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Chen J, Guan Z, Ma Y, Shi Q, Chen T, Waris MI, Lyu L, Lu Y, Qi G. Juvenile hormone induces reproduction via miR-1175-3p in the red imported fire ant, Solenopsis invicta. INSECT SCIENCE 2024; 31:371-386. [PMID: 37933419 DOI: 10.1111/1744-7917.13291] [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: 06/05/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 11/08/2023]
Abstract
Juvenile hormone (JH) acts in the regulation of caste differentiation between queens and workers (i.e., with or without reproductive capacity) during vitellin synthesis and oogenesis in social insects. However, the regulatory mechanisms have not yet been elucidated. Here, we identified a highly expressed microRNA (miRNA), miR-1175-3p, in the red imported fire ant, Solenopsis invicta. We found that miR-1175-3p is prominently present in the fat bodies and ovaries of workers. Furthermore, miR-1175-3p interacts with its target gene, broad-complex core (Br-C), in the fat bodies. By utilizing miR-1175-3p agomir, we successfully suppressed the expression of the Br-C protein in queens, resulting in reduced vitellogenin expression, fewer eggs, and poorly developed ovaries. Conversely, decreasing miR-1175-3p levels led to the increased expression of Br-C and vitellogenin in workers, triggering the "re-development" of the ovaries. Moreover, when queens were fed with JH, the expression of miR-1175-3p decreased, whereas the expression of vitellogenin-2 and vitellogenin-3 increased. Notably, the suppression of fertility in queens caused by treatment with agomir miR-1175-3p was completely rescued by the increased vitellogenin expression induced by being fed with JH. These results suggest the critical role of miR-1175-3p in JH-regulated reproduction, shedding light on the molecular mechanism underlying miRNA-mediated fecundity in social insects and providing a novel strategy for managing S. invicta.
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Affiliation(s)
- Jie Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Ziying Guan
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Yunjie Ma
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Qingxing Shi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Ting Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Muhammad Irfan Waris
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Lihua Lyu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Yongyue Lu
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Guojun Qi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
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Du H, Huang R, Chen DS, Zhuang T, Huang X, Zhang H, Li Z. Regulation of soldier caste differentiation by microRNAs in Formosan subterranean termite ( Coptotermes formosanus Shiraki). PeerJ 2024; 12:e16843. [PMID: 38436016 PMCID: PMC10909360 DOI: 10.7717/peerj.16843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/05/2024] [Indexed: 03/05/2024] Open
Abstract
The soldier caste is one of the most distinguished castes inside the termite colony. The mechanism of soldier caste differentiation has mainly been studied at the transcriptional level, but the function of microRNAs (miRNAs) in soldier caste differentiation is seldom studied. In this study, the workers of Coptotermes formosanus Shiraki were treated with methoprene, a juvenile hormone analog which can induce workers to transform into soldiers. The miRNomes of the methoprene-treated workers and the controls were sequenced. Then, the differentially expressed miRNAs (DEmiRs) were corrected with the differentially expressed genes DEGs to construct the DEmiR-DEG regulatory network. Afterwards, the DEmiR-regulated DEGs were subjected to GO enrichment and KEGG enrichment analysis. A total of 1,324 miRNAs were identified, among which 116 miRNAs were screened as DEmiRs between the methoprene-treated group and the control group. A total of 4,433 DEmiR-DEG pairs were obtained. No GO term was recognized as significant in the cellular component, molecular function, or biological process categories. The KEGG enrichment analysis of the DEmiR-regulated DEGs showed that the ribosome biogenesis in eukaryotes and circadian rhythm-fly pathways were enriched. This study demonstrates that DEmiRs and DEGs form a complex network regulating soldier caste differentiation in termites.
