in sexual dimorphism. We found that the cotton mealybug has two copies of PsDnmt1, but Dnmt3 is absent. We then amplified the full-length cDNAs of PsDnmt1A (2,225 bp) and PsDnmt1B (2,862 bp) using rapid amplification cDNA ends (RACE). Quantitative reverse transcriptase PCR shows that both PsDnmt1A and PsDnmt1B are highly expressed in adult males, while the expression of PsDnmt1B is 30-fold higher in gravid females than in virgin females. We knocked down PsDnmt1A and PsDnmt1B with small interfering RNAs (siRNAs), and both genes were successfully down-regulated after 24 h or 72 h in adult females and pupa (t-test, p < 0.05). Down-regulating the expression of these two DNMT genes led to offspring lethality and abnormal body color in adult females. Furthermore, the silencing of PsDnmt1B induced abnormal wing development in emerged adult males. Our results provide evidence that PsDnmt1 plays a crucial role in regulating sexual dimorphism in the cotton mealybug.
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Affiliation(s)
- Mohamed A.A. Omar
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
- Department of Plant Protection, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt
| | - Meizhen Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
| | - Feiling Liu
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
| | - Kang He
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
| | - Muhammad Qasim
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
| | - Huamei Xiao
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
- College of Life Sciences and Resource Environment/Key Laboratory of Crop Growth and Development Regulation, Yichun University, Jiangxi Province, Yichun 336000, China
| | - Mingxing Jiang
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
| | - Fei Li
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, China (M.L.); (F.L.); (K.H.); (M.Q.); (H.X.); (M.J.)
- Correspondence:
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Abstract
Cognitive abilities can vary dramatically among species. The relative importance of social and ecological challenges in shaping cognitive evolution has been the subject of a long-running and recently renewed debate, but little work has sought to understand the selective dynamics underlying the evolution of cognitive abilities. Here, we investigate recent selection related to cognition in the paper wasp Polistes fuscatus-a wasp that has uniquely evolved visual individual recognition abilities. We generate high quality de novo genome assemblies and population genomic resources for multiple species of paper wasps and use a population genomic framework to interrogate the probable mode and tempo of cognitive evolution. Recent, strong, hard selective sweeps in P. fuscatus contain loci annotated with functions in long-term memory formation, mushroom body development, and visual processing, traits which have recently evolved in association with individual recognition. The homologous pathways are not under selection in closely related wasps that lack individual recognition. Indeed, the prevalence of candidate cognition loci within the strongest selective sweeps suggests that the evolution of cognitive abilities has been among the strongest selection pressures in P. fuscatus' recent evolutionary history. Detailed analyses of selective sweeps containing candidate cognition loci reveal multiple cases of hard selective sweeps within the last few thousand years on de novo mutations, mainly in noncoding regions. These data provide unprecedented insight into some of the processes by which cognition evolves.
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Li B, Hu P, Zhu LB, You LL, Cao HH, Wang J, Zhang SZ, Liu MH, Toufeeq S, Huang SJ, Xu JP. DNA Methylation Is Correlated with Gene Expression during Diapause Termination of Early Embryonic Development in the Silkworm ( Bombyx mori). Int J Mol Sci 2020; 21:E671. [PMID: 31968548 PMCID: PMC7013401 DOI: 10.3390/ijms21020671] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 01/16/2020] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
DNA modification is a naturally occurring DNA modification in prokaryotic and eukaryotic organisms and is involved in several biological processes. Although genome-wide methylation has been studied in many insects, the understanding of global and genomic DNA methylation during insect early embryonic development, is lacking especially for insect diapause. In this study, we analyzed the relationship between DNA methylomes and transcriptomes in diapause-destined eggs compared to diapause-terminated eggs in the silkworm, Bombyx mori (B. mori). The results revealed that methylation was sparse in this species, as previously reported. Moreover, methylation levels in diapause-terminated eggs (HCl-treated) were 0.05% higher than in non-treated eggs, mainly due to the contribution of CG methylation sites. Methylation tends to occur in the coding sequences and promoter regions, especially at transcription initiation sites and short interspersed elements. Additionally, 364 methylome- and transcriptome-associated genes were identified, which showed significant differences in methylation and expression levels in diapause-destined eggs when compared with diapause-terminated eggs, and 74% of methylome and transcriptome associated genes showed both hypermethylation and elevated expression. Most importantly, Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses showed that methylation may be positively associated with Bombyx mori embryonic development, by regulating cell differentiation, metabolism, apoptosis pathways and phosphorylation. Through analyzing the G2/M phase-specific E3 ubiquitin-protein ligase (G2E3), we speculate that methylation may affect embryo diapause by regulating the cell cycle in Bombyx mori. These findings will help unravel potential linkages between DNA methylation and gene expression during early insect embryonic development and insect diapause.
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Affiliation(s)
- Bing Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei 230061, Anhui, China;
| | - Pei Hu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Lin-Bao Zhu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Ling-Ling You
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Hui-Hua Cao
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Jie Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Shang-Zhi Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Ming-Hui Liu
- Institute of Sericulture, Anhui Academy of Agricultural Sciences, Hefei 230061, Anhui, China;
| | - Shahzad Toufeeq
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Shou-Jun Huang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
| | - Jia-Ping Xu
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, Anhui, China; (B.L.); (P.H.); (L.-B.Z.); (L.-L.Y.); (H.-H.C.); (J.W.); (S.-Z.Z.); (S.T.)
- Anhui International Joint Research and Developmental Center of Sericulture Resources Utilization, Hefei 230036, Anhui, China
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Sharko FS, Nedoluzhko AV, Lê BM, Tsygankova SV, Boulygina ES, Rastorguev SM, Sokolov AS, Rodriguez F, Mazur AM, Polilov AA, Benton R, Evgen'ev MB, Arkhipova IR, Prokhortchouk EB, Skryabin KG. A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum. PLoS One 2019; 14:e0226485. [PMID: 31869362 PMCID: PMC6927652 DOI: 10.1371/journal.pone.0226485] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect-the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, compared to other chalcid wasps the gene content of M. amalphitanum is remarkably conserved. Intriguingly, we observed significant changes in M. amalphitanum transposable element dynamics over time, in which an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Overall, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.
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Affiliation(s)
- Fedor S. Sharko
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
| | - Artem V. Nedoluzhko
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Nord University, Faculty of Biosciences and Aquaculture, Bodø, Norway
| | - Brandon M. Lê
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | | | | | | | - Alexey S. Sokolov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Fernando Rodriguez
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Alexander M. Mazur
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey A. Polilov
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Richard Benton
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | | | - Irina R. Arkhipova
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, United States of America
| | - Egor B. Prokhortchouk
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
| | - Konstantin G. Skryabin
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
- National Research Center “Kurchatov Institute”, Moscow, Russia
- Lomonosov Moscow State University, Faculty of Biology, Moscow, Russia
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65
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High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Rep 2019; 23:3078-3090. [PMID: 29874592 PMCID: PMC6023404 DOI: 10.1016/j.celrep.2018.05.014] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 12/31/2022] Open
Abstract
Ants are an emerging model system for neuroepigenetics, as embryos with virtually identical genomes develop into different adult castes that display diverse physiology, morphology, and behavior. Although a number of ant genomes have been sequenced to date, their draft quality is an obstacle to sophisticated analyses of epigenetic gene regulation. We reassembled de novo high-quality genomes for two ant species, Camponotus floridanus and Harpegnathos saltator. Using long reads enabled us to span large repetitive regions and improve genome contiguity, leading to comprehensive and accurate protein-coding annotations that facilitated the identification of a Gp-9-like gene as differentially expressed in Harpegnathos castes. The new assemblies also enabled us to annotate long non-coding RNAs in ants, revealing caste-, brain-, and developmental-stage-specific long non-coding RNAs (lncRNAs) in Harpegnathos. These upgraded genomes, along with the new gene annotations, will aid future efforts to identify epigenetic mechanisms of phenotypic and behavioral plasticity in ants.
