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He J, Kang L. Regulation of insect behavior by non-coding RNAs. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1106-1118. [PMID: 38443665 DOI: 10.1007/s11427-023-2482-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 10/26/2023] [Indexed: 03/07/2024]
Abstract
The adaptation of insects to environments relies on a sophisticated set of behaviors controlled by molecular and physiological processes. Over the past several decades, accumulating studies have unveiled the roles of non-coding RNAs (ncRNAs) in regulating insect behaviors. ncRNAs assume particularly pivotal roles in the behavioral plasticity of insects by rapidly responding to environmental stimuli. ncRNAs also contribute to the maintenance of homeostasis of insects by fine-tuning the expression of target genes. However, a comprehensive review of ncRNAs' roles in regulating insect behaviors has yet to be conducted. Here, we present the recent progress in our understanding of how ncRNAs regulate various insect behaviors, including flight and movement, social behavior, reproduction, learning and memory, and feeding. We refine the intricate mechanisms by which ncRNAs modulate the function of neural, motor, reproductive, and other physiological systems, as well as gene expression in insects like fruit flies, social insects, locusts, and mosquitos. Furthermore, we discuss potential avenues for future studies in ncRNA-mediated insect behaviors.
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Affiliation(s)
- Jing He
- 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.
- Beijing Institutes of Life Sciences, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Science, Hebei University, Baoding, 071002, China.
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2
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Wang X, Zhai Y, Zheng H. Deciphering the cellular heterogeneity of the insect brain with single-cell RNA sequencing. INSECT SCIENCE 2024; 31:314-327. [PMID: 37702319 DOI: 10.1111/1744-7917.13270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023]
Abstract
Insects show highly complicated adaptive and sophisticated behaviors, including spatial orientation skills, learning ability, and social interaction. These behaviors are controlled by the insect brain, the central part of the nervous system. The tiny insect brain consists of millions of highly differentiated and interconnected cells forming a complex network. Decades of research has gone into an understanding of which parts of the insect brain possess particular behaviors, but exactly how they modulate these functional consequences needs to be clarified. Detailed description of the brain and behavior is required to decipher the complexity of cell types, as well as their connectivity and function. Single-cell RNA-sequencing (scRNA-seq) has emerged recently as a breakthrough technology to understand the transcriptome at cellular resolution. With scRNA-seq, it is possible to uncover the cellular heterogeneity of brain cells and elucidate their specific functions and state. In this review, we first review the basic structure of insect brains and the links to insect behaviors mainly focusing on learning and memory. Then the scRNA applications on insect brains are introduced by representative studies. Single-cell RNA-seq has allowed researchers to classify cell subpopulations within different insect brain regions, pinpoint single-cell developmental trajectories, and identify gene regulatory networks. These developments empower the advances in neuroscience and shed light on the intricate problems in understanding insect brain functions and behaviors.
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Affiliation(s)
- Xiaofei Wang
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
| | - Yifan Zhai
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Jinan, China
- Shandong Provincial Engineering Technology Research Center on Biocontrol of Crops Diseases and In-sect Pests, Jinan, China
| | - Hao Zheng
- Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
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3
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Roggenbuck EC, Hall EA, Hanson IB, Roby AA, Zhang KK, Alkatib KA, Carter JA, Clewner JE, Gelfius AL, Gong S, Gordon FR, Iseler JN, Kotapati S, Li M, Maysun A, McCormick EO, Rastogi G, Sengupta S, Uzoma CU, Wolkov MA, Clowney EJ. Let's talk about sex: Mechanisms of neural sexual differentiation in Bilateria. WIREs Mech Dis 2024; 16:e1636. [PMID: 38185860 DOI: 10.1002/wsbm.1636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/09/2024]
Abstract
In multicellular organisms, sexed gonads have evolved that facilitate release of sperm versus eggs, and bilaterian animals purposefully combine their gametes via mating behaviors. Distinct neural circuits have evolved that control these physically different mating events for animals producing eggs from ovaries versus sperm from testis. In this review, we will describe the developmental mechanisms that sexually differentiate neural circuits across three major clades of bilaterian animals-Ecdysozoa, Deuterosomia, and Lophotrochozoa. While many of the mechanisms inducing somatic and neuronal sex differentiation across these diverse organisms are clade-specific rather than evolutionarily conserved, we develop a common framework for considering the developmental logic of these events and the types of neuronal differences that produce sex-differentiated behaviors. This article is categorized under: Congenital Diseases > Stem Cells and Development Neurological Diseases > Stem Cells and Development.
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Affiliation(s)
- Emma C Roggenbuck
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elijah A Hall
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Isabel B Hanson
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Alyssa A Roby
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Katherine K Zhang
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Kyle A Alkatib
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Joseph A Carter
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jarred E Clewner
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Anna L Gelfius
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Shiyuan Gong
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Finley R Gordon
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Jolene N Iseler
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Samhita Kotapati
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Marilyn Li
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Areeba Maysun
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Elise O McCormick
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Geetanjali Rastogi
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Srijani Sengupta
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Chantal U Uzoma
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - Madison A Wolkov
- MCDB 464 - Cellular Diversity: Sex Differentiation of the Brain, University of Michigan, Ann Arbor, Michigan, USA
| | - E Josephine Clowney
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Neuroscience Institute Affiliate, University of Michigan, Ann Arbor, Michigan, USA
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4
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Fu Z, Shi Y, Yu S, Zhao Q, Mo H, Yang P. Variation of gene expression of fatty acid acyl CoA reductase associated with wax secretion of a scale insect, Ericerus pela, and identification of its regulation factors through the accessible chromatin analyses and yeast one-hybrid. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2024; 115:e22101. [PMID: 38500444 DOI: 10.1002/arch.22101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/11/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024]
Abstract
The Chinese white wax scale insect (CWWSI), Ericerus pela, can secret an amount of wax equivalent to their body weight. Previous studies demonstrated the fatty acyl-CoA reductase (far3) plays a pivotal role in wax secretion of CWWSI. The high expression of far3 is crucial for the massive wax secretion. However, the transcription regulation of far3 was not clear. To identify regulatory factors that control the expression of far3, the assay for transposase-accessible chromatin (ATAC) and yeast one-hybrid (Y1H) were carried out in this study. The ATAC sequencing of the CWWSI at the early wax-secretion stage ATAC-seq resulted in 22.75 GB raw data, generated 75,827,225 clean reads and revealed 142,771 peaks. There was one significant peak in the 3 kb upstream regulation regions. The peak sequence is located between -1000 and -670 bp upstream of the far3 transcription start site, spanning a length of 331 bp. This peak sequence served as bait for creating the pAbAi-peak recombinant vector, used in Y1H screenings to identify proteins interacting with far3 gene. The results indicate a successful CWWSI cDNA library construction with a capacity of 1.2 × 107 colony forming unit, a 95.8% recombination rate, and insert sizes between 1,000 and 2,000 bp. Self-activation tests established that 100 ng/mL of AbA effectively inhibited bait vector self-activation. Finally, a total of 88 positive clones were selected. After sequencing and removal of duplication, 63 unique clones were obtained from these screened colonies. By aligning the clone sequences with full-length transcriptome and genome of CWWSI, the full-length coding sequences of these clones were obtained. BlastX analysis identified a transcription factor, nuclear transcription factor Y beta, and two co-activators, cAMP-response-element-binding-protein-binding protein and WW domain binding protein 2. Reverse transcription quantitative polymerase chain reaction analysis confirmed that their expression patterns were consistent with the developmental stages preceding wax secretion and matched the wax secretion characteristics during ovulation periods. These results are beneficial for further research into the regulatory mechanisms of wax secretion of CWWSI.
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Affiliation(s)
- Zuoyi Fu
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, China
- Nanjing Forestry University, Nanjing, China
| | - Yuanchong Shi
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, China
| | - Shuhui Yu
- College of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Qiuyu Zhao
- College of Agriculture and Life Sciences, Kunming University, Kunming, China
| | - Haifeng Mo
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, China
| | - Pu Yang
- Institute of Highland Forest Science, Chinese Academy of Forestry, Kunming, China
- Key Laboratory of Breeding and Utilization of Resource Insects of National Forestry and Grassland Administration, Kunming, China
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5
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Lin S, Elsner D, Ams L, Korb J, Rosengaus R. A genetic toolkit underlying the queen phenotype in termites with totipotent workers. Sci Rep 2024; 14:2214. [PMID: 38278833 PMCID: PMC10817970 DOI: 10.1038/s41598-024-51772-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/09/2024] [Indexed: 01/28/2024] Open
Abstract
Social insect castes (e.g., queens, workers) are prime examples of phenotypic plasticity (i.e., different phenotypes arising from the same genotype). Yet, the mechanisms that give rise to highly fertile, long-lived queens versus non-reproducing, short-lived workers are not well understood. Recently, a module of co-expressed genes has been identified that characterizes queens compared to workers of the termite Cryptotermes secundus (Kalotermitidae): the Queen Central Module (QCM). We tested whether the QCM is shared in termite species, in which queens gradually develop via early larval and late larval instars, the latter functioning as totipotent workers (linear development). Similar as in C. secundus, gene expression profiles revealed an enrichment of QCM genes in Zootermopsis angusticollis queens, a species from another termite family (Archotermopsidae). The expression of these QCM genes became gradually enriched during development from early larval instars via workers to queens. Thus, our results support the hypothesis of a conserved genetic toolkit that characterizes termite queens with gradual linear development. Our data also imply a strong caste-specific tissue specificity with the QCM signal being restricted to head-prothorax tissues in termite queens. This tissue-specific expression of key aging-related genes might have facilitated the evolution of a long lifespan in termite queens.
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Affiliation(s)
- Silu Lin
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany
| | - Daniel Elsner
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany
| | - Leon Ams
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany
| | - Judith Korb
- Evolutionary Biology and Ecology, University of Freiburg, 79104, Freiburg, Germany.
- Research Institute for the Environment and Livelihoods, Charles Darwin University, Casuarina Campus, Darwin, NT, 0909, Australia.
| | - Rebeca Rosengaus
- Department of Marine and Environmental Sciences, Northeastern University, Boston, MA, 02115, USA.
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Taylor BA, Taylor D, Bodrug‐Schepers A, Câmara Ferreira F, Stralis‐Pavese N, Himmelbauer H, Guigó R, Reuter M, Sumner S. Molecular signatures of alternative reproductive strategies in a facultatively social hover wasp. Mol Ecol 2024; 33:e17217. [PMID: 38014715 PMCID: PMC10953455 DOI: 10.1111/mec.17217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 11/09/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
Social insect reproductives and non-reproductives represent ideal models with which to understand the expression and regulation of alternative phenotypes. Most research in this area has focused on the developmental regulation of reproductive phenotypes in obligately social taxa such as honey bees, while relatively few studies have addressed the molecular correlates of reproductive differentiation in species in which the division of reproductive labour is established only in plastic dominance hierarchies. To address this knowledge gap, we generate the first genome for any stenogastrine wasp and analyse brain transcriptomic data for non-reproductives and reproductives of the facultatively social species Liostenogaster flavolineata, a representative of one of the simplest forms of social living. By experimentally manipulating the reproductive 'queues' exhibited by social colonies of this species, we show that reproductive division of labour in this species is associated with transcriptomic signatures that are more subtle and variable than those observed in social taxa in which colony living has become obligate; that variation in gene expression among non-reproductives reflects their investment into foraging effort more than their social rank; and that genes associated with reproductive division of labour overlap to some extent with those underlying division of labour in the separate polistine origin of wasp sociality but only explain a small portion of overall variation in this trait. These results indicate that broad patterns of within-colony transcriptomic differentiation in this species are similar to those in Polistinae but offer little support for the existence of a strongly conserved 'toolkit' for sociality.