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Affiliation(s)
- He Du
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Runmei Huang
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Da-Song Chen
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Tianyong Zhuang
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Xueyi Huang
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
| | - Huan Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Zhiqiang Li
- Guangdong Key Laboratory of Integrated Pest Management in Agriculture, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Institute of Zoology, Guangdong Academy of Sciences, Guangzhou, China
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Monthony AS, de Ronne M, Torkamaneh D. Exploring ethylene-related genes in Cannabis sativa: implications for sexual plasticity. PLANT REPRODUCTION 2024:10.1007/s00497-023-00492-5. [PMID: 38218931 DOI: 10.1007/s00497-023-00492-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 12/11/2023] [Indexed: 01/15/2024]
Abstract
KEY MESSAGE Presented here are model Yang cycle, ethylene biosynthesis and signaling pathways in Cannabis sativa. C. sativa floral transcriptomes were used to predict putative ethylene-related genes involved in sexual plasticity in the species. Sexual plasticity is a phenomenon, wherein organisms possess the ability to alter their phenotypic sex in response to environmental and physiological stimuli, without modifying their sex chromosomes. Cannabis sativa L., a medically valuable plant species, exhibits sexual plasticity when subjected to specific chemicals that influence ethylene biosynthesis and signaling. Nevertheless, the precise contribution of ethylene-related genes (ERGs) to sexual plasticity in cannabis remains unexplored. The current study employed Arabidopsis thaliana L. as a model organism to conduct gene orthology analysis and reconstruct the Yang Cycle, ethylene biosynthesis, and ethylene signaling pathways in C. sativa. Additionally, two transcriptomic datasets comprising male, female, and chemically induced male flowers were examined to identify expression patterns in ERGs associated with sexual determination and sexual plasticity. These ERGs involved in sexual plasticity were categorized into two distinct expression patterns: floral organ concordant (FOC) and unique (uERG). Furthermore, a third expression pattern, termed karyotype concordant (KC) expression, was proposed, which plays a role in sex determination. The study revealed that CsERGs associated with sexual plasticity are dispersed throughout the genome and are not limited to the sex chromosomes, indicating a widespread regulation of sexual plasticity in C. sativa.
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Affiliation(s)
- Adrian S Monthony
- Département de Phytologie, Université Laval, Québec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Centre de Recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada
| | - Maxime de Ronne
- Département de Phytologie, Université Laval, Québec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada
- Centre de Recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, Québec, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, Québec, Canada.
- Centre de Recherche et d'innovation sur les végétaux (CRIV), Université Laval, Québec City, Québec, Canada.
- Institut intelligence et données (IID), Université Laval, Québec City, Québec, Canada.
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Panyushev N, Selitskiy M, Melnichenko V, Lebedev E, Okorokova L, Adonin L. Dynamic Evolution of Repetitive Elements and Chromatin States in Apis mellifera Subspecies. Genes (Basel) 2024; 15:89. [PMID: 38254978 PMCID: PMC10815273 DOI: 10.3390/genes15010089] [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: 12/15/2023] [Revised: 01/07/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
In this study, we elucidate the contribution of repetitive DNA sequences to the establishment of social structures in honeybees (Apis mellifera). Despite recent advancements in understanding the molecular mechanisms underlying the formation of honeybee castes, primarily associated with Notch signaling, the comprehensive identification of specific genomic cis-regulatory sequences remains elusive. Our objective is to characterize the repetitive landscape within the genomes of two honeybee subspecies, namely A. m. mellifera and A. m. ligustica. An observed recent burst of repeats in A. m. mellifera highlights a notable distinction between the two subspecies. After that, we transitioned to identifying differentially expressed DNA elements that may function as cis-regulatory elements. Nevertheless, the expression of these sequences showed minimal disparity in the transcriptome during caste differentiation, a pivotal process in honeybee eusocial organization. Despite this, chromatin segmentation, facilitated by ATAC-seq, ChIP-seq, and RNA-seq data, revealed a distinct chromatin state associated with repeats. Lastly, an analysis of sequence divergence among elements indicates successive changes in repeat states, correlating with their respective time of origin. Collectively, these findings propose a potential role of repeats in acquiring novel regulatory functions.
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Affiliation(s)
- Nick Panyushev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
- Bioinformatics Institute, 197342 St. Petersburg, Russia;
| | - Max Selitskiy
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
| | - Vasilina Melnichenko
- International Scientific and Research Institute of Bioengineering, ITMO University, 197101 St. Petersburg, Russia;
| | - Egor Lebedev
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
| | | | - Leonid Adonin
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (N.P.); (M.S.)