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66
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Marshall H, Lonsdale ZN, Mallon EB. Methylation and gene expression differences between reproductive and sterile bumblebee workers. Evol Lett 2019; 3:485-499. [PMID: 31636941 PMCID: PMC6791180 DOI: 10.1002/evl3.129] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on its role in other bee species. In this study, we analyzed whole genome bisulfite sequencing and RNA-seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found that genome-wide methylation in B. terrestris is similar to other holometabolous insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However, we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high intercolony variation in methylation. These findings suggest that methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste-specific methylome as well as its interaction with gene expression and caste-specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in insects.
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Affiliation(s)
- Hollie Marshall
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
| | - Zoë N. Lonsdale
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
| | - Eamonn B. Mallon
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
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67
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Mathers TC, Mugford ST, Percival-Alwyn L, Chen Y, Kaithakottil G, Swarbreck D, Hogenhout SA, van Oosterhout C. Sex-specific changes in the aphid DNA methylation landscape. Mol Ecol 2019; 28:4228-4241. [PMID: 31472081 PMCID: PMC6857007 DOI: 10.1111/mec.15216] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/22/2019] [Indexed: 12/15/2022]
Abstract
Aphids present an ideal system to study epigenetics as they can produce diverse, but genetically identical, morphs in response to environmental stimuli. Here, using whole genome bisulphite sequencing and transcriptome sequencing of the green peach aphid (Myzus persicae), we present the first detailed analysis of cytosine methylation in an aphid and investigate differences in the methylation and transcriptional landscapes of male and asexual female morphs. We found that methylation primarily occurs in a CG dinucleotide (CpG) context and that exons are highly enriched for methylated CpGs, particularly at the 3' end of genes. Methylation is positively associated with gene expression, and methylated genes are more stably expressed than unmethylated genes. Male and asexual female morphs have distinct methylation profiles. Strikingly, these profiles are divergent between the sex chromosome and the autosomes; autosomal genes are hypomethylated in males compared to asexual females, whereas genes belonging to the sex chromosome, which is haploid in males, are hypermethylated. Overall, we found correlated changes in methylation and gene expression between males and asexual females, and this correlation was particularly strong for genes located on the sex chromosome. Our results suggest that differential methylation of sex-biased genes plays a role in aphid sexual differentiation.
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Affiliation(s)
- Thomas C Mathers
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Sam T Mugford
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Yazhou Chen
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | | | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, UK
| | - Cock van Oosterhout
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, UK
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68
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Hilliard AT, Xie D, Ma Z, Snyder MP, Fernald RD. Genome-wide effects of social status on DNA methylation in the brain of a cichlid fish, Astatotilapia burtoni. BMC Genomics 2019; 20:699. [PMID: 31506062 PMCID: PMC6737626 DOI: 10.1186/s12864-019-6047-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Successful social behavior requires real-time integration of information about the environment, internal physiology, and past experience. The molecular substrates of this integration are poorly understood, but likely modulate neural plasticity and gene regulation. In the cichlid fish species Astatotilapia burtoni, male social status can shift rapidly depending on the environment, causing fast behavioral modifications and a cascade of changes in gene transcription, the brain, and the reproductive system. These changes can be permanent but are also reversible, implying the involvement of a robust but flexible mechanism that regulates plasticity based on internal and external conditions. One candidate mechanism is DNA methylation, which has been linked to social behavior in many species, including A. burtoni. But, the extent of its effects after A. burtoni social change were previously unknown. RESULTS We performed the first genome-wide search for DNA methylation patterns associated with social status in the brains of male A. burtoni, identifying hundreds of Differentially Methylated genomic Regions (DMRs) in dominant versus non-dominant fish. Most DMRs were inside genes supporting neural development, synapse function, and other processes relevant to neural plasticity, and DMRs could affect gene expression in multiple ways. DMR genes were more likely to be transcription factors, have a duplicate elsewhere in the genome, have an anti-sense lncRNA, and have more splice variants than other genes. Dozens of genes had multiple DMRs that were often seemingly positioned to regulate specific splice variants. CONCLUSIONS Our results revealed genome-wide effects of A. burtoni social status on DNA methylation in the brain and strongly suggest a role for methylation in modulating plasticity across multiple biological levels. They also suggest many novel hypotheses to address in mechanistic follow-up studies, and will be a rich resource for identifying the relationships between behavioral, neural, and transcriptional plasticity in the context of social status.
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Affiliation(s)
| | - Dan Xie
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Zhihai Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Michael P. Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
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69
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Arsenault SV, Glastad KM, Hunt BG. Leveraging technological innovations to investigate evolutionary transitions to eusociality. CURRENT OPINION IN INSECT SCIENCE 2019; 34:27-32. [PMID: 31247414 DOI: 10.1016/j.cois.2019.03.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 02/19/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
The study of the major transition to eusociality presents several challenges to researchers, largely resulting from the importance of complex behavioral phenotypes and the shift from individual to group level selection. These challenges are being met with corresponding technological improvements. Advances in resource development for non-model taxa, behavioral tracking, nucleic acid sequencing, and reverse genetics are facilitating studies of hypotheses that were previously intractable. These innovations are resulting in the development of new model systems tailored to the exploration of specific behavioral phenotypes and the querying of underlying molecular mechanisms that drive eusocial behaviors. Here, we present a brief overview of how methodological innovations are advancing our understanding of the evolution of eusociality.
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Affiliation(s)
- Samuel V Arsenault
- Department of Entomology, University of Georgia, Athens, GA 30602, United States
| | - Karl M Glastad
- Department of Cell & Developmental Biology, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA 30602, United States.
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70
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Taylor BA, Reuter M, Sumner S. Patterns of reproductive differentiation and reproductive plasticity in the major evolutionary transition to superorganismality. CURRENT OPINION IN INSECT SCIENCE 2019; 34:40-47. [PMID: 31247416 DOI: 10.1016/j.cois.2019.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/05/2019] [Accepted: 02/21/2019] [Indexed: 06/09/2023]
Abstract
Major evolutionary transitions in individuality are characterised by the formation of new levels of biological complexity from the cooperation of previously independent lower-level units. The evolution of superorganismality in insects is one such major transition, and is characterised by an extreme division of reproductive labour between ancestrally autonomous units, in the form of queen and worker castes. Here, we discuss the nature of plasticity in the emergence of castes across the major transition to superorganismality in insects. We identify key changes in plasticity which act at different levels of selection: a loss of reproductivity plasticity at the individual level is matched by a gain in plasticity at the colony level. Taking multi-level selection into consideration has important implications for formulating testable hypotheses regarding the nature of plasticity in a major transition from a lower to a higher level of biological complexity.
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Affiliation(s)
- Benjamin A Taylor
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Max Reuter
- Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Seirian Sumner
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom.
