1
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Zhang X, Xie N, Ding G, Ning D, Dai W, Xiong Z, Zhong W, Zuo D, Zhao J, Zhang P, Liu C, Li Q, Ran H, Liu W, Zhang G. An evolutionarily conserved pathway mediated by neuroparsin-A regulates reproductive plasticity in ants. PLoS Biol 2024; 22:e3002763. [PMID: 39133741 PMCID: PMC11398701 DOI: 10.1371/journal.pbio.3002763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 09/13/2024] [Accepted: 07/23/2024] [Indexed: 09/14/2024] Open
Abstract
Phenotypic plasticity displayed by an animal in response to different environmental conditions is supposedly crucial for its survival and reproduction. The female adults of some ant lineages display phenotypic plasticity related to reproductive role. In pharaoh ant queens, insemination induces substantial physiological/behavioral changes and implicates remarkable gene regulatory network (GRN) shift in the brain. Here, we report a neuropeptide neuroparsin A (NPA) showing a conserved expression pattern associated with reproductive activity across ant species. Knock-down of NPA in unmated queen enhances ovary activity, whereas injection of NPA peptide in fertilized queen suppresses ovary activity. We found that NPA mainly affected the downstream gene JHBP in the ovary, which is positively regulated by NPA and suppression of which induces elevated ovary activity, and shadow which is negatively regulated by NPA. Furthermore, we show that NPA was also employed into the brain-ovary axis in regulating the worker reproductive changes in other distantly related species, such as Harpegnathos venator ants.
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Affiliation(s)
- Xiafang Zhang
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Nianxia Xie
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI Research, Wuhan, China
| | - Guo Ding
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou, China
| | - Dongdong Ning
- College of Agriculture and Biotechnology, Institute of Insect Science, Zhejiang University, Hangzhou, China
| | | | | | - Wenjiang Zhong
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Dashuang Zuo
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Jie Zhao
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Pei Zhang
- BGI Research, Wuhan, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Chengyuan Liu
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou, China
| | - Qiye Li
- BGI Research, Wuhan, China
- State Key Laboratory of Agricultural Genomics, BGI Research, Shenzhen, China
| | - Hao Ran
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Weiwei Liu
- Key Laboratory of Genetic Evolution & Animal Models, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- Center of Evolutionary & Organismal Biology, and Women's Hospital at Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
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2
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Chee FT, Harun S, Mohd Daud K, Sulaiman S, Nor Muhammad NA. Exploring gene regulation and biological processes in insects: Insights from omics data using gene regulatory network models. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 189:1-12. [PMID: 38604435 DOI: 10.1016/j.pbiomolbio.2024.04.002] [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: 11/02/2023] [Revised: 12/18/2023] [Accepted: 04/03/2024] [Indexed: 04/13/2024]
Abstract
Gene regulatory network (GRN) comprises complicated yet intertwined gene-regulator relationships. Understanding the GRN dynamics will unravel the complexity behind the observed gene expressions. Insect gene regulation is often complicated due to their complex life cycles and diverse ecological adaptations. The main interest of this review is to have an update on the current mathematical modelling methods of GRNs to explain insect science. Several popular GRN architecture models are discussed, together with examples of applications in insect science. In the last part of this review, each model is compared from different aspects, including network scalability, computation complexity, robustness to noise and biological relevancy.
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Affiliation(s)
- Fong Ting Chee
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Sarahani Harun
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia
| | - Kauthar Mohd Daud
- Faculty of Information Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Suhaila Sulaiman
- FGV R&D Sdn Bhd, FGV Innovation Center, PT23417 Lengkuk Teknologi, Bandar Baru Enstek, 71760 Nilai, Negeri Sembilan, Malaysia
| | - Nor Azlan Nor Muhammad
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor, Malaysia.
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3
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Carmona-Aldana F, Yong LW, Reinberg D, Desplan C. Phenomenon of reproductive plasticity in ants. CURRENT OPINION IN INSECT SCIENCE 2024; 63:101197. [PMID: 38583769 PMCID: PMC11139587 DOI: 10.1016/j.cois.2024.101197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/26/2024] [Accepted: 03/31/2024] [Indexed: 04/09/2024]
Abstract
Ant colonies are organized in castes with distinct behaviors that together allow the colony to strive. Reproduction relies on one or a few queens that stay in the nest producing eggs, while females of the worker caste do not reproduce and instead engage in colony maintenance and brood caretaking. Yet, in spite of this clear separation of functions, workers can become reproductive under defined circumstances. Here, we review the context in which workers become reproductive, exhibiting asexual or sexual reproduction depending on the species. Remarkably, the activation of reproduction in these workers can be quite stable, with changes that include behavior and a dramatic extension of lifespan. We compare these changes between species that do or do not have a queen caste. We discuss how the mechanisms underlying reproductive plasticity include changes in hormonal functions and in epigenetic configurations. Further studies are warranted to elucidate not only how reproductive functions have been gradually restricted to the queen caste during evolution but also how reproductive plasticity remains possible in workers of some species.