- Institute of Biomedical Chemistry, Group of Mechanisms for Nanosystems Targeted Delivery, 119121 Moscow, Russia
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5
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Chen J, Ma Y, Guan Z, Liu Q, Shi Q, Qi G, Chen T, Lyu L. Labor division of worker ants can be controlled by insulin synthesis targeted through miR-279c-5p in Solenopsis invicta (Hymenoptera: Formicidae). PEST MANAGEMENT SCIENCE 2023; 79:5029-5043. [PMID: 37552557 DOI: 10.1002/ps.7704] [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: 05/08/2023] [Revised: 07/24/2023] [Accepted: 08/08/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND In social insects, the labor division of workers is ubiquitous and controlled by genetic and environmental factors. However, how they modulate this coordinately remains poorly understood. RESULTS We report miR-279c-5p participation in insulin synthesis and behavioral transition by negatively regulating Rab8A in Solenopsis invicta. Eusocial specific miR-279c-5p is age-associated and highly expressed in nurse workers, and localized in the cytoplasm of neurons, where it is partly co-localized with its target, Rab8A. We determined that miR-279c-5p agomir suppressed Rab8A expression in forager workers, consequently decreasing insulin content, resulting in the behavioral shift to 'nurse-like' behaviors, while the decrease in miR-279c-5p increased Rab8A expression and increased insulin content in nurse workers, leading to the behavioral shift to 'foraging-like' behaviors. Moreover, insulin could rescue the 'foraging behavior' induced by feeding miR-279c-5p to nurse workers. The overexpression and suppression of miR-279c-5p in vivo caused an obvious behavioral transition between foragers and nurses, and insulin synthesis was affected by miR-279c-5p by regulating the direct target Rab8A. CONCLUSION We first report that miR-279c-5p is a novel regulator that promotes labor division by negatively regulating the target gene Rab8A by controlling insulin production in ants. This miRNA-mediated mechanism is significant for understanding the behavioral plasticity of social insects between complex factors and potentially provides new targets for controlling red imported fire ants. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Jie Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Yunjie Ma
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
- Department of Entomology, College of Plant Protection, South China Agricultural University, Guangzhou, China
| | - Ziying Guan
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Qin Liu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Qingxing Shi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Guojun Qi
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Ting Chen
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Lihua Lyu
- Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
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Fan X, Gao X, Zang H, Guo S, Jing X, Zhang Y, Liu X, Zou P, Chen M, Huang Z, Chen D, Guo R. Diverse Regulatory Manners and Potential Roles of lncRNAs in the Developmental Process of Asian Honey Bee ( Apis cerana) Larval Guts. Int J Mol Sci 2023; 24:15399. [PMID: 37895079 PMCID: PMC10607868 DOI: 10.3390/ijms242015399] [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: 09/06/2023] [Revised: 10/15/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are crucial modulators in a variety of biological processes, such as gene expression, development, and immune defense. However, little is known about the function of lncRNAs in the development of Asian honey bee (Apis cerana) larval guts. Here, on the basis of our previously obtained deep-sequencing data from the 4-, 5-, and 6-day-old larval guts of A. cerana workers (Ac4, Ac5, and Ac6 groups), an in-depth transcriptome-wide investigation was conducted to decipher the expression pattern, regulatory manners, and potential roles of lncRNAs during the developmental process of A. cerana worker larval guts, followed by the verification of the relative expression of differentially expressed lncRNAs (DElncRNAs) and the targeting relationships within a competing endogenous RNA (ceRNA) axis. In the Ac4 vs. Ac5 and Ac5 vs. Ac6 comparison groups, 527 and 498 DElncRNAs were identified, respectively, which is suggestive of the dynamic expression of lncRNAs during the developmental process of larval guts. A cis-acting analysis showed that 330 and 393 neighboring genes of the aforementioned DElncRNAs were respectively involved in 29 and 32 functional terms, such as cellular processes and metabolic processes; these neighboring genes were also respectively engaged in 246 and 246 pathways such as the Hedgehog signaling pathway and the Wnt signaling pathway. Additionally, it was found that 79 and 76 DElncRNAs as potential antisense lncRNAs may, respectively, interact with 72 and 60 sense-strand mRNAs. An investigation of competing endogenous RNA (ceRNA) networks suggested that 75 (155) DElncRNAs in the Ac4 vs. Ac5 (Ac5 vs. Ac6) comparison group could target 7 (5) DEmiRNAs and further bind to 334 (248) DEmRNAs, which can be annotated to 33 (29) functional terms and 186 (210) pathways, including 12 (16) cellular- and humoral-immune pathways (lysosome pathway, necroptosis, MAPK signaling pathway, etc.) and 11 (10) development-associated signaling pathways (Wnt, Hippo, AMPK, etc.). The RT-qPCR detection of five randomly selected DElncRNAs confirmed the reliability of the used sequencing data. Moreover, the results of a dual-luciferase reporter assay were indicative of the binding relationship between MSTRG.11294.1 and miR-6001-y and between miR-6001-y and ncbi_107992440. These results demonstrate that DElncRNAs are likely to modulate the developmental process of larval guts via the regulation of the source genes' transcription, interaction with mRNAs, and ceRNA networks. Our findings not only yield new insights into the developmental mechanism underlying A. cerana larval guts, but also provide a candidate ceRNA axis for further functional dissection.