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71
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Ceolin Mariano DO, de Oliveira ÚC, Zaharenko AJ, Pimenta DC, Rádis-Baptista G, Prieto-da-Silva ÁRDB. Bottom-Up Proteomic Analysis of Polypeptide Venom Components of the Giant Ant Dinoponera Quadriceps. Toxins (Basel) 2019; 11:toxins11080448. [PMID: 31362422 PMCID: PMC6722740 DOI: 10.3390/toxins11080448] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 07/10/2019] [Accepted: 07/26/2019] [Indexed: 12/26/2022] Open
Abstract
Ant species have specialized venom systems developed to sting and inoculate a biological cocktail of organic compounds, including peptide and polypeptide toxins, for the purpose of predation and defense. The genus Dinoponera comprises predatory giant ants that inoculate venom capable of causing long-lasting local pain, involuntary shaking, lymphadenopathy, and cardiac arrhythmias, among other symptoms. To deepen our knowledge about venom composition with regard to protein toxins and their roles in the chemical-ecological relationship and human health, we performed a bottom-up proteomics analysis of the crude venom of the giant ant D. quadriceps, popularly known as the "false" tocandiras. For this purpose, we used two different analytical approaches: (i) gel-based proteomics approach, wherein the crude venom was resolved by denaturing sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and all protein bands were excised for analysis; (ii) solution-based proteomics approach, wherein the crude venom protein components were directly fragmented into tryptic peptides in solution for analysis. The proteomic data that resulted from these two methodologies were compared against a previously annotated transcriptomic database of D. quadriceps, and subsequently, a homology search was performed for all identified transcript products. The gel-based proteomics approach unequivocally identified nine toxins of high molecular mass in the venom, as for example, enzymes [hyaluronidase, phospholipase A1, dipeptidyl peptidase and glucose dehydrogenase/flavin adenine dinucleotide (FAD) quinone] and diverse venom allergens (homologous of the red fire ant Selenopsis invicta) and venom-related proteins (major royal jelly-like). Moreover, the solution-based proteomics revealed and confirmed the presence of several hydrolases, oxidoreductases, proteases, Kunitz-like polypeptides, and the less abundant inhibitor cysteine knot (ICK)-like (knottin) neurotoxins and insect defensin. Our results showed that the major components of the D. quadriceps venom are toxins that are highly likely to damage cell membranes and tissue, to cause neurotoxicity, and to induce allergic reactions, thus, expanding the knowledge about D. quadriceps venom composition and its potential biological effects on prey and victims.
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Affiliation(s)
| | | | | | - Daniel Carvalho Pimenta
- Laboratory of Biochemistry and Biophysics, Instituto Butantan, São Paulo SP 05503-900, Brazil
| | - Gandhi Rádis-Baptista
- Laboratorio of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza CE 60165-081, Brazil.
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72
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Rubin BER, Jones BM, Hunt BG, Kocher SD. Rate variation in the evolution of non-coding DNA associated with social evolution in bees. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180247. [PMID: 31154980 PMCID: PMC6560270 DOI: 10.1098/rstb.2018.0247] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2019] [Indexed: 11/12/2022] Open
Abstract
The evolutionary origins of eusociality represent increases in complexity from individual to caste-based, group reproduction. These behavioural transitions have been hypothesized to go hand in hand with an increased ability to regulate when and where genes are expressed. Bees have convergently evolved eusociality up to five times, providing a framework to test this hypothesis. To examine potential links between putative gene regulatory elements and social evolution, we compare alignable, non-coding sequences in 11 diverse bee species, encompassing three independent origins of reproductive division of labour and two elaborations of eusocial complexity. We find that rates of evolution in a number of non-coding sequences correlate with key social transitions in bees. Interestingly, while we find little evidence for convergent rate changes associated with independent origins of social behaviour, a number of molecular pathways exhibit convergent rate changes in conjunction with subsequent elaborations of social organization. We also present evidence that many novel non-coding regions may have been recruited alongside the origin of sociality in corbiculate bees; these loci could represent gene regulatory elements associated with division of labour within this group. Thus, our findings are consistent with the hypothesis that gene regulatory innovations are associated with the evolution of eusociality and illustrate how a thorough examination of both coding and non-coding sequence can provide a more complete understanding of the molecular mechanisms underlying behavioural evolution. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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Affiliation(s)
- Benjamin E. R. Rubin
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Beryl M. Jones
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois, Urbana, IL, USA
| | - Brendan G. Hunt
- Department of Entomology, University of Georgia, Griffin, GA, USA
| | - Sarah D. Kocher
- Department of Ecology and Evolutionary Biology; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
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73
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Core transcriptional signatures of phase change in the migratory locust. Protein Cell 2019; 10:883-901. [PMID: 31292921 PMCID: PMC6881432 DOI: 10.1007/s13238-019-0648-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 06/17/2019] [Indexed: 01/21/2023] Open
Abstract
Phenotypic plasticity plays fundamental roles in successful adaptation of animals in response to environmental variations. Here, to reveal the transcriptome reprogramming in locust phase change, a typical phenotypic plasticity, we conducted a comprehensive analysis of multiple phase-related transcriptomic datasets of the migratory locust. We defined PhaseCore genes according to their contribution to phase differentiation by the adjustment for confounding principal components analysis algorithm (AC-PCA). Compared with other genes, PhaseCore genes predicted phase status with over 87.5% accuracy and displayed more unique gene attributes including the faster evolution rate, higher CpG content and higher specific expression level. Then, we identified 20 transcription factors (TFs) named PhaseCoreTF genes that are associated with the regulation of PhaseCore genes. Finally, we experimentally verified the regulatory roles of three representative TFs (Hr4, Hr46, and grh) in phase change by RNAi. Our findings revealed that core transcriptional signatures are involved in the global regulation of locust phase changes, suggesting a potential common mechanism underlying phenotypic plasticity in insects. The expression and network data are accessible in an online resource called LocustMine (http://www.locustmine.org:8080/locustmine).
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74
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Saleh NW, Ramírez SR. Sociality emerges from solitary behaviours and reproductive plasticity in the orchid bee Euglossa dilemma. Proc Biol Sci 2019; 286:20190588. [PMID: 31288697 DOI: 10.1098/rspb.2019.0588] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The evolution of eusociality and sterile worker castes represents a major transition in the history of life. Despite this, little is known about the mechanisms involved in the initial transition from solitary to social behaviour. It has been hypothesized that plasticity from ancestral solitary life cycles was coopted to create queen and worker castes in insect societies. Here, we tested this hypothesis by examining gene expression involved in the transition from solitary to social behaviour in the orchid bee Euglossa dilemma. To this end, we conducted observations that allowed us to classify bees into four distinct categories of solitary and social behaviour. Then, by sequencing brain and ovary transcriptomes from these behavioural phases, we identified gene expression changes overlapping with socially associated genes across multiple eusocial lineages. We find that genes involved in solitary E. dilemma ovarian plasticity overlap extensively with genes showing differential expression between fertile and sterile workers-or between queens and workers in other eusocial bees. We also find evidence that sociality in E. dilemma reflects gene expression patterns involved in solitary foraging and non-foraging nest care behaviours. Our results provide strong support for the hypothesis that eusociality emerges from plasticity found across solitary life cycles.
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Affiliation(s)
- Nicholas W Saleh
- Center for Population Biology, University of California , Davis, CA , USA
| | - Santiago R Ramírez
- Center for Population Biology, University of California , Davis, CA , USA
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75
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Bebane PSA, Hunt BJ, Pegoraro M, Jones ARC, Marshall H, Rosato E, Mallon EB. The effects of the neonicotinoid imidacloprid on gene expression and DNA methylation in the buff-tailed bumblebee Bombus terrestris. Proc Biol Sci 2019; 286:20190718. [PMID: 31213186 PMCID: PMC6599982 DOI: 10.1098/rspb.2019.0718] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023] Open
Abstract
Neonicotinoids are effective insecticides used on many important arable and horticultural crops. They are nicotinic acetylcholine receptor agonists which disrupt the function of insect neurons and cause paralysis and death. In addition to direct mortality, there are numerous sublethal effects of low doses of neonicotinoids on bees. We hypothesize that some of these large array of effects could be a consequence of epigenetic changes in bees induced by neonicotinoids. We compared whole methylome (BS-seq) and RNA-seq libraries of the brains of buff-tailed bumblebee Bombus terrestris workers exposed to field-realistic doses of the neonicotinoid imidacloprid to libraries from control workers. We found numerous genes which show differential expression between neonicotinoid-treated bees and control bees, but no differentially methylated cytosines in any context. We found CpG methylation to be focused mainly in exons and associated with highly expressed genes. We discuss the implications of our results for future legislation.