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Affiliation(s)
- Benjamin A. Taylor
- Centre for Biodiversity & Environment ResearchUniversity College LondonLondonUK
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
| | - Daisy Taylor
- School of Biological SciencesUniversity of BristolBristolUK
| | | | | | - Nancy Stralis‐Pavese
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Heinz Himmelbauer
- Department of BiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Roderic Guigó
- Centre for Genomic RegulationBarcelona Institute of Science and TechnologyBarcelonaSpain
- Universitat Pompeu FabraBarcelonaSpain
| | - Max Reuter
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
- Centre for Life's Origins and EvolutionUniversity College LondonLondonUK
| | - Seirian Sumner
- Centre for Biodiversity & Environment ResearchUniversity College LondonLondonUK
- Department of Genetics, Evolution & EnvironmentUniversity College LondonLondonUK
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7
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Zhao Z, Li L, Zeng R, Lin L, Yuan D, Wen Y, Li N, Cui Y, Zhu S, Zhang ZM, Li S, Ren C. 5mC modification orchestrates choriogenesis and fertilization by preventing prolonged ftz-f1 expression. Nat Commun 2023; 14:8234. [PMID: 38086980 PMCID: PMC10716119 DOI: 10.1038/s41467-023-43987-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/23/2023] [Indexed: 12/18/2023] Open
Abstract
DNA methylation at the fifth position of cytosine (5-methylcytosine, 5mC) is a crucial epigenetic modification for regulating gene expression, but little is known about how it regulates gene expression in insects. Here, we pursue the detailed molecular mechanism by which DNMT1-mediated 5mC maintenance regulates female reproduction in the German cockroach, Blattella germanica. Our results show that Dnmt1 knockdown decreases the level of 5mC in the ovary, upregulating numerous genes during choriogenesis, especially the transcription factor ftz-f1. The hypomethylation at the ftz-f1 promoter region increases and prolongs ftz-f1 expression in ovarian follicle cells during choriogenesis, which consequently causes aberrantly high levels of 20-hydroxyecdysone and excessively upregulates the extracellular matrix remodeling gene Mmp1. These changes further impair choriogenesis and disrupt fertilization by causing anoikis of the follicle cells, a shortage of chorion proteins, and malformation of the sponge-like bodies. This study significantly advances our understanding of how DNA 5mC modification regulates female reproduction in insects.
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Affiliation(s)
- Zheng Zhao
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510631, China
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, 514779, China
| | - Liang Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Ruichen Zeng
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Liangguan Lin
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Dongwei Yuan
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yejie Wen
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Na Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, 514779, China
| | - Yingying Cui
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Shiming Zhu
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhi-Min Zhang
- College of Pharmacy, Jinan University, 510632, Guangzhou, China
| | - Sheng Li
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510631, China.
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, 514779, China.
| | - Chonghua Ren
- Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, Guangzhou Key Laboratory of Insect Development Regulation and Application Research, Institute of Insect Science and Technology & School of Life Sciences, South China Normal University, Guangzhou, 510631, China.
- Guangmeiyuan R&D Center, Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology, South China Normal University, Meizhou, 514779, China.
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8
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Kucharski R, Ellis N, Jurkowski TP, Hurd PJ, Maleszka R. The PWWP domain and the evolution of unique DNA methylation toolkits in Hymenoptera. iScience 2023; 26:108193. [PMID: 37920666 PMCID: PMC10618690 DOI: 10.1016/j.isci.2023.108193] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/11/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023] Open
Abstract
DNMT3 in Hymenoptera has a unique duplication of the essential PWWP domain. Using GST-tagged PWWP fusion proteins and histone arrays we show that these domains have gained new properties and represent the first case of PWWP domains binding to H3K27 chromatin modifications, including H3K27me3, a key modification that is important during development. Phylogenetic analyses of 107 genomes indicate that the duplicated PWWP domains separated into two sister clades, and their distinct binding capacities are supported by 3D modeling. Other features of this unique DNA methylation system include variable copies, losses, and duplications of DNMT1 and DNMT3, and combinatorial generations of DNMT3 isoforms including variants missing the catalytic domain. Some of these losses and duplications of are found only in parasitic wasps. We discuss our findings in the context of the crosstalk between DNA methylation and histone methylation, and the expanded potential of epigenomic modifications in Hymenoptera to drive evolutionary novelties.
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Affiliation(s)
- Robert Kucharski
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Nancy Ellis
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | | | - Paul J. Hurd
- School of Biological & Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ryszard Maleszka
- Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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9
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Koludarov I, Velasque M, Senoner T, Timm T, Greve C, Hamadou AB, Gupta DK, Lochnit G, Heinzinger M, Vilcinskas A, Gloag R, Harpur BA, Podsiadlowski L, Rost B, Jackson TNW, Dutertre S, Stolle E, von Reumont BM. Prevalent bee venom genes evolved before the aculeate stinger and eusociality. BMC Biol 2023; 21:229. [PMID: 37867198 PMCID: PMC10591384 DOI: 10.1186/s12915-023-01656-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 06/29/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND Venoms, which have evolved numerous times in animals, are ideal models of convergent trait evolution. However, detailed genomic studies of toxin-encoding genes exist for only a few animal groups. The hyper-diverse hymenopteran insects are the most speciose venomous clade, but investigation of the origin of their venom genes has been largely neglected. RESULTS Utilizing a combination of genomic and proteo-transcriptomic data, we investigated the origin of 11 toxin genes in 29 published and 3 new hymenopteran genomes and compiled an up-to-date list of prevalent bee venom proteins. Observed patterns indicate that bee venom genes predominantly originate through single gene co-option with gene duplication contributing to subsequent diversification. CONCLUSIONS Most Hymenoptera venom genes are shared by all members of the clade and only melittin and the new venom protein family anthophilin1 appear unique to the bee lineage. Most venom proteins thus predate the mega-radiation of hymenopterans and the evolution of the aculeate stinger.
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Affiliation(s)
- Ivan Koludarov
- Justus Liebig University of Gießen, Institute for Insect Biotechnology, Heinrich-Buff-Ring 58, 35392, Giessen, Germany.
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany.
| | - Mariana Velasque
- Genomics & Regulatory Systems Unit, Okinawa Institute of Science & Technology, Tancha, Okinawa, 1919, Japan
| | - Tobias Senoner
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
| | - Thomas Timm
- Protein Analytics, Institute of Biochemistry, Justus Liebig University, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Carola Greve
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Alexander Ben Hamadou
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Deepak Kumar Gupta
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany
| | - Günter Lochnit
- Protein Analytics, Institute of Biochemistry, Justus Liebig University, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Michael Heinzinger
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
| | - Andreas Vilcinskas
- Justus Liebig University of Gießen, Institute for Insect Biotechnology, Heinrich-Buff-Ring 58, 35392, Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Department of Bioresources, Ohlebergsweg 12, 35392, Giessen, Germany
| | - Rosalyn Gloag
- Rosalyn Gloag - School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Brock A Harpur
- Brock A. Harpur - Department of Entomology, Purdue University, 901 W. State Street, West Lafayette, IN, 47907, USA
| | - Lars Podsiadlowski
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Centre of Molecular Biodiversity Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology, i12, Technical University of Munich, Boltzmannstr. 3, Garching, 85748, Munich, Germany
| | - Timothy N W Jackson
- Australian Venom Research Unit, Department of Biochemistry and Pharmacology, University of Melbourne, Grattan Street, Parkville, Viktoria, 3010, Australia
| | | | - Eckart Stolle
- Leibniz Institute for the Analysis of Biodiversity Change, Zoological Research Museum Alexander Koenig, Centre of Molecular Biodiversity Research, Adenauerallee 160, 53113, Bonn, Germany
| | - Björn M von Reumont
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Senckenberganlage 25, 60325, Frankfurt, Germany.
- Faculty of Biological Sciences, Group of Applied Bioinformatics, Goethe University Frankfurt, Max-Von-Laue Str. 13, 60438, Frankfurt, Germany.
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10
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Vertacnik KL, Herrig DK, Godfrey RK, Hill T, Geib SM, Unckless RL, Nelson DR, Linnen CR. Evolution of five environmentally responsive gene families in a pine-feeding sawfly, Neodiprion lecontei (Hymenoptera: Diprionidae). Ecol Evol 2023; 13:e10506. [PMID: 37791292 PMCID: PMC10542623 DOI: 10.1002/ece3.10506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 10/05/2023] Open
Abstract
A central goal in evolutionary biology is to determine the predictability of adaptive genetic changes. Despite many documented cases of convergent evolution at individual loci, little is known about the repeatability of gene family expansions and contractions. To address this void, we examined gene family evolution in the redheaded pine sawfly Neodiprion lecontei, a noneusocial hymenopteran and exemplar of a pine-specialized lineage evolved from angiosperm-feeding ancestors. After assembling and annotating a draft genome, we manually annotated multiple gene families with chemosensory, detoxification, or immunity functions before characterizing their genomic distributions and molecular evolution. We find evidence of recent expansions of bitter gustatory receptor, clan 3 cytochrome P450, olfactory receptor, and antimicrobial peptide subfamilies, with strong evidence of positive selection among paralogs in a clade of gustatory receptors possibly involved in the detection of bitter compounds. In contrast, these gene families had little evidence of recent contraction via pseudogenization. Overall, our results are consistent with the hypothesis that in response to novel selection pressures, gene families that mediate ecological interactions may expand and contract predictably. Testing this hypothesis will require the comparative analysis of high-quality annotation data from phylogenetically and ecologically diverse insect species and functionally diverse gene families. To this end, increasing sampling in under-sampled hymenopteran lineages and environmentally responsive gene families and standardizing manual annotation methods should be prioritized.