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Affiliation(s)
- Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - He Zang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Xin Jing
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Xiaoyu Liu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Peiyuan Zou
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Mengjun Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Zhijian Huang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.F.); (X.G.); (H.Z.); (S.G.); (X.J.); (Y.Z.); (X.L.); (P.Z.); (M.C.); (Z.H.); (D.C.)
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
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Fan X, Zhang W, Guo S, Zhu L, Zhang Y, Zhao H, Gao X, Jiang H, Zhang T, Chen D, Guo R, Niu Q. Expression Profile, Regulatory Network, and Putative Role of microRNAs in the Developmental Process of Asian Honey Bee Larval Guts. INSECTS 2023; 14:insects14050469. [PMID: 37233097 DOI: 10.3390/insects14050469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/09/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
MiRNAs, as a kind of key regulators in gene expression, play vital roles in numerous life activities from cellular proliferation and differentiation to development and immunity. However, little is known about the regulatory manner of miRNAs in the development of Asian honey bee (Apis cerana) guts. Here, on basis of our previously gained high-quality transcriptome data, transcriptome-wide identification of miRNAs in the larval guts of Apis cerana cerana was conducted, followed by investigation of the miRNAs' differential expression profile during the gut development. In addition to the regulatory network, the potential function of differentially expressed miRNAs (DEmiRNAs) was further analyzed. In total, 330, 351, and 321 miRNAs were identified in the 4-, 5-, and 6-day-old larval guts, respectively; among these, 257 miRNAs were shared, while 38, 51, and 36 ones were specifically expressed. Sequences of six miRNAs were confirmed by stem-loop RT-PCR and Sanger sequencing. Additionally, in the "Ac4 vs. Ac5" comparison group, there were seven up-regulated and eight down-regulated miRNAs; these DEmiRNAs could target 5041 mRNAs, involving a series of GO terms and KEGG pathways associated with growth and development, such as cellular process, cell part, Wnt, and Hippo. Comparatively, four up-regulated and six down-regulated miRNAs detected in the "Ac5 vs. Ac6" comparison group and the targets were associated with diverse development-related terms and pathways, including cell, organelle, Notch and Wnt. Intriguingly, it was noticed that miR-6001-y presented a continuous up-regulation trend across the developmental process of larval guts, implying that miR-6001-y may be a potential essential modulator in the development process of larval guts. Further investigation indicated that 43 targets in the "Ac4 vs. Ac5" comparison group and 31 targets in the "Ac5 vs. Ac6" comparison group were engaged in several crucial development-associated signaling pathways such as Wnt, Hippo, and Notch. Ultimately, the expression trends of five randomly selected DEmiRNAs were verified using RT-qPCR. These results demonstrated that dynamic expression and structural alteration of miRNAs were accompanied by the development of A. c. cerana larval guts, and DEmiRNAs were likely to participate in the modulation of growth as well as development of larval guts by affecting several critical pathways via regulation of the expression of target genes. Our data offer a basis for elucidating the developmental mechanism underlying Asian honey bee larval guts.