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Affiliation(s)
| | - Luok Wen Yong
- Department of Biology, New York University, NY 10003, USA
| | - Danny Reinberg
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Coral Gables, FL 33124, USA.
| | - Claude Desplan
- Department of Biology, New York University, NY 10003, USA; Center for Genomics and Systems Biology, New York University, Abu Dhabi 51133, United Arab Emirates.
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4
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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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5
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Hou L, Wang N, Sun T, Wang X. Neuropeptide regulations on behavioral plasticity in social insects. CURRENT OPINION IN INSECT SCIENCE 2023; 60:101119. [PMID: 37741615 DOI: 10.1016/j.cois.2023.101119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/25/2023]
Abstract
Social insects demonstrate remarkable behavioral flexibility in response to complex external and social environments. One of the most striking examples of this adaptability is the context-dependent division of labor among workers of bees and ants. Neuropeptides, the brain's most diverse group of messenger molecules, play an essential role in modulating this phenotypic plasticity related to labor division in social insects. Integrated omics research and mass spectrometry imaging technology have greatly accelerated the identification and spatiotemporal analysis of neuropeptides. Moreover, key roles of several neuropeptides in age- and caste-dependent behavioral plasticity have been uncovered. This review summarizes recent advances in the characterization, expression, distribution, and functions of neuropeptides in controlling behavioral plasticity in social insects, particularly bees and ants. The article concludes with a discussion of future directions and challenges in understanding the regulation of social behavior by neuropeptides.
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Affiliation(s)
- Li Hou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, PR China.
| | - Nanying Wang
- College of Life Sciences, Hebei University, Baoding 071002, China
| | - Tianle Sun
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, PR China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, PR China; CAS Centre for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, PR China.
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6
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Ju L, Glastad KM, Sheng L, Gospocic J, Kingwell CJ, Davidson SM, Kocher SD, Bonasio R, Berger SL. Hormonal gatekeeping via the blood-brain barrier governs caste-specific behavior in ants. Cell 2023; 186:4289-4309.e23. [PMID: 37683635 PMCID: PMC10807403 DOI: 10.1016/j.cell.2023.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/10/2023] [Accepted: 08/01/2023] [Indexed: 09/10/2023]
Abstract
Here, we reveal an unanticipated role of the blood-brain barrier (BBB) in regulating complex social behavior in ants. Using scRNA-seq, we find localization in the BBB of a key hormone-degrading enzyme called juvenile hormone esterase (Jhe), and we show that this localization governs the level of juvenile hormone (JH3) entering the brain. Manipulation of the Jhe level reprograms the brain transcriptome between ant castes. Although ant Jhe is retained and functions intracellularly within the BBB, we show that Drosophila Jhe is naturally extracellular. Heterologous expression of ant Jhe into the Drosophila BBB alters behavior in fly to mimic what is seen in ants. Most strikingly, manipulation of Jhe levels in ants reprograms complex behavior between worker castes. Our study thus uncovers a remarkable, potentially conserved role of the BBB serving as a molecular gatekeeper for a neurohormonal pathway that regulates social behavior.
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Affiliation(s)
- Linyang Ju
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Karl M Glastad
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
| | - Lihong Sheng
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Janko Gospocic
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; 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, Freiburg, Germany
| | - Callum J Kingwell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Shawn M Davidson
- Lewis-Sigler Institute for Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA; Lewis-Sigler Institute for Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Roberto Bonasio
- Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Shelley L Berger
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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7
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Kishner M, Habaz L, Meshnik L, Meidan TD, Polonsky A, Ben-Zvi A. Gonadotropin-releasing hormone-like receptor 2 inversely regulates somatic proteostasis and reproduction in Caenorhabditis elegans. Front Cell Dev Biol 2022; 10:951199. [PMID: 36105349 PMCID: PMC9465036 DOI: 10.3389/fcell.2022.951199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
The quality control machinery regulates the cellular proteome to ensure proper protein homeostasis (proteostasis). In Caenorhabditis elegans, quality control networks are downregulated cell-nonautonomously by the gonadal longevity pathway or metabolic signaling at the onset of reproduction. However, how signals are mediated between the gonad and the somatic tissues is not known. Gonadotropin-releasing hormone (GnRH)-like signaling functions in the interplay between development and reproduction and have conserved roles in regulating reproduction, metabolism, and stress. We, therefore, asked whether GnRH-like signaling is involved in proteostasis collapse at the onset of reproduction. Here, we examine whether C. elegans orthologues of GnRH receptors modulate heat shock survival. We find that gnrr-2 is required for proteostasis remodeling in different somatic tissues during the transition to adulthood. We show that gnrr-2 likely functions in neurons downstream of the gonad in the gonadal-longevity pathway and modulate the somatic regulation of transcription factors HSF-1, DAF-16, and PQM-1. In parallel, gnrr-2 modulates egg-laying rates, vitellogenin production, and thus reproductive capacity. Taken together, our data suggest that gnrr-2 plays a GnRH-associated role, mediating the cross-talk between the reproduction system and the soma in the decision to commit to reproduction.