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Affiliation(s)
- Kim L. Vertacnik
- Department of EntomologyUniversity of KentuckyLexingtonKentuckyUSA
| | | | - R. Keating Godfrey
- McGuire Center for Lepidoptera and Biodiversity, University of FloridaGainesvilleFloridaUSA
| | - Tom Hill
- National Institute of Allergy and Infectious DiseasesBethesdaMarylandUSA
| | - Scott M. Geib
- Tropical Crop and Commodity Protection Research UnitUnited States Department of Agriculture: Agriculture Research Service Pacific Basin Agricultural Research CenterHiloHawaiiUSA
| | - Robert L. Unckless
- Department of Molecular BiosciencesUniversity of KansasLawrenceKansasUSA
| | - David R. Nelson
- Department of Microbiology, Immunology and BiochemistryUniversity of Tennessee Health Science CenterMemphisTennesseeUSA
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11
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Brůna T, Li H, Guhlin J, Honsel D, Herbold S, Stanke M, Nenasheva N, Ebel M, Gabriel L, Hoff KJ. Galba: genome annotation with miniprot and AUGUSTUS. BMC Bioinformatics 2023; 24:327. [PMID: 37653395 PMCID: PMC10472564 DOI: 10.1186/s12859-023-05449-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
BACKGROUND The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. RESULTS Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein-to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. CONCLUSIONS Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.
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Affiliation(s)
- Tomáš Brůna
- U.S. Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, 02215 MA USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, 02215 MA USA
| | - Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, Dunedin, 9016 New Zealand
| | - Daniel Honsel
- Institute of Computer Science, University of Göttingen, 37077 Göttingen, Germany
| | - Steffen Herbold
- Faculty for Computer Science and Mathematics, University of Passau, 94032 Passau, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Natalia Nenasheva
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Matthis Ebel
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Lars Gabriel
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Katharina J. Hoff
- Institute of Mathematics and Computer Science, and Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
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12
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Okwaro LA, Korb J. Epigenetic regulation and division of labor in social insects. CURRENT OPINION IN INSECT SCIENCE 2023; 58:101051. [PMID: 37164259 DOI: 10.1016/j.cois.2023.101051] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/12/2023]
Abstract
Analogous to multicellular organisms, social insect colonies are characterized by division of labor with queens and workers reflecting germline and soma, respectively. In multicellular organisms, such division is achieved through epigenetic factors regulating cell differentiation during development. Analogously, epigenetic regulation is postulated to regulate caste differences in social insects. We summarize recent findings about the role of epigenetics in social insects, focusing on DNA methylation and histone modifications. We specifically address (i) queen versus worker caste differentiation, (ii) queen versus worker caste differences, and (iii) division of labor among workers. Our review provides an overview of an exciting and controversially discussed field in developmental and molecular biology. It shows that our current understanding about the role of epigenetics in regulating division of labor in social insects is still fragmentary but that refined methods with well-replicated samples and targeted questions offer promising insights into this emerging field of socio-epigenomics.
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Affiliation(s)
- Louis A Okwaro
- University of Freiburg, Evolutionary Biology and Ecology D-79104 Freiburg, Germany
| | - Judith Korb
- University of Freiburg, Evolutionary Biology and Ecology D-79104 Freiburg, Germany.
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13
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Zhu W, Yang C, Liu Q, Peng M, Li Q, Wang H, Chen X, Zhang B, Feng P, Chen T, Zeng D, Zhao Y. Integrated Analysis of DNA Methylome and Transcriptome Reveals Epigenetic Regulation of Cold Tolerance in Litopenaeus vannamei. Int J Mol Sci 2023; 24:11573. [PMID: 37511332 PMCID: PMC10380378 DOI: 10.3390/ijms241411573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
DNA methylation is an important epigenetic modification that has been shown to be associated with responses to non-biological stressors. However, there is currently no research on DNA methylation in response to environmental signals in shrimp. In this study, we conducted a comprehensive comparative analysis of DNA methylation profiles and differentially expressed genes between two strains of Litopenaeus vannamei with significantly different cold tolerance through whole genome bisulfite sequencing (WGBS) and transcriptome sequencing. Between Lv-C and Lv-T (constant temperature of 28 °C and low temperatures of 18 °C and 10 °C) under cytosine-guanine (CG) environments, 39,100 differentially methylated regions (DMRs) were identified, corresponding to 9302 DMR-related genes (DMRGs). The DMRs were mainly located in the gene body (exons and introns). Gene Ontology (GO) analysis showed that these DMRGs were significantly enriched in cell parts, catalytic activity, and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed significant enrichment of these DMRGs in pathways such as proteasome (ko03050), oxidative phosphorylation (ko00190), mTOR signaling pathway (ko04150), fatty acid metabolism (ko01212), and fatty acid degradation (ko00071). The comprehensive results suggested that L. vannamei mainly regulates gene expression in response to low temperatures through hypermethylation or demethylation of some genes involved in thermogenesis, glycolysis, the autophagy pathway, the peroxisome, and drug metabolism pathways. These results provide important clues for studying DNA methylation patterns and identifying cold tolerance genes in shrimp.
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Affiliation(s)
- Weilin Zhu
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Chunling Yang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qingyun Liu
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Min Peng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Qiangyong Li
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Huanling Wang
- Key Lab of Freshwater Animal Breeding, Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education, College of Fishery Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Bin Zhang
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Pengfei Feng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Tiancong Chen
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Digang Zeng
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
| | - Yongzhen Zhao
- Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Guangxi Academy of Fishery Sciences, Nanning 530021, China
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14
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Toga K, Bono H. Meta-Analysis of Public RNA Sequencing Data Revealed Potential Key Genes Associated with Reproductive Division of Labor in Social Hymenoptera and Termites. Int J Mol Sci 2023; 24:ijms24098353. [PMID: 37176060 PMCID: PMC10179490 DOI: 10.3390/ijms24098353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Eusociality in insects has evolved independently many times. One of the most notable characteristics of eusociality is the reproductive division of labor. In social insects, the reproductive division of labor is accomplished by queens and workers. Transcriptome analyses of queens and workers have been conducted for various eusocial species. However, the genes that regulate the reproductive division of labor across all or multiple eusocial species have not yet been fully elucidated. Therefore, we conducted a meta-analysis using publicly available RNA-sequencing data from four major groups of social insects. In this meta-analysis, we collected 258 pairs (queen vs. worker) of RNA-sequencing data from 34 eusocial species. The meta-analysis identified a total of 20 genes that were differentially expressed in queens or workers. Out of these, 12 genes have not previously been reported to be involved in the reproductive division of labor. Functional annotation of these 20 genes in other organisms revealed that they could be regulators of behaviors and physiological states related to the reproductive division of labor. These 20 genes, revealed using massive datasets of numerous eusocial insects, may be key regulators of the reproductive division of labor.
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Affiliation(s)
- Kouhei Toga
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
| | - Hidemasa Bono
- Laboratory of BioDX, PtBio Co-Creation Research Center, Genome Editing Innovation Center, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
- Laboratory of Genome Informatics, Graduate School of Integrated Sciences for Life, Hiroshima University, 3-10-23 Kagamiyama, Higashi-Hiroshima City 739-0046, Hiroshima, Japan
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15
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Favreau E, Cini A, Taylor D, Câmara Ferreira F, Bentley MA, Cappa F, Cervo R, Privman E, Schneider J, Thiéry D, Mashoodh R, Wyatt CDR, Brown RL, Bodrug-Schepers A, Stralis-Pavese N, Dohm JC, Mead D, Himmelbauer H, Guigo R, Sumner S. Putting hornets on the genomic map. Sci Rep 2023; 13:6232. [PMID: 37085574 PMCID: PMC10121689 DOI: 10.1038/s41598-023-31932-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 03/20/2023] [Indexed: 04/23/2023] Open
Abstract
Hornets are the largest of the social wasps, and are important regulators of insect populations in their native ranges. Hornets are also very successful as invasive species, with often devastating economic, ecological and societal effects. Understanding why these wasps are such successful invaders is critical to managing future introductions and minimising impact on native biodiversity. Critical to the management toolkit is a comprehensive genomic resource for these insects. Here we provide the annotated genomes for two hornets, Vespa crabro and Vespa velutina. We compare their genomes with those of other social Hymenoptera, including the northern giant hornet Vespa mandarinia. The three hornet genomes show evidence of selection pressure on genes associated with reproduction, which might facilitate the transition into invasive ranges. Vespa crabro has experienced positive selection on the highest number of genes, including those putatively associated with molecular binding and olfactory systems. Caste-specific brain transcriptomic analysis also revealed 133 differentially expressed genes, some of which are associated with olfactory functions. This report provides a spring-board for advancing our understanding of the evolution and ecology of hornets, and opens up opportunities for using molecular methods in the future management of both native and invasive populations of these over-looked insects.
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Affiliation(s)
- Emeline Favreau
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
| | - Alessandro Cini
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
- Department of Biology, Università di Pisa, Via Volta 6, 56126, Pisa, Italy
| | - Daisy Taylor
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | | | - Michael A Bentley
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Federico Cappa
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Rita Cervo
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Abba Hushi 199, 3498838, Haifa, Israel
| | - Jadesada Schneider
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Denis Thiéry
- INRAe, UMR 1065 Santé et Agroécologie du Vignoble, Bordeaux Sciences Agro, ISVV, Université de Bordeaux, 33883, Villenave d'Ornon, France
| | - Rahia Mashoodh
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christopher D R Wyatt
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Robert L Brown
- Manaaki Whenua - Landcare Research, 54 Gerald Street, Lincoln, 7608, New Zealand
| | - Alexandrina Bodrug-Schepers
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Nancy Stralis-Pavese
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Juliane C Dohm
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Daniel Mead
- Tree of Life Programme, Wellcome Sanger Institute, Hinxton, CB10 1SA, UK
| | - Heinz Himmelbauer
- Department of Biotechnology, Institute of Computational Biology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Roderic Guigo
- Centre for Genomic Regulation, Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Seirian Sumner
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK.
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16
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Ivasyk I, Olivos-Cisneros L, Valdés-Rodríguez S, Droual M, Jang H, Schmitz RJ, Kronauer DJC. DNMT1 mutant ants develop normally but have disrupted oogenesis. Nat Commun 2023; 14:2201. [PMID: 37072475 PMCID: PMC10113331 DOI: 10.1038/s41467-023-37945-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 04/06/2023] [Indexed: 04/20/2023] Open
Abstract
Although DNA methylation is an important gene regulatory mechanism in mammals, its function in arthropods remains poorly understood. Studies in eusocial insects have argued for its role in caste development by regulating gene expression and splicing. However, such findings are not always consistent across studies, and have therefore remained controversial. Here we use CRISPR/Cas9 to mutate the maintenance DNA methyltransferase DNMT1 in the clonal raider ant, Ooceraea biroi. Mutants have greatly reduced DNA methylation, but no obvious developmental phenotypes, demonstrating that, unlike mammals, ants can undergo normal development without DNMT1 or DNA methylation. Additionally, we find no evidence of DNA methylation regulating caste development. However, mutants are sterile, whereas in wild-type ants, DNMT1 is localized to the ovaries and maternally provisioned into nascent oocytes. This supports the idea that DNMT1 plays a crucial but unknown role in the insect germline.
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Affiliation(s)
- Iryna Ivasyk
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
| | | | - Stephany Valdés-Rodríguez
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
- Howard Hughes Medical Institute, New York, NY, USA
| | - Marie Droual
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA
| | - Hosung Jang
- Department of Genetics, University of Georgia, Athens, GA, USA
| | | | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, New York, NY, USA.