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Affiliation(s)
- P S A Bebane
- 1 Department of Genetics and Genome Biology, University of Leicester, University Road , Leicester LE1 7RH , UK
| | - B J Hunt
- 2 School of Natural Sciences and Psychology, John Moores University Liverpool , Liverpool L3 3AF , UK
| | - M Pegoraro
- 1 Department of Genetics and Genome Biology, University of Leicester, University Road , Leicester LE1 7RH , UK
| | - A R C Jones
- 1 Department of Genetics and Genome Biology, University of Leicester, University Road , Leicester LE1 7RH , UK
| | - H Marshall
- 1 Department of Genetics and Genome Biology, University of Leicester, University Road , Leicester LE1 7RH , UK
| | - E Rosato
- 1 Department of Genetics and Genome Biology, University of Leicester, University Road , Leicester LE1 7RH , UK
| | - E B Mallon
- 1 Department of Genetics and Genome Biology, University of Leicester, University Road , Leicester LE1 7RH , UK
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76
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Warner MR, Qiu L, Holmes MJ, Mikheyev AS, Linksvayer TA. Convergent eusocial evolution is based on a shared reproductive groundplan plus lineage-specific plastic genes. Nat Commun 2019; 10:2651. [PMID: 31201311 PMCID: PMC6570765 DOI: 10.1038/s41467-019-10546-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 05/14/2019] [Indexed: 12/31/2022] Open
Abstract
Eusociality has convergently evolved multiple times, but the genomic basis of caste-based division of labor and degree to which independent origins of eusociality have utilized common genes remain largely unknown. Here we characterize caste-specific transcriptomic profiles across development and adult body segments from pharaoh ants (Monomorium pharaonis) and honey bees (Apis mellifera), representing two independent origins of eusociality. We identify a substantial shared core of genes upregulated in the abdomens of queen ants and honey bees that also tends to be upregulated in mated female flies, suggesting that these genes are part of a conserved insect reproductive groundplan. Outside of this shared groundplan, few genes are differentially expressed in common. Instead, the majority of the thousands of caste-associated genes are plastically expressed, rapidly evolving, and relatively evolutionarily young. These results emphasize that the recruitment of both highly conserved and lineage-specific genes underlie the convergent evolution of novel traits such as eusociality. Eusocial caste systems have evolved independently multiple times. Here, Warner et al. investigate the amount of shared vs. lineage-specific genes involved in the evolution of caste in pharaoh ants and honey bees by comparing transcriptomes across tissues, developmental stages, and castes.
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Affiliation(s)
| | - Lijun Qiu
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Michael J Holmes
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,School of Life and Environmental Science, University of Sydney, Sydney, 2006, Australia
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan.,Research School of Biology, Australian National University, Canberra, 0200, Australia
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77
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Rubenstein DR, Ågren JA, Carbone L, Elde NC, Hoekstra HE, Kapheim KM, Keller L, Moreau CS, Toth AL, Yeaman S, Hofmann HA. Coevolution of Genome Architecture and Social Behavior. Trends Ecol Evol 2019; 34:844-855. [PMID: 31130318 DOI: 10.1016/j.tree.2019.04.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/03/2019] [Accepted: 04/17/2019] [Indexed: 01/02/2023]
Abstract
Although social behavior can have a strong genetic component, it can also result in selection on genome structure and function, thereby influencing the evolution of the genome itself. Here we explore the bidirectional links between social behavior and genome architecture by considering variation in social and/or mating behavior among populations (social polymorphisms) and across closely related species. We propose that social behavior can influence genome architecture via associated demographic changes due to social living. We establish guidelines to exploit emerging whole-genome sequences using analytical approaches that examine genome structure and function at different levels (regulatory vs structural variation) from the perspective of both molecular biology and population genetics in an ecological context.
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Affiliation(s)
- Dustin R Rubenstein
- Columbia University, Department of Ecology, Evolution, and Environmental Biology and Center for Integrative Animal Behavior, New York, NY 10027, USA.
| | - J Arvid Ågren
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138, USA
| | - Lucia Carbone
- Oregon Health & Science University, Department of Medicine, KCVI, Portland, OR 97239, USA; Oregon National Primate Research Center, Division of Genetics, Beaverton, OR 97006, USA
| | - Nels C Elde
- University of Utah School of Medicine, Department of Human Genetics, Salt Lake City, UT 84112, USA
| | - Hopi E Hoekstra
- Harvard University, Department of Organismic and Evolutionary Biology, Cambridge, MA 02138, USA; Harvard University, Howard Hughes Medical Institute, Department of Molecular and Cellular Biology, Cambridge, MA 02138, USA
| | - Karen M Kapheim
- Utah State University, Department of Biology, Logan, UT 84322, USA
| | - Laurent Keller
- University of Lausanne, Department of Ecology and Evolution, Biophore, UNIL, 1015 Lausanne, Switzerland
| | - Corrie S Moreau
- Cornell University, Departments of Entomology and Ecology and Evolutionary Biology, Ithaca, NY 14850, USA
| | - Amy L Toth
- Iowa State University, Department of Ecology, Evolution, and Organismal Biology and Department of Entomology, Ames, IA 50011, USA
| | - Sam Yeaman
- University of Calgary, Department of Biological Sciences, Calgary, AB T2N 1N4, Canada
| | - Hans A Hofmann
- The University of Texas at Austin, Department of Integrative Biology and Institute for Cellular and Molecular Biology, 2415 Speedway C-0990, Austin, TX 78712, USA.
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78
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Morandin C, Brendel VP, Sundström L, Helanterä H, Mikheyev AS. Changes in gene DNA methylation and expression networks accompany caste specialization and age-related physiological changes in a social insect. Mol Ecol 2019; 28:1975-1993. [PMID: 30809873 DOI: 10.1111/mec.15062] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 02/21/2019] [Accepted: 02/21/2019] [Indexed: 12/14/2022]
Abstract
Social insects provide systems for studying epigenetic regulation of phenotypes, particularly with respect to differentiation of reproductive and worker castes, which typically arise from a common genetic background. The role of gene expression in caste specialization has been extensively studied, but the role of DNA methylation remains controversial. Here, we perform well replicated, integrated analyses of DNA methylation and gene expression in brains of an ant (Formica exsecta) with distinct female castes using traditional approaches (tests of differential methylation) combined with a novel approach (analysis of co-expression and co-methylation networks). We found differences in expression and methylation profiles between workers and queens at different life stages, as well as some overlap between DNA methylation and expression at the functional level. Large portions of the transcriptome and methylome are organized into "modules" of genes, some significantly associated with phenotypic traits of castes and developmental stages. Several gene co-expression modules are preserved in co-methylation networks, consistent with possible regulation of caste-specific gene expression by DNA methylation. Surprisingly, brain co-expression modules were highly preserved when compared with a previous study that examined whole-body co-expression patterns in 16 ant species, suggesting that these modules are evolutionarily conserved and for specific functions in various tissues. Altogether, these results suggest that DNA methylation participates in regulation of caste specialization and age-related physiological changes in social insects.