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Affiliation(s)
- Xiaoxue Fan
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Wende Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Sijia Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Leran Zhu
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiqiong Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haodong Zhao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xuze Gao
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Haibin Jiang
- Apiculture Science Institute of Jilin Province, Jilin 132000, China
| | - Tianze Zhang
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Dafu Chen
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Rui Guo
- College of Animal Sciences (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Apitherapy Research Institute of Fujian Province, Fuzhou 350002, China
| | - Qingsheng Niu
- Apiculture Science Institute of Jilin Province, Jilin 132000, China
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8
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Chi X, Wang Z, Wang Y, Liu Z, Wang H, Xu B. Cross-Kingdom Regulation of Plant-Derived miRNAs in Modulating Insect Development. Int J Mol Sci 2023; 24:ijms24097978. [PMID: 37175684 PMCID: PMC10178792 DOI: 10.3390/ijms24097978] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/15/2023] Open
Abstract
MicroRNAs (miRNAs), a class of non-coding small RNAs, are crucial regulatory factors in plants and animals at the post-transcriptional level. These tiny molecules suppress gene expression by complementary oligonucleotide binding to sites in the target messenger. Recently, the discovery of plant-derived miRNAs with cross-kingdom abilities to regulate gene expression in insects has promoted exciting discussion, although some controversies exist regarding the modulation of insect development by plant-derived miRNAs. Here, we review current knowledge about the mechanisms of miRNA biogenesis, the roles of miRNAs in coevolution between insects and plants, the regulation of insect development by plant-derived miRNAs, the cross-kingdom transport mechanisms of plant-derived miRNAs, and cross-kingdom regulation. In addition, the controversy regarding the modulation of insect development by plant-derived miRNAs also was discussed. Our review provides new insights for understanding complex plant-insect interactions and discovering new strategies for pest management and even crop genetic improvement.
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Affiliation(s)
- Xuepeng Chi
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Zhe Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Ying Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Zhenguo Liu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Hongfang Wang
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
| | - Baohua Xu
- College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271002, China
- Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai'an 271018, China
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9
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Jin MJ, Wang ZL, Wu ZH, He XJ, Zhang Y, Huang Q, Zhang LZ, Wu XB, Yan WY, Zeng ZJ. Phenotypic dimorphism between honeybee queen and worker is regulated by complicated epigenetic modifications. iScience 2023; 26:106308. [PMID: 36942051 PMCID: PMC10024153 DOI: 10.1016/j.isci.2023.106308] [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: 05/23/2022] [Revised: 01/12/2023] [Accepted: 02/24/2023] [Indexed: 03/14/2023] Open
Abstract
Phenotypic dimorphism between queens and workers is an important biological characteristic of honeybees that has been the subject of intensive research. The enormous differences in morphology, lifespan, physiology, and behavior between queens and workers are caused by a complicated set of factors. Epigenetic modifications are considered to play an important role in this process. In this study, we analyzed the differences in chromosome interactions and H3K27ac and H3K4me1 modifications between the queens and workers using high-throughput chromosome conformation capture (Hi-C) and Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) technologies. We found that the queens contain more chromosome interactions and more unique H3K27ac modifications than workers; in contrast, workers have more H3K4me1 modifications than queens. Moreover, we identified Map3k15 as a potential caste gene in queen-worker differentiation. Our results suggest that chromosomal conformation and H3K27ac and H3K4me1 modifications are involved in regulating queen-worker differentiation, which reveals that the queen-worker phenotypic dimorphism is regulated by multiple epigenetic modifications.
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Affiliation(s)
- Meng Jie Jin
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zhi Hao Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Yong Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P.R.China
- Jiangxi Province Honeybee Biology and Beekeeping, Nanchang, Jiangxi 330045, P. R. China
- Corresponding author
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10
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Jones BM, Rubin BER, Dudchenko O, Kingwell CJ, Traniello IM, Wang ZY, Kapheim KM, Wyman ES, Adastra PA, Liu W, Parsons LR, Jackson SR, Goodwin K, Davidson SM, McBride MJ, Webb AE, Omufwoko KS, Van Dorp N, Otárola MF, Pham M, Omer AD, Weisz D, Schraiber J, Villanea F, Wcislo WT, Paxton RJ, Hunt BG, Aiden EL, Kocher SD. Convergent and complementary selection shaped gains and losses of eusociality in sweat bees. Nat Ecol Evol 2023; 7:557-569. [PMID: 36941345 DOI: 10.1038/s41559-023-02001-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/18/2023] [Indexed: 03/23/2023]
Abstract
Sweat bees have repeatedly gained and lost eusociality, a transition from individual to group reproduction. Here we generate chromosome-length genome assemblies for 17 species and identify genomic signatures of evolutionary trade-offs associated with transitions between social and solitary living. Both young genes and regulatory regions show enrichment for these molecular patterns. We also identify loci that show evidence of complementary signals of positive and relaxed selection linked specifically to the convergent gains and losses of eusociality in sweat bees. This includes two pleiotropic proteins that bind and transport juvenile hormone (JH)-a key regulator of insect development and reproduction. We find that one of these proteins is primarily expressed in subperineurial glial cells that form the insect blood-brain barrier and that brain levels of JH vary by sociality. Our findings are consistent with a role of JH in modulating social behaviour and suggest that eusocial evolution was facilitated by alteration of the proteins that bind and transport JH, revealing how an ancestral developmental hormone may have been co-opted during one of life's major transitions. More broadly, our results highlight how evolutionary trade-offs have structured the molecular basis of eusociality in these bees and demonstrate how both directional selection and release from constraint can shape trait evolution.