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17
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Brůna T, Li H, Guhlin J, Honsel D, Herbold S, Stanke M, Nenasheva N, Ebel M, Gabriel L, Hoff KJ. GALBA: Genome Annotation with Miniprot and AUGUSTUS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.10.536199. [PMID: 37090650 PMCID: PMC10120627 DOI: 10.1101/2023.04.10.536199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
The Earth Biogenome Project has rapidly increased the number of available eukaryotic genomes, but most released genomes continue to lack annotation of protein-coding genes. In addition, no transcriptome data is available for some genomes. Various gene annotation tools have been developed but each has its limitations. Here, we introduce GALBA, a fully automated pipeline that utilizes miniprot, a rapid protein- to-genome aligner, in combination with AUGUSTUS to predict genes with high accuracy. Accuracy results indicate that GALBA is particularly strong in the annotation of large vertebrate genomes. We also present use cases in insects, vertebrates, and a previously unannotated land plant. GALBA is fully open source and available as a docker image for easy execution with Singularity in high-performance computing environments. Our pipeline addresses the critical need for accurate gene annotation in newly sequenced genomes, and we believe that GALBA will greatly facilitate genome annotation for diverse organisms.
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Affiliation(s)
- Tomáš Brůna
- US Department of Energy Joint Genome Institute, Berkeley, CA 94720, USA
| | - Heng Li
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA & Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Joseph Guhlin
- Genomics Aotearoa and Laboratory for Evolution and Development, Department of Biochemistry, University of Otago, PO Box 56, Dunedin 9016, New Zealand
| | - Daniel Honsel
- Institute of Computer Science, University of Göttingen, 37077 Göttingen, Germany
| | - Steffen Herbold
- Faculty for Computer Science and Mathematics, University of Passau, 94032 Passau, Germany
| | - Mario Stanke
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Natalia Nenasheva
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Matthis Ebel
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Lars Gabriel
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
| | - Katharina J. Hoff
- Institute of Mathematics and Computer Science & Center for Functional Genomics of Microbes, University of Greifswald, 17489 Greifswald, Germany
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18
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Sumner S, Favreau E, Geist K, Toth AL, Rehan SM. Molecular patterns and processes in evolving sociality: lessons from insects. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220076. [PMID: 36802779 PMCID: PMC9939270 DOI: 10.1098/rstb.2022.0076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/16/2022] [Indexed: 02/21/2023] Open
Abstract
Social insects have provided some of the clearest insights into the origins and evolution of collective behaviour. Over 20 years ago, Maynard Smith and Szathmáry defined the most complex form of insect social behaviour-superorganismality-among the eight major transitions in evolution that explain the emergence of biological complexity. However, the mechanistic processes underlying the transition from solitary life to superorganismal living in insects remain rather elusive. An overlooked question is whether this major transition arose via incremental or step-wise modes of evolution. We suggest that examination of the molecular processes underpinning different levels of social complexity represented across the major transition from solitary to complex sociality can help address this question. We present a framework for using molecular data to assess to what extent the mechanistic processes that take place in the major transition to complex sociality and superorganismality involve nonlinear (implying step-wise evolution) or linear (implying incremental evolution) changes in the underlying molecular mechanisms. We assess the evidence for these two modes using data from social insects and discuss how this framework can be used to test the generality of molecular patterns and processes across other major transitions. This article is part of a discussion meeting issue 'Collective behaviour through time'.
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Affiliation(s)
- Seirian Sumner
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Emeline Favreau
- Centre for Biodiversity and Environmental Research, Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Katherine Geist
- Department of Ecology, Evolution and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Amy L. Toth
- Department of Ecology, Evolution and Organismal Biology, and Department of Entomology, Iowa State University, Ames, IA 50011, USA
| | - Sandra M. Rehan
- Department of Biology, York University, Toronto, Canada M3J 1P3
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19
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Marshall H, Nicholas MT, van Zweden JS, Wäckers F, Ross L, Wenseleers T, Mallon EB. DNA methylation is associated with codon degeneracy in a species of bumblebee. Heredity (Edinb) 2023; 130:188-195. [PMID: 36658299 PMCID: PMC10076500 DOI: 10.1038/s41437-023-00591-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Social insects display extreme phenotypic differences between sexes and castes even though the underlying genome can be almost identical. Epigenetic processes have been proposed as a possible mechanism for mediating these phenotypic differences. Using whole genome bisulfite sequencing of queens, males, and reproductive female workers we have characterised the sex- and caste-specific methylome of the bumblebee Bombus terrestris. We have identified a potential role for DNA methylation in histone modification processes which may influence sex and caste phenotypic differences. We also find differentially methylated genes generally show low levels of DNA methylation which may suggest a separate function for lowly methylated genes in mediating transcriptional plasticity, unlike highly methylated genes which are usually involved in housekeeping functions. We also examined the relationship between the underlying genome and the methylome using whole genome re-sequencing of the same queens and males. We find DNA methylation is enriched at zero-fold degenerate sites. We suggest DNA methylation may be acting as a targeted mutagen at these sites, providing substrate for selection via non-synonymous changes in the underlying genome. However, we did not see any relationship between DNA methylation and rates of positive selection in our samples. In order to fully assess a possible role for DNA methylation in adaptive processes a specifically designed study using natural population data is needed.
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Affiliation(s)
- H Marshall
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK.
| | - M T Nicholas
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK
| | - J S van Zweden
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - F Wäckers
- Biobest Belgium N.V., Westerlo, Belgium
- The Lancaster Environmental Centre, University of Lancaster, Lancaster, UK
| | - L Ross
- The Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - T Wenseleers
- Laboratory of Socioecology and Social Evolution, Department of Biology, KU Leuven, Leuven, Belgium
| | - E B Mallon
- Department of Genetics and Genome Biology, The University of Leicester, Leicester, UK.
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20
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Wyatt CDR, Bentley MA, Taylor D, Favreau E, Brock RE, Taylor BA, Bell E, Leadbeater E, Sumner S. Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps. Nat Commun 2023; 14:1046. [PMID: 36828829 PMCID: PMC9958023 DOI: 10.1038/s41467-023-36456-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/31/2023] [Indexed: 02/26/2023] Open
Abstract
A key mechanistic hypothesis for the evolution of division of labour in social insects is that a shared set of genes co-opted from a common solitary ancestral ground plan (a genetic toolkit for sociality) regulates caste differentiation across levels of social complexity. Using brain transcriptome data from nine species of vespid wasps, we test for overlap in differentially expressed caste genes and use machine learning models to predict castes using different gene sets. We find evidence of a shared genetic toolkit across species representing different levels of social complexity. We also find evidence of additional fine-scale differences in predictive gene sets, functional enrichment and rates of gene evolution that are related to level of social complexity, lineage and of colony founding. These results suggest that the concept of a shared genetic toolkit for sociality may be too simplistic to fully describe the process of the major transition to sociality.
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Affiliation(s)
- Christopher Douglas Robert Wyatt
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK.
| | - Michael Andrew Bentley
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Daisy Taylor
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Emeline Favreau
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Ryan Edward Brock
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich, Norfolk, NR4 7UH, UK
| | - Benjamin Aaron Taylor
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Emily Bell
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Ellouise Leadbeater
- Department of Biological Sciences, Royal Holloway University of London, Egham, TW20 0EX, UK
| | - Seirian Sumner
- Centre for Biodiversity and Environment Research, Dept Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK.
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21
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Favreau E, Geist KS, Wyatt CDR, Toth AL, Sumner S, Rehan SM. Co-expression Gene Networks and Machine-learning Algorithms Unveil a Core Genetic Toolkit for Reproductive Division of Labour in Rudimentary Insect Societies. Genome Biol Evol 2022; 15:6926469. [PMID: 36527688 PMCID: PMC9830183 DOI: 10.1093/gbe/evac174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
The evolution of eusociality requires that individuals forgo some or all their own reproduction to assist the reproduction of others in their group, such as a primary egg-laying queen. A major open question is how genes and genetic pathways sculpt the evolution of eusociality, especially in rudimentary forms of sociality-those with smaller cooperative nests when compared with species such as honeybees that possess large societies. We lack comprehensive comparative studies examining shared patterns and processes across multiple social lineages. Here we examine the mechanisms of molecular convergence across two lineages of bees and wasps exhibiting such rudimentary societies. These societies consist of few individuals and their life histories range from facultative to obligately social. Using six species across four independent origins of sociality, we conduct a comparative meta-analysis of publicly available transcriptomes. Standard methods detected little similarity in patterns of differential gene expression in brain transcriptomes among reproductive and non-reproductive individuals across species. By contrast, both supervised machine learning and consensus co-expression network approaches uncovered sets of genes with conserved expression patterns among reproductive and non-reproductive phenotypes across species. These sets overlap substantially, and may comprise a shared genetic "toolkit" for sociality across the distantly related taxa of bees and wasps and independently evolved lineages of sociality. We also found many lineage-specific genes and co-expression modules associated with social phenotypes and possible signatures of shared life-history traits. These results reveal how taxon-specific molecular mechanisms complement a core toolkit of molecular processes in sculpting traits related to the evolution of eusociality.
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Affiliation(s)
| | | | - Christopher D R Wyatt
- Department of Genetics, Environment, Evolution, University College London, London WC1E 6BT, United Kingdom
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22
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Renard T, Gueydan C, Aron S. DNA methylation and expression of the egfr gene are associated with worker size in monomorphic ants. Sci Rep 2022; 12:21228. [PMID: 36481802 PMCID: PMC9732050 DOI: 10.1038/s41598-022-25675-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022] Open
Abstract
The reproductive division of labour is a hallmark of eusocial Hymenoptera. Females are either reproductive queens or non-reproductive workers. In ants, workers often display further task specialisation that is associated with variation in size and/or morphology. Because female polyphenism is typically under environmental control, it is thought epigenetic mechanisms (such as DNA methylation) play a central role since they mediate gene-by-environment interactions. Methylation of the growth-promoting gene epidermal growth factor receptor (egfr) was indeed shown to control worker size in a highly polymorphic ant. However, it remains unknown if egfr methylation could also regulate worker size in monomorphic species. By combining experimental pharmacology and molecular biology, we show that worker size is associated with egfr methylation in two monomorphic ants. Furthermore, we functionally demonstrate that EGFR signalling affects worker size. These results indicate that worker size regulation by egfr methylation has been mechanistically conserved in ants but remains unexploited in monomorphic species.