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Affiliation(s)
- Claire Morandin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Environmental and Marine Biology, Faculty of Science and Engineering, Åbo Akademi University, Åbo, Finland.,Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - Volker P Brendel
- Department of Biology, Indiana University, Bloomington, Indiana.,Department of Computer Science, Indiana University, Bloomington, Indiana
| | - Liselotte Sundström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Tvärminne Zoological Station, University of Helsinki, Hanko, Finland
| | - Heikki Helanterä
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland.,Ecology and Genetics Research Unit, Faculty of Science, University of Oulu, Oulu, Finland
| | - Alexander S Mikheyev
- Okinawa Institute of Science and Technology, Okinawa, Japan.,Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
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79
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Cassill DL. Extending r/K selection with a maternal risk-management model that classifies animal species into divergent natural selection categories. Sci Rep 2019; 9:6111. [PMID: 30992495 PMCID: PMC6467907 DOI: 10.1038/s41598-019-42562-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 04/03/2019] [Indexed: 01/13/2023] Open
Abstract
Reproduction is a defining process of biological systems. Every generation, across all species, breeding females repopulate ecosystems with offspring. r/K selection was the first theory to classify animal species by linking the rates with which breeding females repopulated ecosystems, to the stability of ecosystems. Here, I introduce a species classification scheme that extends the reach of r-K selection and CSR selection by linking breeder investments in offspring quantity, quality, and diversity to specific natural selection pressures. The species classification scheme is predicated on the assumption that high rates of predation favor breeders that invest more in offspring quantity than quality; and that spatiotemporal scarcity favors breeders that investment more in offspring quality than quantity. I present equations that convert the species classification scheme into a maternal risk-management model. Thereafter, using the equations, I classify eighty-seven animal species into the model's natural selection categories. Species of reptiles, fish, and marine invertebrates clustered in the predation selection category. Species of birds and mammals clustered in the scarcity selection category. Several species of apex predators clustered in the weak selection category. Several species of social insects and social mammals clustered in the convergent selection category. In summary, by acknowledging breeding females as the individuals upon which natural selection acts to repopulate ecosystems with offspring, the proposed maternal risk-management model offers a testable, theoretical framework for the field of ecology.
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Affiliation(s)
- Deby L Cassill
- Department of Biological Sciences, USF St. Petersburg, St, Petersburg, Florida, 33701, USA.
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80
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Norman VC, Pamminger T, Nascimento F, Hughes WOH. The role of juvenile hormone in regulating reproductive physiology and dominance in Dinoponera quadriceps ants. PeerJ 2019; 7:e6512. [PMID: 30842903 PMCID: PMC6398374 DOI: 10.7717/peerj.6512] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 01/24/2019] [Indexed: 12/18/2022] Open
Abstract
Unequal reproductive output among members of the same sex (reproductive skew) is a common phenomenon in a wide range of communally breeding animals. In such species, reproductive dominance is often acquired during antagonistic interactions between group members that establish a reproductive hierarchy in which only a few individuals reproduce. Rank-specific syndromes of behavioural and physiological traits characterize such hierarchies, but how antagonistic behavioural interactions translate into stable rank-specific syndromes remains poorly understood. The pleiotropic nature of hormones makes them prime candidates for generating such syndromes as they physiologically integrate environmental (social) information, and often affect reproduction and behaviour simultaneously. Juvenile hormone (JH) is one of several hormones that occupy such a central regulatory role in insects and has been suggested to regulate reproductive hierarchies in a wide range of social insects including ants. Here we use experimental manipulation to investigate the effect of JH levels on reproductive physiology and social dominance in high-ranked workers of the eusocial ant Dinoponera quadriceps, a species that has secondarily reverted to queenless, simple societies. We show that JH regulated reproductive physiology, with ants in which JH levels were experimentally elevated having more regressed ovaries. In contrast, we found no evidence of JH levels affecting dominance in social interactions. This could indicate that JH and ovary development are decoupled from dominance in this species, however only high-ranked workers were investigated. The results therefore confirm that the regulatory role of JH in reproductive physiology in this ant species is in keeping with its highly eusocial ancestors rather than its secondary reversion to simple societies, but more investigation is needed to disentangle the relationships between hormones, behaviour and hierarchies.
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Affiliation(s)
- Victoria C Norman
- School of Biology, University of Leeds, Leeds, United Kingdom.,School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Tobias Pamminger
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Fabio Nascimento
- Departamento de Biologia, Universidade de São Paulo, Ribeirão Preto, Brazil
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81
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Tupec M, Buček A, Janoušek V, Vogel H, Prchalová D, Kindl J, Pavlíčková T, Wenzelová P, Jahn U, Valterová I, Pichová I. Expansion of the fatty acyl reductase gene family shaped pheromone communication in Hymenoptera. eLife 2019; 8:e39231. [PMID: 30714899 PMCID: PMC6361591 DOI: 10.7554/elife.39231] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 01/10/2019] [Indexed: 12/20/2022] Open
Abstract
Fatty acyl reductases (FARs) are involved in the biosynthesis of fatty alcohols that serve a range of biological roles. Insects typically harbor numerous FAR gene family members. While some FARs are involved in pheromone biosynthesis, the biological significance of the large number of FARs in insect genomes remains unclear. Using bumble bee (Bombini) FAR expression analysis and functional characterization, hymenopteran FAR gene tree reconstruction, and inspection of transposable elements (TEs) in the genomic environment of FARs, we uncovered a massive expansion of the FAR gene family in Hymenoptera, presumably facilitated by TEs. The expansion occurred in the common ancestor of bumble bees and stingless bees (Meliponini). We found that bumble bee FARs from the expanded FAR-A ortholog group contribute to the species-specific pheromone composition. Our results indicate that expansion and functional diversification of the FAR gene family played a key role in the evolution of pheromone communication in Hymenoptera.
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Affiliation(s)
- Michal Tupec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
- Department of Biochemistry, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Aleš Buček
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
- Okinawa Institute of Science and Technology Graduate UniversityOkinawaJapan
| | - Václav Janoušek
- Department of Zoology, Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Heiko Vogel
- Department of EntomologyMax Planck Institute for Chemical EcologyJenaGermany
| | - Darina Prchalová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Jiří Kindl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Tereza Pavlíčková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Petra Wenzelová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Irena Valterová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesPragueCzech Republic
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82
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Cunningham CB, Ji L, McKinney EC, Benowitz KM, Schmitz RJ, Moore AJ. Changes of gene expression but not cytosine methylation are associated with male parental care reflecting behavioural state, social context and individual flexibility. J Exp Biol 2019; 222:jeb188649. [PMID: 30446546 PMCID: PMC10681020 DOI: 10.1242/jeb.188649] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/08/2018] [Indexed: 11/29/2023]
Abstract
Behaviour is often a front line response to changing environments. Recent studies show behavioural changes are associated with changes of gene expression; however, these studies have primarily focused on discrete behavioural states. We build on these studies by addressing additional contexts that produce qualitatively similar behavioural changes. We measured levels of gene expression and cytosine methylation, which is hypothesized to regulate the transcriptional architecture of behavioural transitions, within the brain during male parental care of the burying beetle Nicrophorus vespilloides in a factorial design. Male parenting is a suitably plastic behaviour because although male N. vespilloides typically do not provide direct care (i.e. feed offspring) when females are present, levels of feeding by a male equivalent to the female can be induced by removing the female. We examined three different factors: behavioural state (caring versus non-caring), social context (with or without a female mate) and individual flexibility (if a male switched to direct care after his mate was removed). The greatest number of differentially expressed genes were associated with behavioural state, followed by social context and individual flexibility. Cytosine methylation was not associated with changes of gene expression in any of the factors. Our results suggest a hierarchical association between gene expression and the different factors, but that this process is not controlled by cytosine methylation. Our results further suggest that the extent a behaviour is transient plays an underappreciated role in determining its underpinning molecular mechanisms.