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8
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Li Q, Wang M, Zhang P, Liu Y, Guo Q, Zhu Y, Wen T, Dai X, Zhang X, Nagel M, Dethlefsen BH, Xie N, Zhao J, Jiang W, Han L, Wu L, Zhong W, Wang Z, Wei X, Dai W, Liu L, Xu X, Lu H, Yang H, Wang J, Boomsma JJ, Liu C, Zhang G, Liu W. A single-cell transcriptomic atlas tracking the neural basis of division of labour in an ant superorganism. Nat Ecol Evol 2022; 6:1191-1204. [PMID: 35711063 PMCID: PMC9349048 DOI: 10.1038/s41559-022-01784-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/03/2022] [Indexed: 01/21/2023]
Abstract
Ant colonies with permanent division of labour between castes and highly distinct roles of the sexes have been conceptualized to be superorganisms, but the cellular and molecular mechanisms that mediate caste/sex-specific behavioural specialization have remained obscure. Here we characterized the brain cell repertoire of queens, gynes (virgin queens), workers and males of Monomorium pharaonis by obtaining 206,367 single-nucleus transcriptomes. In contrast to Drosophila, the mushroom body Kenyon cells are abundant in ants and display a high diversity with most subtypes being enriched in worker brains, the evolutionarily derived caste. Male brains are as specialized as worker brains but with opposite trends in cell composition with higher abundances of all optic lobe neuronal subtypes, while the composition of gyne and queen brains remained generalized, reminiscent of solitary ancestors. Role differentiation from virgin gynes to inseminated queens induces abundance changes in roughly 35% of cell types, indicating active neurogenesis and/or programmed cell death during this transition. We also identified insemination-induced cell changes probably associated with the longevity and fecundity of the reproductive caste, including increases of ensheathing glia and a population of dopamine-regulated Dh31-expressing neurons. We conclude that permanent caste differentiation and extreme sex-differentiation induced major changes in the neural circuitry of ants. Using single-cell transcriptomics, the authors generate a brain cell atlas for the pharaoh ant including individuals of different sexes and castes and show changes in cell composition underlying division of labour and reproductive specialization.
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Affiliation(s)
- Qiye Li
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Qunfei Guo
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | | | | | - Xueqin Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xiafang Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Manuel Nagel
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Bjarke Hamberg Dethlefsen
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Nianxia Xie
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jie Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Lei Han
- BGI-Shenzhen, Shenzhen, China
| | - Liang Wu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenjiang Zhong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | | | | | - Wei Dai
- BGI-Shenzhen, Shenzhen, China
| | - Longqi Liu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Shenzhen Bay Laboratory, Shenzhen, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China.,Guangdong Provincial Key Laboratory of Genome Read and Write, Shenzhen, China
| | - Haorong Lu
- China National GeneBank, BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jian Wang
- BGI-Shenzhen, Shenzhen, China.,James D. Watson Institute of Genome Science, Hangzhou, China
| | - Jacobus J Boomsma
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Guojie Zhang
- BGI-Shenzhen, Shenzhen, China. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China. .,Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark. .,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China. .,Evolutionary and Organismal Biology Research Center, School of Medicine, Zhejiang University, Hangzhou, China.
| | - Weiwei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.
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9
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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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10
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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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11
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Opachaloemphan C, Mancini G, Konstantinides N, Parikh A, Mlejnek J, Yan H, Reinberg D, Desplan C. Early behavioral and molecular events leading to caste switching in the ant Harpegnathos. Genes Dev 2021; 35:410-424. [PMID: 33602869 PMCID: PMC7919410 DOI: 10.1101/gad.343699.120] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022]
Abstract
Ant societies show a division of labor in which a queen is in charge of reproduction while nonreproductive workers maintain the colony. In Harpegnathos saltator, workers retain reproductive ability, inhibited by the queen pheromones. Following the queen loss, the colony undergoes social unrest with an antennal dueling tournament. Most workers quickly abandon the tournament while a few workers continue the dueling for months and become gamergates (pseudoqueens). However, the temporal dynamics of the social behavior and molecular mechanisms underlining the caste transition and social dominance remain unclear. By tracking behaviors, we show that the gamergate fate is accurately determined 3 d after initiation of the tournament. To identify genetic factors responsible for this commitment, we compared transcriptomes of different tissues between dueling and nondueling workers. We found that juvenile hormone is globally repressed, whereas ecdysone biosynthesis in the ovary is increased in gamergates. We show that molecular changes in the brain serve as earliest caste predictors compared with other tissues. Thus, behavioral and molecular data indicate that despite the prolonged social upheaval, the gamergate fate is rapidly established, suggesting a robust re-establishment of social structure.
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Affiliation(s)
- Comzit Opachaloemphan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
| | - Giacomo Mancini
- Department of Biology, New York University, New York, New York 10003, USA
| | | | - Apurva Parikh
- Department of Biology, New York University, New York, New York 10003, USA
| | - Jakub Mlejnek
- Department of Biology, New York University, New York, New York 10003, USA
| | - Hua Yan
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Danny Reinberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA
- Howard Hughes Medical Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Claude Desplan
- Department of Biology, New York University, New York, New York 10003, USA
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