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Affiliation(s)
- Thibaut Renard
- grid.4989.c0000 0001 2348 0746Evolutionary Biology and Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt, 50, 1050 Brussels, Belgium
| | - Cyril Gueydan
- grid.4989.c0000 0001 2348 0746Molecular Biology of the Gene, Université Libre de Bruxelles, Rue Prof. Jeener et Brachet, 12, 6041 Gosselies, Belgium
| | - Serge Aron
- grid.4989.c0000 0001 2348 0746Evolutionary Biology and Ecology, Université Libre de Bruxelles, Avenue F.D. Roosevelt, 50, 1050 Brussels, Belgium
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23
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Patalano S, Alsina A, Gregorio-Rodríguez C, Bachman M, Dreier S, Hernando-Herraez I, Nana P, Balasubramanian S, Sumner S, Reik W, Rulands S. Self-organization of plasticity and specialization in a primitively social insect. Cell Syst 2022; 13:768-779.e4. [PMID: 36044898 PMCID: PMC9512265 DOI: 10.1016/j.cels.2022.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 04/10/2022] [Accepted: 08/05/2022] [Indexed: 01/26/2023]
Abstract
Biological systems have the capacity to not only build and robustly maintain complex structures but also to rapidly break up and rebuild such structures. Here, using primitive societies of Polistes wasps, we show that both robust specialization and rapid plasticity are emergent properties of multi-scale dynamics. We combine theory with experiments that, after perturbing the social structure by removing the queen, correlate time-resolved multi-omics with video recordings. We show that the queen-worker dimorphism relies on the balance between the development of a molecular queen phenotype in all insects and colony-scale inhibition of this phenotype via asymmetric interactions. This allows Polistes to be stable against intrinsic perturbations of molecular states while reacting plastically to extrinsic cues affecting the whole society. Long-term stability of the social structure is reinforced by dynamic DNA methylation. Our study provides a general principle of how both specialization and plasticity can be achieved in biological systems. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Solenn Patalano
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK.
| | - Adolfo Alsina
- Max Planck Institute for the Physics of Complex Systems, Noethnitzer Str. 38, 01187 Dresden, Germany
| | - Carlos Gregorio-Rodríguez
- Departamento de Sistemas Informáticos y Computación, Universidad Complutense de Madrid, Plaza de Ciencias, 3, 28040 Madrid, Spain
| | - Martin Bachman
- Discovery Science and Technology, Medicines Discovery Catapult, Alderley Park, Cheshire SK10 4GT, UK; Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 ORE, UK; Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Stephanie Dreier
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | | | - Paulin Nana
- Faculty of Agronomy and Agricultural Sciences, School of Wood, Water and Natural Resources, University of Dschang, Ebolowa Campus, P.O. Box 786, Ebolowa, Cameroon
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge CB2 ORE, UK; Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK; School of Clinical Medicine, University of Cambridge, CB2 0SP, Cambridge, UK
| | - Seirian Sumner
- Centre for Biodiversity and Environment Research, Department of Genetics Evolution and Environment, Division of Biosciences, University College London, Gower Street, London WC1E 6BT, UK
| | - Wolf Reik
- Epigenetics Programme, 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.
| | - Steffen Rulands
- Max Planck Institute for the Physics of Complex Systems, Noethnitzer Str. 38, 01187 Dresden, Germany; Center for Systems Biology Dresden, Pfotenhauer Str. 108, 01307 Dresden, Germany.
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24
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Differential Gene Expression Correlates with Behavioural Polymorphism during Collective Behaviour in Cockroaches. Animals (Basel) 2022; 12:ani12182354. [PMID: 36139214 PMCID: PMC9495117 DOI: 10.3390/ani12182354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary It is currently well accepted that animals differ from one another in their behaviour and tendency to perform actions, a property we refer to as animal personality. In group-living animals, variation in animal personality can be important to determine group survival, as it determines how individuals interact with each other and with their environment. However, we have little knowledge of the proximal mechanisms underlying personality, particularly in group-living organisms. Here, we investigate the relationship between gene expression and two behavioural types (bold and shy) in a gregarious species: the American cockroach. Our results show that bold individuals have upregulated genes with functions associated with sensory activity (phototaxis and odour detection) and aggressive/dominant behaviour, and suggest that social context can modulate gene expression related to bold/shy characteristics. This work could help identify genes important in the earliest stages of group living and social life, and provides a first step toward establishing cockroaches as a focal group for the study of the evolution of sociality. Abstract Consistent inter-individual variation in the propensity to perform different tasks (animal personality) can contribute significantly to the success of group-living organisms. The distribution of different personalities in a group influences collective actions and therefore how these organisms interact with their environment. However, we have little understanding of the proximate mechanisms underlying animal personality in animal groups, and research on this theme has often been biased towards organisms with advanced social systems. The goal of this study is to investigate the mechanistic basis for personality variation during collective behaviour in a species with rudimentary societies: the American cockroach. We thus use an approach which combines experimental classification of individuals into behavioural phenotypes (‘bold’ and ‘shy’ individuals) with comparative gene expression. Our analyses reveal differences in gene expression between behavioural phenotypes and suggest that social context may modulate gene expression related to bold/shy characteristics. We also discuss how cockroaches could be a valuable model for the study of genetic mechanisms underlying the early steps in the evolution of social behaviour and social complexity. This study provides a first step towards a better understanding of the molecular mechanisms associated with differences in boldness and behavioural plasticity in these organisms.
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25
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Ramasamy D, Rao AKDM, Rajkumar T, Mani S. Experimental and Computational Approaches for Non-CpG Methylation Analysis. EPIGENOMES 2022; 6:epigenomes6030024. [PMID: 35997370 PMCID: PMC9397002 DOI: 10.3390/epigenomes6030024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
Cytosine methylation adjacent to adenine, thymine, and cytosine residues but not guanine of the DNA is distinctively known as non-CpG methylation. This CA/CT/CC methylation accounts for 15% of the total cytosine methylation and varies among different cell and tissue types. The abundance of CpG methylation has largely concealed the role of non-CpG methylation. Limitations in the early detection methods could not distinguish CpG methylation from non-CpG methylation. Recent advancements in enrichment strategies and high throughput sequencing technologies have enabled the detection of non-CpG methylation. This review discusses the advanced experimental and computational approaches to detect and describe the genomic distribution and function of non-CpG methylation. We present different approaches such as enzyme-based and antibody-based enrichment, which, when coupled, can also improve the sensitivity and specificity of non-CpG detection. We also describe the current bioinformatics pipelines and their specific application in computing and visualizing the imbalance of CpG and non-CpG methylation. Enrichment modes and the computational suites need to be further developed to ease the challenges of understanding the functional role of non-CpG methylation.
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Affiliation(s)
| | | | | | - Samson Mani
- Correspondence: ; Tel.: +91-44-22350131 (ext. 196)
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26
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Miller SE, Legan AW, Uy FMK, Sheehan MJ. Highly contiguous genome assemblies of the Guinea paper wasp (Polistes exclamans) and Mischocyttarus mexicanus. Genome Biol Evol 2022; 14:6649880. [PMID: 35880292 PMCID: PMC9346566 DOI: 10.1093/gbe/evac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2022] [Indexed: 12/01/2022] Open
Abstract
Paper wasps are a model system for the study of social evolution due to a high degree of inter- and intraspecific variation in cooperation, aggression, and visual signals of social status. Increasing the taxonomic coverage of genomic resources for this diverse clade will aid comparative genomic approaches for testing predictions about the molecular basis of social evolution. Here, we provide draft genome assemblies for two well-studied species of paper wasps, Polistes exclamans and Mischocyttarus mexicanus. The P. exclamans genome assembly is 221.5 Mb in length with a scaffold N50 of 4.11 Mb. The M. mexicanus genome assembly is 227 Mb in length with a scaffold N50 of 1.1 Mb. Genomes have low repeat content (9.54–10.75%) and low GC content (32.06–32.4%), typical of other social hymenopteran genomes. The DNA methyltransferase gene, Dnmt3 , was lost early in the evolution of Polistinae. We identified a second independent loss of Dnmt3 within hornets (genus: Vespa).
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Affiliation(s)
- Sara E Miller
- Cornell University, Department of Neurobiology and Behavior, Ithaca, NY, USA
| | - Andrew W Legan
- Cornell University, Department of Neurobiology and Behavior, Ithaca, NY, USA
| | - Floria M K Uy
- University of Rochester, Department of Biology, Rochester, NY, USA
| | - Michael J Sheehan
- Cornell University, Department of Neurobiology and Behavior, Ithaca, NY, USA
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27
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Harrison MC, Dohmen E, George S, Sillam-Dussès D, Séité S, Vasseur-Cognet M. Complex regulatory role of DNA methylation in caste- and age-specific expression of a termite. Open Biol 2022; 12:220047. [PMID: 35857972 PMCID: PMC9256085 DOI: 10.1098/rsob.220047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The reproductive castes of eusocial insects are often characterized by extreme lifespans and reproductive output, indicating an absence of the fecundity/longevity trade-off. The role of DNA methylation in the regulation of caste- and age-specific gene expression in eusocial insects is controversial. While some studies find a clear link to caste formation in honeybees and ants, others find no correlation when replication is increased across independent colonies. Although recent studies have identified transcription patterns involved in the maintenance of high reproduction throughout the long lives of queens, the role of DNA methylation in the regulation of these genes is unknown. We carried out a comparative analysis of DNA methylation in the regulation of caste-specific transcription and its importance for the regulation of fertility and longevity in queens of the higher termite Macrotermes natalensis. We found evidence for significant, well-regulated changes in DNA methylation in mature compared to young queens, especially in several genes related to ageing and fecundity in mature queens. We also found a strong link between methylation and caste-specific alternative splicing. This study reveals a complex regulatory role of fat body DNA methylation both in the division of labour in termites, and during the reproductive maturation of queens.
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Affiliation(s)
- Mark C. Harrison
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Elias Dohmen
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | | | - David Sillam-Dussès
- University Sorbonne Paris Nord, Laboratory of Experimental and Comparative Ethology (LEEC), UR4443, Villetaneuse, France
| | - Sarah Séité
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRAE 1392, Institute of Ecology and Environmental Sciences of Paris, Paris 7 113, Bondy, France,University of Paris-Est, Créteil, France
| | - Mireille Vasseur-Cognet
- UMR IRD 242, UPEC, CNRS 7618, UPMC 113, INRAE 1392, Institute of Ecology and Environmental Sciences of Paris, Paris 7 113, Bondy, France,University of Paris-Est, Créteil, France,INSERM, Paris, France
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28
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Nakajima Y, Ogura A. Genomics and effective trait candidates of edible insects. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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29
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Falk S, Broad GR. The genome sequence of the tree wasp, Dolichovespula sylvestris Scopoli, 1763. Wellcome Open Res 2022; 7:113. [PMID: 36451628 PMCID: PMC9672531 DOI: 10.12688/wellcomeopenres.17783.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/01/2023] Open
Abstract
We present a genome assembly from an individual male Dolichovespula sylvestris (the tree wasp; Arthropoda; Insecta; Hymenoptera; Vespidae). The genome sequence is 233 megabases in span. The majority of the assembly (95.56%) is scaffolded into 26 chromosomal pseudomolecules. The mitochondrial genome was also assembled and is 21.3 kilobases in length.