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Affiliation(s)
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | | | - Kyle M Benowitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Allen J Moore
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
- Department of Entomology, University of Georgia, Athens, GA 30602, USA
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83
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Park J, Kwon W, Park J. The complete mitochondrial genome of Cryptopone sauteriWheeler, W.M., 1906 (Hymenoptera: Formicidae). MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2018.1561231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Jonghyun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Woochan Kwon
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
| | - Jongsun Park
- InfoBoss Co., Ltd., Seoul, Republic of Korea
- InfoBoss Research Center, Seoul, Republic of Korea
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84
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Bewick AJ, Sanchez Z, Mckinney EC, Moore AJ, Moore PJ, Schmitz RJ. Dnmt1 is essential for egg production and embryo viability in the large milkweed bug, Oncopeltus fasciatus. Epigenetics Chromatin 2019; 12:6. [PMID: 30616649 PMCID: PMC6322253 DOI: 10.1186/s13072-018-0246-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/18/2018] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The function of cytosine (DNA) methylation in insects remains inconclusive due to a lack of mutant and/or genetic studies. RESULTS Here, we provide evidence for the functional role of the maintenance DNA methyltransferase 1 (Dnmt1) in an insect using experimental manipulation. Through RNA interference (RNAi), we successfully posttranscriptionally knocked down Dnmt1 in ovarian tissue of the hemipteran Oncopeltus fasciatus (the large milkweed bug). Individuals depleted for Dnmt1, and subsequently DNA methylation, failed to reproduce. Eggs were inviable and declined in number, and nuclei structure of follicular epithelium was aberrant. Erasure of DNA methylation from gene or transposon element bodies did not reveal a direct causal link to steady-state mRNA levels in somatic cells. These results reveal an important function of Dnmt1 seemingly not contingent on directly controlling gene expression. CONCLUSIONS This study provides direct experimental evidence for a functional role of Dnmt1 in egg production and embryo viability and uncovers a trivial role, if any, for DNA methylation in control of gene expression in O. fasciatus.
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Affiliation(s)
- Adam J. Bewick
- Department of Genetics, University of Georgia, Athens, GA 30602 USA
| | - Zachary Sanchez
- Department of Entomology, University of Georgia, Athens, GA 30602 USA
| | | | - Allen J. Moore
- Department of Entomology, University of Georgia, Athens, GA 30602 USA
| | - Patricia J. Moore
- Department of Entomology, University of Georgia, Athens, GA 30602 USA
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85
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Helliwell EE, Faber‐Hammond J, Lopez ZC, Garoutte A, Wettberg E, Friesen ML, Porter SS. Rapid establishment of a flowering cline in
Medicago polymorpha
after invasion of North America. Mol Ecol 2018; 27:4758-4774. [DOI: 10.1111/mec.14898] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 10/01/2018] [Accepted: 10/03/2018] [Indexed: 12/11/2022]
Affiliation(s)
- Emily E. Helliwell
- School of Biological Sciences Washington State University Vancouver Washington
| | | | - Zoie C. Lopez
- School of Biological Sciences Washington State University Vancouver Washington
| | - Aaron Garoutte
- Department of Plant Biology Michigan State University East Lansing Michigan
| | - Eric Wettberg
- Department of Plant and Soil Science The University of Vermont Burlington Vermont
| | - Maren L. Friesen
- Department of Plant Biology Michigan State University East Lansing Michigan
- Department of Plant Pathology Washington State University Pullman Washington
- Department of Crop and Soil Sciences Washington State University Pullman Washington
| | - Stephanie S. Porter
- School of Biological Sciences Washington State University Vancouver Washington
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86
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Qiu B, Larsen RS, Chang NC, Wang J, Boomsma JJ, Zhang G. Towards reconstructing the ancestral brain gene-network regulating caste differentiation in ants. Nat Ecol Evol 2018; 2:1782-1791. [PMID: 30349091 PMCID: PMC6217981 DOI: 10.1038/s41559-018-0689-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 09/06/2018] [Indexed: 12/15/2022]
Abstract
Specialized queens and life-time unmated workers evolved once in the common ancestor of all ants, but whether caste development across ants continues to be at least partly regulated by a single core set of genes remains obscure. We analysed brain transcriptomes from five ant species (three subfamilies) and reconstructed the origins of genes with caste-biased expression. Ancient genes predating the Neoptera were more likely to regulate gyne (virgin queen) phenotypes, while caste differentiation roles of younger, ant-lineage-specific genes varied. Transcriptome profiling showed that the ancestral network for caste-specific gene-regulation has been maintained, but that signatures of common ancestry are obscured by later modifications. Adjusting for such differences, we identified a core gene-set that: 1. consistently displayed similar directions and degrees of caste-differentiated expression, and 2. have mostly not been reported as being involved in caste differentiation. These core regulatory genes exist in the genomes of ant species that secondarily lost the queen caste, but expression differences for reproductive and sterile workers are minor and similar to social paper wasps that lack differentiated castes. Many caste-biased ant genes have caste-differentiated expression in honeybees, but directions of caste bias were uncorrelated, as expected when permanent castes evolved independently in both lineages.
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Affiliation(s)
- Bitao Qiu
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Stenbak Larsen
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ni-Chen Chang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - John Wang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Guojie Zhang
- Centre for Social Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,China National GeneBank, BGI-Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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87
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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: 60] [Impact Index Per Article: 10.0] [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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88
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Rehan SM, Glastad KM, Steffen MA, Fay CR, Hunt BG, Toth AL. Conserved Genes Underlie Phenotypic Plasticity in an Incipiently Social Bee. Genome Biol Evol 2018; 10:2749-2758. [PMID: 30247544 PMCID: PMC6190964 DOI: 10.1093/gbe/evy212] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2018] [Indexed: 11/13/2022] Open
Abstract
Despite a strong history of theoretical work on the mechanisms of social evolution, relatively little is known of the molecular genetic changes that accompany transitions from solitary to eusocial forms. Here, we provide the first genome of an incipiently social bee that shows both solitary and social colony organization in sympatry, the Australian carpenter bee Ceratina australensis. Through comparative analysis, we provide support for the role of conserved genes and cis-regulation of gene expression in the phenotypic plasticity observed in nest-sharing, a rudimentary form of sociality. Additionally, we find that these conserved genes are associated with caste differences in advanced eusocial species, suggesting these types of mechanisms could pave the molecular pathway from solitary to eusocial living. Genes associated with social nesting in this species show signatures of being deeply conserved, in contrast to previous studies in other bees showing novel and faster-evolving genes are associated with derived sociality. Our data provide support for the idea that the earliest social transitions are driven by changes in gene regulation of deeply conserved genes.
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Affiliation(s)
- Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire
| | - Karl M Glastad
- Department of Cell & Developmental Biology, University of Pennsylvania
| | | | - Cameron R Fay
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
| | | | - Amy L Toth
- Department of Ecology, Evolution and Organismal Biology, Iowa State University
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89
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Piekarski PK, Carpenter JM, Lemmon AR, Moriarty Lemmon E, Sharanowski BJ. Phylogenomic Evidence Overturns Current Conceptions of Social Evolution in Wasps (Vespidae). Mol Biol Evol 2018; 35:2097-2109. [PMID: 29924339 PMCID: PMC6107056 DOI: 10.1093/molbev/msy124] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The hypothesis that eusociality originated once in Vespidae has shaped interpretation of social evolution for decades and has driven the supposition that preimaginal morphophysiological differences between castes were absent at the outset of eusociality. Many researchers also consider casteless nest-sharing an antecedent to eusociality. Together, these ideas endorse a stepwise progression of social evolution in wasps (solitary → casteless nest-sharing → eusociality with rudimentary behavioral castes → eusociality with preimaginal caste-biasing (PCB) → morphologically differentiated castes). Here, we infer the phylogeny of Vespidae using sequence data generated via anchored hybrid enrichment from 378 loci across 136 vespid species and perform ancestral state reconstructions to test whether rudimentary and monomorphic castes characterized the initial stages of eusocial evolution. Our results reject the single origin of eusociality hypothesis, contest the supposition that eusociality emerged from a casteless nest-sharing ancestor, and suggest that eusociality in Polistinae + Vespinae began with castes having morphological differences. An abrupt appearance of castes with ontogenetically established morphophysiological differences conflicts with the current conception of stepwise social evolution and suggests that the climb up the ladder of sociality does not occur through sequential mutation. Phenotypic plasticity and standing genetic variation could explain how cooperative brood care evolved in concert with nest-sharing and how morphologically dissimilar castes arose without a rudimentary intermediate. Furthermore, PCB at the outset of eusociality implicates a subsocial route to eusociality in Polistinae + Vespinae, emphasizing the role of mother-daughter interactions and subfertility (i.e. the cost component of kin selection) in the origin of workers.
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Affiliation(s)
| | - James M Carpenter
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
| | - Alan R Lemmon
- Department of Scientific Computing, Florida State University, Tallahassee, FL
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90
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Libbrecht R, Oxley PR, Kronauer DJC. Clonal raider ant brain transcriptomics identifies candidate molecular mechanisms for reproductive division of labor. BMC Biol 2018; 16:89. [PMID: 30103762 PMCID: PMC6090591 DOI: 10.1186/s12915-018-0558-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/31/2018] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Division of labor between reproductive queens and workers that perform brood care is a hallmark of insect societies. However, studies of the molecular basis of this fundamental dichotomy are limited by the fact that the caste of an individual cannot typically be experimentally manipulated at the adult stage. Here we take advantage of the unique biology of the clonal raider ant, Ooceraea biroi, to study brain gene expression dynamics during experimentally induced transitions between reproductive and brood care behavior. RESULTS Introducing larvae that inhibit reproduction and induce brood care behavior causes much faster changes in adult gene expression than removing larvae. In addition, the general patterns of gene expression differ depending on whether ants transition from reproduction to brood care or vice versa, indicating that gene expression changes between phases are cyclic rather than pendular. Finally, we identify genes that could play upstream roles in regulating reproduction and behavior because they show large and early expression changes in one or both transitions. CONCLUSIONS Our analyses reveal that the nature and timing of gene expression changes differ substantially depending on the direction of the transition, and identify a suite of promising candidate molecular regulators of reproductive division of labor that can now be characterized further in both social and solitary animal models. This study contributes to understanding the molecular regulation of reproduction and behavior, as well as the organization and evolution of insect societies.
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Affiliation(s)
- Romain Libbrecht
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128, Mainz, Germany.
| | - Peter R Oxley
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
- Samuel J. Wood Library, Weill Cornell Medicine, 1300 York Avenue, New York, NY, 10065, USA
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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91
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Kronauer DJ, Libbrecht R. Back to the roots: the importance of using simple insect societies to understand the molecular basis of complex social life. CURRENT OPINION IN INSECT SCIENCE 2018; 28:33-39. [PMID: 30551765 DOI: 10.1016/j.cois.2018.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 06/09/2023]
Abstract
The evolutionary trajectories toward insect eusociality come in two broad forms. In species like wasps, bees, and ants, the first helpers remained at the nest primarily to help with brood care. In species like aphids and termites, on the other hand, nest defense was initially the primary ecological driving force. To better understand the molecular basis of these two alternative evolutionary trajectories, it is therefore important to study the mechanistic basis of brood care and nest defense behavior. So far, most studies have compared morphologically distinct castes in advanced eusocial species of ants, bees, wasps, and termites. However, the interpretation of such comparisons is limited by multiple confounding factors and the fact that castes are typically fixed and cannot be manipulated at the adult stage. In this review, we argue that conducting molecular studies of brood care and nest defense in simpler, more flexible insect societies may complement studies of advanced eusocial insects and provide avenues toward more functional analyses. We review the available literature and propose candidate study systems for future molecular investigations of brood care and nest defense in social insects.
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Affiliation(s)
- Daniel Jc Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, USA
| | - Romain Libbrecht
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Mainz, Germany.
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92
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Taylor D, Bentley MA, Sumner S. Social wasps as models to study the major evolutionary transition to superorganismality. CURRENT OPINION IN INSECT SCIENCE 2018; 28:26-32. [PMID: 30551764 DOI: 10.1016/j.cois.2018.04.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 06/09/2023]
Abstract
The major evolutionary transition to superorganismality has taken place several times in the insects. Although there has been much consideration of the ultimate evolutionary explanations for superorganismality, we know relatively little about what proximate mechanisms constrain or promote this major transition. Here, we propose that Vespid wasps represent an understudied, but potentially very useful, model system for studying the mechanisms underpinning superorganismality. We highlight how there is an abundance of behavioural data for many wasp species, confirming their utility in studies of social evolution; however, there is a sparsity of genomic data from which we can test proximate and ultimate hypotheses on this major evolutionary transition.
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Affiliation(s)
- Daisy Taylor
- Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| | - Michael A Bentley
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Seirian Sumner
- Centre for Biodiversity & Environment Research, Department of Genetics, Evolution & Environment, University College London, Gower Street, London WC1E 6BT, United Kingdom.
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93
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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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94
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Chandra V, Fetter-Pruneda I, Oxley PR, Ritger AL, McKenzie SK, Libbrecht R, Kronauer DJC. Social regulation of insulin signaling and the evolution of eusociality in ants. Science 2018; 361:398-402. [PMID: 30049879 PMCID: PMC6178808 DOI: 10.1126/science.aar5723] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/01/2018] [Accepted: 05/30/2018] [Indexed: 12/15/2022]
Abstract
Queens and workers of eusocial Hymenoptera are considered homologous to the reproductive and brood care phases of an ancestral subsocial life cycle. However, the molecular mechanisms underlying the evolution of reproductive division of labor remain obscure. Using a brain transcriptomics screen, we identified a single gene, insulin-like peptide 2 (ilp2), which is always up-regulated in ant reproductives, likely because they are better nourished than their nonreproductive nestmates. In clonal raider ants (Ooceraea biroi), larval signals inhibit adult reproduction by suppressing ilp2, thus producing a colony reproductive cycle reminiscent of ancestral subsociality. However, increasing ILP2 peptide levels overrides larval suppression, thereby breaking the colony cycle and inducing a stable division of labor. These findings suggest a simple model for the origin of ant eusociality via nutritionally determined reproductive asymmetries potentially amplified by larval signals.
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Affiliation(s)
- Vikram Chandra
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Ingrid Fetter-Pruneda
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
| | - Peter R Oxley
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Samuel J. Wood Library, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Amelia L Ritger
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Department of Ecology and Evolution, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Romain Libbrecht
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Institute of Organismic and Molecular Evolution, Johannes Gutenberg University, Johannes-von-Müller-Weg 6, 55128 Mainz, Germany
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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95
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Insects with similar social complexity show convergent patterns of adaptive molecular evolution. Sci Rep 2018; 8:10388. [PMID: 29991733 PMCID: PMC6039441 DOI: 10.1038/s41598-018-28489-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/22/2018] [Indexed: 12/30/2022] Open
Abstract
Eusociality has independently evolved multiple times in the hymenoptera, but the patterns of adaptive molecular evolution underlying the evolution and elaboration of eusociality remain uncertain. Here, we performed a population genomics study of primitively eusocial Polistes (paper wasps), and compared their patterns of molecular evolution to two social bees; Bombus (bumblebees), and Apis (honey bees). This species triad allowed us to study molecular evolution across a gradient of social complexity (Polistes < Bombus < Apis) and compare species pairs that have similar (i.e. Polistes and Bombus) or different (i.e. Polistes and Apis) life histories, while controlling for phylogenetic distance. We found that regulatory genes have high levels of positive selection in Polistes; consistent with the prediction that adaptive changes in gene regulation are important during early stages of social evolution. Polistes and Bombus exhibit greater similarity in patterns of adaptive evolution including greater overlap of genes experiencing positive selection, and greater positive selection on queen-biased genes. Our findings suggest that either adaptive evolution of a few key genes underlie the evolution of simpler forms of eusociality, or that the initial stages of social evolution lead to selection on a few key traits orchestrated by orthologous genes and networks.