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Affiliation(s)
- Steven Falk
- Independent Researcher, Kenilworth, Warwickshire, UK
| | | | | | | | | | - Gavin R. Broad
- Department of Life Sciences, Natural History Museum, London, UK
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30
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Kin selection for cooperation in natural bacterial populations. Proc Natl Acad Sci U S A 2022; 119:2119070119. [PMID: 35193981 PMCID: PMC8892524 DOI: 10.1073/pnas.2119070119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 01/03/2023] Open
Abstract
Bacteria secrete many molecules outside the cell, where they provide benefits to other cells. One potential reason for producing these “public goods” is that they benefit closely related cells that share the gene for cooperation (kin selection). While many laboratory studies have supported this hypothesis, there is a lack of evidence that kin selection favors cooperation in natural populations. We examined bacterial genomes from the environment and used population genetics theory to analyze the DNA sequences. Our analyses suggest that public goods cooperation has indeed been favored by kin selection in natural populations. Bacteria produce a range of molecules that are secreted from the cell and can provide a benefit to the local population of cells. Laboratory experiments have suggested that these “public goods” molecules represent a form of cooperation, favored because they benefit closely related cells (kin selection). However, there is a relative lack of data demonstrating kin selection for cooperation in natural populations of bacteria. We used molecular population genetics to test for signatures of kin selection at the genomic level in natural populations of the opportunistic pathogen Pseudomonas aeruginosa. We found consistent evidence from multiple traits that genes controlling putatively cooperative traits have higher polymorphism and greater divergence and are more likely to harbor deleterious mutations relative to genes controlling putatively private traits, which are expressed at similar rates. These patterns suggest that cooperative traits are controlled by kin selection, and we estimate that the relatedness for social interactions in P. aeruginosa is r = 0.84. More generally, our results demonstrate how molecular population genetics can be used to study the evolution of cooperation in natural populations.
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31
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Santos PKF, Galbraith DA, Starkey J, Amsalem E. The effect of the brood and the queen on early gene expression in bumble bee workers' brains. Sci Rep 2022; 12:3018. [PMID: 35194064 PMCID: PMC8863840 DOI: 10.1038/s41598-022-06715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Accepted: 02/04/2022] [Indexed: 11/12/2022] Open
Abstract
Worker reproduction in social insects is often regulated by the queen, but can be regulated by the brood and nestmates, who may use different mechanisms to induce the same outcomes in subordinates. Analysis of brain gene expression patterns in bumble bee workers (Bombus impatiens) in response to the presence of the queen, the brood, both or neither, identified 18 differentially expressed genes, 17 of them are regulated by the queen and none are regulated by the brood. Overall, brain gene expression differences in workers were driven by the queen’s presence, despite recent studies showing that brood reduces worker egg laying and provides context to the queen pheromones. The queen affected important regulators of reproduction and brood care across insects, such as neuroparsin and vitellogenin, and a comparison with similar datasets in the honey bee and the clonal raider ant revealed that neuroparsin is differentially expressed in all species. These data emphasize the prominent role of the queen in regulating worker physiology and behavior. Genes that serve as key regulators of workers’ reproduction are likely to play an important role in the evolution of sociality.
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Affiliation(s)
- Priscila K F Santos
- Department of Entomology, Center for Chemical Ecology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA.
| | - David A Galbraith
- Department of Entomology, Center for Chemical Ecology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Jesse Starkey
- Department of Entomology, Center for Chemical Ecology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
| | - Etya Amsalem
- Department of Entomology, Center for Chemical Ecology, Center for Pollinator Research, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, 16802, USA
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32
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Phenotypic Plasticity: What Has DNA Methylation Got to Do with It? INSECTS 2022; 13:insects13020110. [PMID: 35206684 PMCID: PMC8878681 DOI: 10.3390/insects13020110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 12/14/2022]
Abstract
How does one genome give rise to multiple, often markedly different, phenotypes in response to an environmental cue? This phenomenon, known as phenotypic plasticity, is common amongst plants and animals, but arguably the most striking examples are seen in insects. Well-known insect examples include seasonal morphs of butterfly wing patterns, sexual and asexual reproduction in aphids, and queen and worker castes of eusocial insects. Ultimately, we need to understand how phenotypic plasticity works at a mechanistic level; how do environmental signals alter gene expression, and how are changes in gene expression translated into novel morphology, physiology and behaviour? Understanding how plasticity works is of major interest in evolutionary-developmental biology and may have implications for understanding how insects respond to global change. It has been proposed that epigenetic mechanisms, specifically DNA methylation, are the key link between environmental cues and changes in gene expression. Here, we review the available evidence on the function of DNA methylation of insects, the possible role(s) for DNA methylation in phenotypic plasticity and also highlight key outstanding questions in this field as well as new experimental approaches to address these questions.
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33
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Genomic and transcriptomic analyses of the subterranean termite Reticulitermes speratus: Gene duplication facilitates social evolution. Proc Natl Acad Sci U S A 2022; 119:2110361119. [PMID: 35042774 PMCID: PMC8785959 DOI: 10.1073/pnas.2110361119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
Gene duplication is a major source of evolutionary innovation and is associated with the increases in biological complexity and adaptive radiation. Termites are model social organisms characterized by a sophisticated caste system. We analyzed the genome of the Japanese subterranean termite, an ecologically and economically important insect acting as a destructive pest. The analyses revealed the significance of gene duplication in social evolution. Gene duplication associated with caste-biased gene expression was prevalent in the termite genome. Many of the duplicated genes were related to social functions, such as chemical communication, social immunity, and defense, and they were often expressed in caste-specific organs. We propose that gene duplication facilitates social evolution through regulatory diversification leading to caste-biased expression and functional specialization. Termites are model social organisms characterized by a polyphenic caste system. Subterranean termites (Rhinotermitidae) are ecologically and economically important species, including acting as destructive pests. Rhinotermitidae occupies an important evolutionary position within the clade representing a transitional taxon between the higher (Termitidae) and lower (other families) termites. Here, we report the genome, transcriptome, and methylome of the Japanese subterranean termite Reticulitermes speratus. Our analyses highlight the significance of gene duplication in social evolution in this termite. Gene duplication associated with caste-biased gene expression was prevalent in the R. speratus genome. The duplicated genes comprised diverse categories related to social functions, including lipocalins (chemical communication), cellulases (wood digestion and social interaction), lysozymes (social immunity), geranylgeranyl diphosphate synthase (social defense), and a novel class of termite lineage–specific genes with unknown functions. Paralogous genes were often observed in tandem in the genome, but their expression patterns were highly variable, exhibiting caste biases. Some of the assayed duplicated genes were expressed in caste-specific organs, such as the accessory glands of the queen ovary and the frontal glands of soldier heads. We propose that gene duplication facilitates social evolution through regulatory diversification, leading to caste-biased expression and subfunctionalization and/or neofunctionalization conferring caste-specialized functions.
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Nasrullah, Hussain A, Ahmed S, Rasool M, Shah AJ. DNA methylation across the tree of life, from micro to macro-organism. Bioengineered 2022; 13:1666-1685. [PMID: 34986742 PMCID: PMC8805842 DOI: 10.1080/21655979.2021.2014387] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
DNA methylation is a process in which methyl (CH3) groups are added to the DNA molecule. The DNA segment does not change in the sequence, but DNA methylation could alter the action of DNA. Different enzymes like DNA methyltransferases (DNMTs) take part in methylation of cytosine/adenine nucleosides in DNA. In prokaryotes, DNA methylation is performed to prevent the attack of phage and also plays a role in the chromosome replication and repair. In fungi, DNA methylation is studied to see the transcriptional changes, as in insects, the DNA methylation is not that well-known, it plays a different role like other organisms. In mammals, the DNA methylation is related to different types of cancers and plays the most important role in the placental development and abnormal DNA methylation connected with diseases like cancer, autoimmune diseases, and rheumatoid arthritis.
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Affiliation(s)
- Nasrullah
- Center for Advanced Studies in Vaccinology & Biotechnology (Casvab), University of Baluchistan, Quetta- Pakistan. E-mails:
| | - Abrar Hussain
- Department of Biotechnology, Faculty of Life Sciences, Buitems, Quetta-Pakistan. E-mails:
| | - Sagheer Ahmed
- Department of Basic Medical Sciences, Shifa College of Pharmaceutical Sciences, Shifa Tameer-e-Millat University, Islamabad, Pakistan. E-mails:
| | - Mahmood Rasool
- Center of Excellence in Genomic Medicine Research, Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia. E-mails:
| | - Abdul Jabbar Shah
- Department of Pharmaceutical Sciences, Comsats University, Abbottabad. E-mails:
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35
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Shields EJ, Sorida M, Sheng L, Sieriebriennikov B, Ding L, Bonasio R. Genome annotation with long RNA reads reveals new patterns of gene expression and improves single-cell analyses in an ant brain. BMC Biol 2021; 19:254. [PMID: 34838024 PMCID: PMC8626913 DOI: 10.1186/s12915-021-01188-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 11/10/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Functional genomic analyses rely on high-quality genome assemblies and annotations. Highly contiguous genome assemblies have become available for a variety of species, but accurate and complete annotation of gene models, inclusive of alternative splice isoforms and transcription start and termination sites, remains difficult with traditional approaches. RESULTS Here, we utilized full-length isoform sequencing (Iso-Seq), a long-read RNA sequencing technology, to obtain a comprehensive annotation of the transcriptome of the ant Harpegnathos saltator. The improved genome annotations include additional splice isoforms and extended 3' untranslated regions for more than 4000 genes. Reanalysis of RNA-seq experiments using these annotations revealed several genes with caste-specific differential expression and tissue- or caste-specific splicing patterns that were missed in previous analyses. The extended 3' untranslated regions afforded great improvements in the analysis of existing single-cell RNA-seq data, resulting in the recovery of the transcriptomes of 18% more cells. The deeper single-cell transcriptomes obtained with these new annotations allowed us to identify additional markers for several cell types in the ant brain, as well as genes differentially expressed across castes in specific cell types. CONCLUSIONS Our results demonstrate that Iso-Seq is an efficient and effective approach to improve genome annotations and maximize the amount of information that can be obtained from existing and future genomic datasets in Harpegnathos and other organisms.
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Affiliation(s)
- Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Masato Sorida
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Lihong Sheng
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Bogdan Sieriebriennikov
- Department of Biology, New York University, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Long Ding
- Department of Biology, New York University, New York, NY, USA
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA.
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36
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Gospocic J, Glastad KM, Sheng L, Shields EJ, Berger SL, Bonasio R. Kr-h1 maintains distinct caste-specific neurotranscriptomes in response to socially regulated hormones. Cell 2021; 184:5807-5823.e14. [PMID: 34739833 DOI: 10.1016/j.cell.2021.10.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 07/13/2021] [Accepted: 10/07/2021] [Indexed: 10/19/2022]
Abstract
Behavioral plasticity is key to animal survival. Harpegnathos saltator ants can switch between worker and queen-like status (gamergate) depending on the outcome of social conflicts, providing an opportunity to study how distinct behavioral states are achieved in adult brains. Using social and molecular manipulations in live ants and ant neuronal cultures, we show that ecdysone and juvenile hormone drive molecular and functional differences in the brains of workers and gamergates and direct the transcriptional repressor Kr-h1 to different target genes. Depletion of Kr-h1 in the brain caused de-repression of "socially inappropriate" genes: gamergate genes were upregulated in workers, whereas worker genes were upregulated in gamergates. At the phenotypic level, loss of Kr-h1 resulted in the emergence of worker-specific behaviors in gamergates and gamergate-specific traits in workers. We conclude that Kr-h1 is a transcription factor that maintains distinct brain states established in response to socially regulated hormones.