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96
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Taguchi YH. Tensor decomposition-based and principal-component-analysis-based unsupervised feature extraction applied to the gene expression and methylation profiles in the brains of social insects with multiple castes. BMC Bioinformatics 2018; 19:99. [PMID: 29745827 PMCID: PMC5998888 DOI: 10.1186/s12859-018-2068-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Background Even though coexistence of multiple phenotypes sharing the same genomic background is interesting, it remains incompletely understood. Epigenomic profiles may represent key factors, with unknown contributions to the development of multiple phenotypes, and social-insect castes are a good model for elucidation of the underlying mechanisms. Nonetheless, previous studies have failed to identify genes associated with aberrant gene expression and methylation profiles because of the lack of suitable methodology that can address this problem properly. Methods A recently proposed principal component analysis (PCA)-based and tensor decomposition (TD)-based unsupervised feature extraction (FE) can solve this problem because these two approaches can deal with gene expression and methylation profiles even when a small number of samples is available. Results PCA-based and TD-based unsupervised FE methods were applied to the analysis of gene expression and methylation profiles in the brains of two social insects, Polistes canadensis and Dinoponera quadriceps. Genes associated with differential expression and methylation between castes were identified, and analysis of enrichment of Gene Ontology terms confirmed reliability of the obtained sets of genes from the biological standpoint. Conclusions Biologically relevant genes, shown to be associated with significant differential gene expression and methylation between castes, were identified here for the first time. The identification of these genes may help understand the mechanisms underlying epigenetic control of development of multiple phenotypes under the same genomic conditions. Electronic supplementary material The online version of this article (10.1186/s12859-018-2068-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunkyo-ku, Tokyo, 112-8551, Japan.
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97
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Glastad KM, Arsenault SV, Vertacnik KL, Geib SM, Kay S, Danforth BN, Rehan SM, Linnen CR, Kocher SD, Hunt BG. Variation in DNA Methylation Is Not Consistently Reflected by Sociality in Hymenoptera. Genome Biol Evol 2018; 9:1687-1698. [PMID: 28854636 PMCID: PMC5522706 DOI: 10.1093/gbe/evx128] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2017] [Indexed: 12/12/2022] Open
Abstract
Changes in gene regulation that underlie phenotypic evolution can be encoded directly in the DNA sequence or mediated by chromatin modifications such as DNA methylation. It has been hypothesized that the evolution of eusocial division of labor is associated with enhanced gene regulatory potential, which may include expansions in DNA methylation in the genomes of Hymenoptera (bees, ants, wasps, and sawflies). Recently, this hypothesis garnered support from analyses of a commonly used metric to estimate DNA methylation in silico, CpG content. Here, we test this hypothesis using direct, nucleotide-level measures of DNA methylation across nine species of Hymenoptera. In doing so, we generated new DNA methylomes for three species of interest, including one solitary and one facultatively eusocial halictid bee and a sawfly. We demonstrate that the strength of correlation between CpG content and DNA methylation varies widely among hymenopteran taxa, highlighting shortcomings in the utility of CpG content as a proxy for DNA methylation in comparative studies of taxa with sparse DNA methylomes. We observed strikingly high levels of DNA methylation in the sawfly relative to other investigated hymenopterans. Analyses of molecular evolution suggest the relatively distinct sawfly DNA methylome may be associated with positive selection on functional DNMT3 domains. Sawflies are an outgroup to all ants, bees, and wasps, and no sawfly species are eusocial. We find no evidence that either global expansions or variation within individual ortholog groups in DNA methylation are consistently associated with the evolution of social behavior.
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Affiliation(s)
- Karl M Glastad
- Department of Cell and Developmental Biology, University of Pennsylvania
| | | | | | - Scott M Geib
- U.S. Department of Agriculture-Agricultural Research Service (USDA-ARS), Daniel K. Inouye U.S. Pacific Basin Agricultural Research Center, Hilo, Hawaii
| | - Sasha Kay
- Department of Entomology, University of Georgia
| | | | - Sandra M Rehan
- Department of Biological Sciences, University of New Hampshire, Durham, New Hampshire
| | | | - Sarah D Kocher
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
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Olova N, Krueger F, Andrews S, Oxley D, Berrens RV, Branco MR, Reik W. Comparison of whole-genome bisulfite sequencing library preparation strategies identifies sources of biases affecting DNA methylation data. Genome Biol 2018; 19:33. [PMID: 29544553 PMCID: PMC5856372 DOI: 10.1186/s13059-018-1408-2] [Citation(s) in RCA: 153] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 02/14/2018] [Indexed: 12/20/2022] Open
Abstract
Background Whole-genome bisulfite sequencing (WGBS) is becoming an increasingly accessible technique, used widely for both fundamental and disease-oriented research. Library preparation methods benefit from a variety of available kits, polymerases and bisulfite conversion protocols. Although some steps in the procedure, such as PCR amplification, are known to introduce biases, a systematic evaluation of biases in WGBS strategies is missing. Results We perform a comparative analysis of several commonly used pre- and post-bisulfite WGBS library preparation protocols for their performance and quality of sequencing outputs. Our results show that bisulfite conversion per se is the main trigger of pronounced sequencing biases, and PCR amplification builds on these underlying artefacts. The majority of standard library preparation methods yield a significantly biased sequence output and overestimate global methylation. Importantly, both absolute and relative methylation levels at specific genomic regions vary substantially between methods, with clear implications for DNA methylation studies. Conclusions We show that amplification-free library preparation is the least biased approach for WGBS. In protocols with amplification, the choice of bisulfite conversion protocol or polymerase can significantly minimize artefacts. To aid with the quality assessment of existing WGBS datasets, we have integrated a bias diagnostic tool in the Bismark package and offer several approaches for consideration during the preparation and analysis of WGBS datasets. Electronic supplementary material The online version of this article (10.1186/s13059-018-1408-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nelly Olova
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK.,Present address: MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Simon Andrews
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - David Oxley
- Mass Spectrometry Facility, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Rebecca V Berrens
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK.
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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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Sumner S, Bell E, Taylor D. A molecular concept of caste in insect societies. CURRENT OPINION IN INSECT SCIENCE 2018; 25:42-50. [PMID: 29602361 DOI: 10.1016/j.cois.2017.11.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/21/2017] [Accepted: 11/21/2017] [Indexed: 05/20/2023]
Abstract
The term 'caste' is used to describe the division of reproductive labour that defines eusocial insect societies. The definition of 'caste' has been debated over the last 50 years, specifically with respect to the simplest insect societies; this raises the question of whether a simple categorisation of social behaviour by reproductive state alone is helpful. Gene-level analyses of behaviours of individuals in hymenopteran social insect societies now provide a new empirical base-line for defining caste and understanding the evolution and maintenance of a reproductive division of labour. We review this literature to identify a set of potential molecular signatures that, combined with behavioural, morphological and physiological data, help define caste more precisely; these signatures vary with the type of society, and are likely to be influenced by ecology, life-history, and stage in the colony cycle. We conclude that genomic approaches provide us with additional ways to help quantify and categorise caste, and behaviour in general.
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Affiliation(s)
- Seirian Sumner
- Centre for Biodiversity and Environmental Research, Medawar Building, University College London, Gower Street, London WC1E 6BT, UK.
| | - Emily Bell
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Daisy Taylor
- School of Biological Sciences, Bristol Life Sciences Building, University of Bristol, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
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