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Affiliation(s)
- Janko Gospocic
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Karl M Glastad
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Lihong Sheng
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Emily J Shields
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Urology and Institute of Neuropathology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Shelley L Berger
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Biology, University of Pennsylvania School of Arts and Sciences, Philadelphia, PA 19104, USA.
| | - Roberto Bonasio
- Epigenetics Institute and Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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37
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Walsh AT, Triant DA, Le Tourneau JJ, Shamimuzzaman M, Elsik CG. Hymenoptera Genome Database: new genomes and annotation datasets for improved go enrichment and orthologue analyses. Nucleic Acids Res 2021; 50:D1032-D1039. [PMID: 34747465 PMCID: PMC8728238 DOI: 10.1093/nar/gkab1018] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023] Open
Abstract
We report an update of the Hymenoptera Genome Database (HGD; http://HymenopteraGenome.org), a genomic database of hymenopteran insect species. The number of species represented in HGD has nearly tripled, with fifty-eight hymenopteran species, including twenty bees, twenty-three ants, eleven wasps and four sawflies. With a reorganized website, HGD continues to provide the HymenopteraMine genomic data mining warehouse and JBrowse/Apollo genome browsers integrated with BLAST. We have computed Gene Ontology (GO) annotations for all species, greatly enhancing the GO annotation data gathered from UniProt with more than a ten-fold increase in the number of GO-annotated genes. We have also generated orthology datasets that encompass all HGD species and provide orthologue clusters for fourteen taxonomic groups. The new GO annotation and orthology data are available for searching in HymenopteraMine, and as bulk file downloads.
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Affiliation(s)
- Amy T Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Deborah A Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Md Shamimuzzaman
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA.,Division of Plant Science & Technology, University of Missouri, Columbia, MO 65211, USA.,MU Institute for Data Science & Informatics, University of Missouri, Columbia, MO 65211, USA
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38
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Fuentes D, Molina M, Chorostecki U, Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T. PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Res 2021; 50:D1062-D1068. [PMID: 34718760 PMCID: PMC8728271 DOI: 10.1093/nar/gkab966] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/20/2022] Open
Abstract
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.
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Affiliation(s)
- Diego Fuentes
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Manuel Molina
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Uciel Chorostecki
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | | | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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39
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McKenzie SK, Winston ME, Grewe F, Vargas Asensio G, Rodríguez-Hernández N, Rubin BER, Murillo-Cruz C, von Beeren C, Moreau CS, Suen G, Pinto-Tomás AA, Kronauer DJC. The genomic basis of army ant chemosensory adaptations. Mol Ecol 2021; 30:6627-6641. [PMID: 34582590 PMCID: PMC9292994 DOI: 10.1111/mec.16198] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022]
Abstract
The evolution of mass raiding has allowed army ants to become dominant arthropod predators in the tropics. Although a century of research has led to many discoveries about behavioural, morphological and physiological adaptations in army ants, almost nothing is known about the molecular basis of army ant biology. Here we report the genome of the iconic New World army ant Eciton burchellii, and show that it is unusually compact, with a reduced gene complement relative to other ants. In contrast to this overall reduction, a particular gene subfamily (9‐exon ORs) expressed predominantly in female antennae is expanded. This subfamily has previously been linked to the recognition of hydrocarbons, key olfactory cues used in insect communication and prey discrimination. Confocal microscopy of the brain showed a corresponding expansion in a putative hydrocarbon response centre within the antennal lobe, while scanning electron microscopy of the antenna revealed a particularly high density of hydrocarbon‐sensitive sensory hairs. E. burchellii shares these features with its predatory and more cryptic relative, the clonal raider ant. By integrating genomic, transcriptomic and anatomical analyses in a comparative context, our work thus provides evidence that army ants and their relatives possess a suite of modifications in the chemosensory system that may be involved in behavioural coordination and prey selection during social predation. It also lays the groundwork for future studies of army ant biology at the molecular level.
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Affiliation(s)
- Sean K McKenzie
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Felix Grewe
- Grainger Bioinformatics Center, Science and Education, Field Museum of Natural History, Chicago, Illinois, USA
| | - Gabriel Vargas Asensio
- Centro de Investigación en Biología Molecular y Celular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.,Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Natalia Rodríguez-Hernández
- Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, San José, Costa Rica
| | - Benjamin E R Rubin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, USA
| | - Catalina Murillo-Cruz
- Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, San José, Costa Rica
| | - Christoph von Beeren
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA.,Ecological Networks, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Corrie S Moreau
- Departments of Entomology and Ecology & Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Garret Suen
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Adrian A Pinto-Tomás
- Centro de Investigación en Biología Molecular y Celular (CIBCM), Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Estructuras Microscópicas (CIEMIC), Universidad de Costa Rica, San José, Costa Rica.,Escuela de Medicina, Departamento de Bioquímica, Universidad de Costa Rica, San José, Costa Rica
| | - Daniel J C Kronauer
- Laboratory of Social Evolution and Behavior, The Rockefeller University, New York, New York, USA
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40
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Sieriebriennikov B, Reinberg D, Desplan C. A molecular toolkit for superorganisms. Trends Genet 2021; 37:846-859. [PMID: 34116864 PMCID: PMC8355152 DOI: 10.1016/j.tig.2021.05.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 12/16/2022]
Abstract
Social insects, such as ants, bees, wasps, and termites, draw biologists' attention due to their distinctive lifestyles. As experimental systems, they provide unique opportunities to study organismal differentiation, division of labor, longevity, and the evolution of development. Ants are particularly attractive because several ant species can be propagated in the laboratory. However, the same lifestyle that makes social insects interesting also hampers the use of molecular genetic techniques. Here, we summarize the efforts of the ant research community to surmount these hurdles and obtain novel mechanistic insight into the biology of social insects. We review current approaches and propose novel ones involving genomics, transcriptomics, chromatin and DNA methylation profiling, RNA interference (RNAi), and genome editing in ants and discuss future experimental strategies.
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Affiliation(s)
- Bogdan Sieriebriennikov
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Department of Biology, New York University, New York, NY, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, NYU Grossman School of Medicine, New York, NY, USA.
| | - Claude Desplan
- Department of Biology, New York University, New York, NY, USA.
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41
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Legan AW, Jernigan CM, Miller SE, Fuchs MF, Sheehan MJ. Expansion and Accelerated Evolution of 9-Exon Odorant Receptors in Polistes Paper Wasps. Mol Biol Evol 2021; 38:3832-3846. [PMID: 34151983 PMCID: PMC8383895 DOI: 10.1093/molbev/msab023] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Independent origins of sociality in bees and ants are associated with independent expansions of particular odorant receptor (OR) gene subfamilies. In ants, one clade within the OR gene family, the 9-exon subfamily, has dramatically expanded. These receptors detect cuticular hydrocarbons (CHCs), key social signaling molecules in insects. It is unclear to what extent 9-exon OR subfamily expansion is associated with the independent evolution of sociality across Hymenoptera, warranting studies of taxa with independently derived social behavior. Here, we describe OR gene family evolution in the northern paper wasp, Polistes fuscatus, and compare it to four additional paper wasp species spanning ∼40 million years of evolutionary divergence. We find 200 putatively functional OR genes in P. fuscatus, matching predictions from neuroanatomy, and more than half of these are in the 9-exon subfamily. Most OR gene expansions are tandemly arrayed at orthologous loci in Polistes genomes, and microsynteny analysis shows species-specific gain and loss of 9-exon ORs within tandem arrays. There is evidence of episodic positive diversifying selection shaping ORs in expanded subfamilies. Values of omega (dN/dS) are higher among 9-exon ORs compared to other OR subfamilies. Within the Polistes OR gene tree, branches in the 9-exon OR clade experience relaxed negative (relaxed purifying) selection relative to other branches in the tree. Patterns of OR evolution within Polistes are consistent with 9-exon OR function in CHC perception by combinatorial coding, with both natural selection and neutral drift contributing to interspecies differences in gene copy number and sequence.
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Affiliation(s)
- Andrew W Legan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Christopher M Jernigan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Sara E Miller
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Matthieu F Fuchs
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Michael J Sheehan
- Laboratory for Animal Social Evolution and Recognition, Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
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42
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Zhu D, Ge J, Guo S, Hou L, Shi R, Zhou X, Nie X, Wang X. Independent variations in genome-wide expression, alternative splicing, and DNA methylation in brain tissues among castes of the buff-tailed bumblebee, Bombus terrestris. J Genet Genomics 2021; 48:681-694. [PMID: 34315685 DOI: 10.1016/j.jgg.2021.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/26/2021] [Accepted: 04/02/2021] [Indexed: 10/21/2022]
Abstract
Caste differentiation in social hymenopterans is an intriguing example of phenotypic plasticity. However, the co-ordination among gene regulatory factors to mediate caste differentiation remains inconclusive. In this study, we determined the role of gene regulation and related epigenetic processes in pre-imaginal caste differentiation in the primitively eusocial bumblebee Bombus terrestris. By combining RNA-Seq data from Illumina and PacBio and accurately quantifying methylation at whole-genomic base pair resolution, we found that queens, workers, and drones mainly differentiate in gene expression but not in alternative splicing and DNA methylation. Gynes are the most distinct with the lowest global level of whole-genomic methylation and with the largest number of caste-specific transcripts and alternative splicing events. By contrast, workers exhibit few uniquely expressed or alternatively spliced genes. Moreover, several genes involved in hormone and neurotransmitter metabolism are related to caste differentiation, whereas several neuropeptides are linked with sex differentiation. Despite little genome-wide association among differential gene expression, splicing, and differential DNA methylation, the overlapped gene ontology (GO) terms point to nutrition-related activity. Therefore, variations in gene regulation correlate with the behavioral differences among castes and highlight the specialization of toolkit genes in bumblebee gynes at the beginning of the adult stage.
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Affiliation(s)
- Dan Zhu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jin Ge
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rangjun Shi
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xian Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Nie
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100080, China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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43
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Wilson Rankin EE. Emerging patterns in social wasp invasions. CURRENT OPINION IN INSECT SCIENCE 2021; 46:72-77. [PMID: 33667693 DOI: 10.1016/j.cois.2021.02.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/12/2021] [Accepted: 02/18/2021] [Indexed: 05/06/2023]
Abstract
Invasive species are a main driver of biodiversity loss and ecological change globally. Consequently, there is a need to understand how invaders damage ecosystems and to develop effective management strategies. Social wasps (Hymenoptera: Vespidae) include some of the world's most ecologically damaging invasive insects. In recent decades, the invasive social wasp literature has grown rapidly. This may be due in part to increased rate of introduction as well as greater public awareness of invasive wasps and their potential negative impacts on bees. Here, we investigate trends in invasive social wasp research, identifying the emergence of Vespa invasions, the mechanism-based inquiry into Vespula invasions, and the increased application of molecular methods to track invasive species through the invasion process.
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Affiliation(s)
- Erin E Wilson Rankin
- Department of Entomology, University of California Riverside, 900 University Ave, Riverside, CA 92521, USA.
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44
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45
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Kausar S, Abbas MN, Cui H. A review on the DNA methyltransferase family of insects: Aspect and prospects. Int J Biol Macromol 2021; 186:289-302. [PMID: 34237376 DOI: 10.1016/j.ijbiomac.2021.06.205] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 06/22/2021] [Accepted: 06/30/2021] [Indexed: 12/11/2022]
Abstract
The DNA methyltransferase family contains a conserved set of DNA-modifying enzymatic proteins. They are responsible for epigenetic gene modulation, such as transcriptional silencing, transcription activation, and post-transcriptional modulation. Recent research has revealed that the canonical DNA methyltransferases (DNMTs) biological roles go beyond their traditional functions of establishing and maintaining DNA methylation patterns. Although a complete DNA methylation toolkit is absent in most insect orders, recent evidence indicates the de novo DNA methylation and maintenance function remain conserved. Studies using various molecular approaches provided evidence that DNMTs are multi-functional proteins. However, still in-depth studies on their biological role lack due to the least studied area in insects. Here, we review the DNA methylation toolkit of insects, focusing on recent research on various insect orders, which exhibit DNA methylation at different levels, and for which DNMTs functional studies have become available in recent years. We survey research on the potential roles of DNMTs in the regulation of gene transcription in insect species. DNMTs participate in different physiological processes by interacting with other epigenetic factors. Future studies on insect's DNMTs will benefit to understand developmental processes, responses to various stimuli, and adaptability of insects to different environmental conditions.
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Affiliation(s)
- Saima Kausar
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Muhammad Nadeem Abbas
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China
| | - Hongjuan Cui
- State Key Laboratory of Silkworm Genome Biology, College of Sericulture, Textile and Biomass Sciences, Southwest University, Chongqing, China.
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46
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Oldroyd BP, Yagound B. The role of epigenetics, particularly DNA methylation, in the evolution of caste in insect societies. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200115. [PMID: 33866805 PMCID: PMC8059649 DOI: 10.1098/rstb.2020.0115] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Eusocial insects can be defined as those that live in colonies and have distinct queens and workers. For most species, queens and workers arise from a common genome, and so caste-specific developmental trajectories must arise from epigenetic processes. In this review, we examine the epigenetic mechanisms that may be involved in the regulation of caste dimorphism. Early work on honeybees suggested that DNA methylation plays a causal role in the divergent development of queen and worker castes. This view has now been challenged by studies that did not find consistent associations between methylation and caste in honeybees and other species. Evidence for the involvement of methylation in modulating behaviour of adult workers is also inconsistent. Thus, the functional significance of DNA methylation in social insects remains equivocal. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Benjamin P. Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
- Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193 Berlin, Germany
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences A12, University of Sydney, New South Wales 2006, Australia
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47
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Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. Sci Rep 2021; 11:3654. [PMID: 33574391 PMCID: PMC7878513 DOI: 10.1038/s41598-020-75432-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 10/05/2020] [Indexed: 01/30/2023] Open
Abstract
A striking feature of advanced insect societies is the existence of workers that forgo reproduction. Two broad types of workers exist in eusocial bees: nurses who care for their young siblings and the queen, and foragers who guard the nest and forage for food. Comparisons between these two worker subcastes have been performed in honeybees, but data from other bees are scarce. To understand whether similar molecular mechanisms are involved in nurse-forager differences across distinct species, we compared gene expression and DNA methylation profiles between nurses and foragers of the buff-tailed bumblebee Bombus terrestris and the stingless bee Tetragonisca angustula. These datasets were then compared to previous findings from honeybees. Our analyses revealed that although the expression pattern of genes is often species-specific, many of the biological processes and molecular pathways involved are common. Moreover, the correlation between gene expression and DNA methylation was dependent on the nucleotide context, and non-CG methylation appeared to be a relevant factor in the behavioral changes of the workers. In summary, task specialization in worker bees is characterized by a plastic and mosaic molecular pattern, with species-specific mechanisms acting upon broad common pathways across species.
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48
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Taylor BA, Cini A, Wyatt CDR, Reuter M, Sumner S. The molecular basis of socially mediated phenotypic plasticity in a eusocial paper wasp. Nat Commun 2021; 12:775. [PMID: 33536437 PMCID: PMC7859208 DOI: 10.1038/s41467-021-21095-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 01/12/2021] [Indexed: 01/30/2023] Open
Abstract
Phenotypic plasticity, the ability to produce multiple phenotypes from a single genotype, represents an excellent model with which to examine the relationship between gene expression and phenotypes. Analyses of the molecular foundations of phenotypic plasticity are challenging, however, especially in the case of complex social phenotypes. Here we apply a machine learning approach to tackle this challenge by analyzing individual-level gene expression profiles of Polistes dominula paper wasps following the loss of a queen. We find that caste-associated gene expression profiles respond strongly to queen loss, and that this change is partly explained by attributes such as age but occurs even in individuals that appear phenotypically unaffected. These results demonstrate that large changes in gene expression may occur in the absence of outwardly detectable phenotypic changes, resulting here in a socially mediated de-differentiation of individuals at the transcriptomic level but not at the levels of ovarian development or behavior.
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Affiliation(s)
- Benjamin A Taylor
- Centre for Biodiversity & Environment Research, University College London, London, UK.
- Department of Genetics, Evolution & Environment, University College London, London, UK.
| | - Alessandro Cini
- Centre for Biodiversity & Environment Research, University College London, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Dipartimento di Biologia, Università degli Studi di Firenze, Sesto Fiorentino, Italy
| | - Christopher D R Wyatt
- Centre for Biodiversity & Environment Research, University College London, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
| | - Max Reuter
- Department of Genetics, Evolution & Environment, University College London, London, UK
- Centre for Life's Origins and Evolution, University College London, London, UK
| | - Seirian Sumner
- Centre for Biodiversity & Environment Research, University College London, London, UK
- Department of Genetics, Evolution & Environment, University College London, London, UK
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49
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Miyazaki S, Shimoji H, Suzuki R, Chinushi I, Takayanagi H, Yaguchi H, Miura T, Maekawa K. Expressions of conventional vitellogenin and vitellogenin-like A in worker brains are associated with a nursing task in a ponerine ant. INSECT MOLECULAR BIOLOGY 2021; 30:113-121. [PMID: 33150669 DOI: 10.1111/imb.12682] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 06/11/2023]
Abstract
In eusocial insect colonies, non-reproductive workers often perform different tasks. Tasks of an individual worker are shifted depending on various factors, e.g., age and colony demography. Although a vitellogenin (Vg) gene play regulatory roles in both reproductive and non-reproductive division of labours in a honeybee, it has been shown that the insect Vg underwent multiple gene duplications and sub-functionalisation, especially in apical ant lineages. The regulatory roles of duplicated Vgs were suggested to change evolutionarily among ants, whereas such roles in phylogenetically basal ants remain unclear. Here, we examined the expression patterns of conventional Vg (CVg), Vg-like A, Vg-like B and Vg-like C, as well as Vg receptor, during the task shift in an age-dependent manner and under experimental manipulation of colony demography in a primitive ant Diacamma sp. Expressions of CVg and Vg-like A in a brain were associated with a nursing task. It is suggested that associations of brain expressions of these Vgs with worker tasks were acquired in the basal ant lineage, and that such Vg functions could have sub-functionalised in the derived ant lineage.
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Affiliation(s)
- S Miyazaki
- Graduate School of Agriculture, Tamagawa University, Tokyo, Japan
| | - H Shimoji
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
- School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
| | - R Suzuki
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - I Chinushi
- Graduate School of Agriculture, Tamagawa University, Tokyo, Japan
| | - H Takayanagi
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
| | - H Yaguchi
- School of Science and Technology, Kwansei Gakuin University, Sanda, Japan
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - T Miura
- Faculty of Environmental Earth Science, Hokkaido University, Sapporo, Japan
- Misaki Marine Biological Station, School of Science, The University of Tokyo, Miura, Japan
| | - K Maekawa
- Faculty of Science, Academic Assembly, University of Toyama, Toyama, Japan
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50
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Collins DH, Wirén A, Labédan M, Smith M, Prince DC, Mohorianu I, Dalmay T, Bourke AFG. Gene expression during larval caste determination and differentiation in intermediately eusocial bumblebees, and a comparative analysis with advanced eusocial honeybees. Mol Ecol 2021; 30:718-735. [PMID: 33238067 PMCID: PMC7898649 DOI: 10.1111/mec.15752] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022]
Abstract
The queen‐worker caste system of eusocial insects represents a prime example of developmental polyphenism (environmentally‐induced phenotypic polymorphism) and is intrinsic to the evolution of advanced eusociality. However, the comparative molecular basis of larval caste determination and subsequent differentiation in the eusocial Hymenoptera remains poorly known. To address this issue within bees, we profiled caste‐associated gene expression in female larvae of the intermediately eusocial bumblebee Bombus terrestris. In B. terrestris, female larvae experience a queen‐dependent period during which their caste fate as adults is determined followed by a nutrition‐sensitive period also potentially affecting caste fate but for which the evidence is weaker. We used mRNA‐seq and qRT‐PCR validation to isolate genes differentially expressed between each caste pathway in larvae at developmental stages before and after each of these periods. We show that differences in gene expression between caste pathways are small in totipotent larvae, then peak after the queen‐dependent period. Relatively few novel (i.e., taxonomically‐restricted) genes were differentially expressed between castes, though novel genes were significantly enriched in late‐instar larvae in the worker pathway. We compared sets of caste‐associated genes in B. terrestris with those reported from the advanced eusocial honeybee, Apis mellifera, and found significant but relatively low levels of overlap of gene lists between the two species. These results suggest both the existence of low numbers of shared toolkit genes and substantial divergence in caste‐associated genes between Bombus and the advanced eusocial Apis since their last common eusocial ancestor.
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Affiliation(s)
- David H Collins
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Anders Wirén
- School of Biological Sciences, University of East Anglia, Norwich, UK.,School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marjorie Labédan
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michael Smith
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - David C Prince
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Irina Mohorianu
- School of Biological Sciences, University of East Anglia, Norwich, UK.,Jeffrey Cheah Biomedical Centre, WT-MRC Cambridge Stem Cell Institute, Cambridge, UK
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Andrew F G Bourke
- School of Biological Sciences, University of East Anglia, Norwich, UK
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