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Affiliation(s)
- Beryl M Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Benjamin E R Rubin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Callum J Kingwell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Ian M Traniello
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Z Yan Wang
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Karen M Kapheim
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
- Department of Biology, Utah State University, Logan, UT, USA
| | - Eli S Wyman
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Per A Adastra
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Weijie Liu
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Lance R Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - S RaElle Jackson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Katharine Goodwin
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Shawn M Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Matthew J McBride
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
- Department of Chemistry, Princeton University, Princeton, NJ, USA
| | - Andrew E Webb
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Kennedy S Omufwoko
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Nikki Van Dorp
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Mauricio Fernández Otárola
- Biodiversity and Tropical Ecology Research Center (CIBET) and School of Biology, University of Costa Rica, San José, Costa Rica
| | - Melanie Pham
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Arina D Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David Weisz
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Joshua Schraiber
- Department of Biology, Temple University, Philadelphia, PA, USA
- Illumina Artificial Intelligence Laboratory, Illumina Inc, San Diego, CA, USA
| | - Fernando Villanea
- Department of Biology, Temple University, Philadelphia, PA, USA
- Department of Anthropology, University of Colorado Boulder, Boulder, CO, USA
| | - William T Wcislo
- Smithsonian Tropical Research Institute, Panama City, Republic of Panama
| | - Robert J Paxton
- Institute of Biology, Martin-Luther University Halle-Wittenberg, Halle, Germany
- German Centre for Integrative Biodiversity Research (iDiv), Halle-Jena-Leipzig, Germany
| | - Brendan G Hunt
- Department of Entomology, University of Georgia, Athens, GA, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Theoretical Biological Physics, Rice University, Houston, TX, USA
| | - Sarah D Kocher
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA.
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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11
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Chen X, Wang D, An J. Circular RNA ame_circ_2015 Function as microRNA Sponges in Regulating Egg-Laying of Honeybees ( Apis mellifera). LIFE (BASEL, SWITZERLAND) 2023; 13:life13010161. [PMID: 36676110 PMCID: PMC9865145 DOI: 10.3390/life13010161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
Abstract
Honeybees (Apis mellifera) are critical to maintaining ecological balance and are important pollinators. The oviposition behavior in honeybees is important and complex. Circular RNAs (circRNAs) are found to form circRNA-miRNA crosstalk and play important roles in reproduction processes. Here, dual luciferase reporter was used to confirm the crosstalk between ame_circ_2015 and ame_miR-14-3p. Functional experiments in vitro and in vivo were performed to investigate the biological functions of ame_circ_2015 in egg-laying of queens. The results showed that ame_circ_2015 directly target ame_miR-14-3p, and the expression of ame_circ_2015 was negatively correlated with ame_miR-14-3p expression. Overexpression results showed that ame_circ_2015 promoted the number of eggs laid and knockdown of ame_circ_2015 suppressed the number of eggs laid. It demonstrates that up-regulated ame_circ_2015 promotes the number of eggs laid by sponging ame_miR-14-3p. The study will provide information towards a better understanding of circRNA-miRNA crosstalk in egg-laying in honeybees.
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Affiliation(s)
- Xiao Chen
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-1013426240519
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jiandong An
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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12
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Abbas MN, Kausar S, Asma B, Ran W, Li J, Lin Z, Li T, Cui H. MicroRNAs reshape the immunity of insects in response to bacterial infection. Front Immunol 2023; 14:1176966. [PMID: 37153604 PMCID: PMC10161253 DOI: 10.3389/fimmu.2023.1176966] [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: 03/01/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
The interaction between bacteria and insects can significantly impact a wide range of different areas because bacteria and insects are widely distributed around the globe. The bacterial-insect interactions have the potential to directly affect human health since insects are vectors for disease transmission, and their interactions can also have economic consequences. In addition, they have been linked to high mortality rates in economically important insects, resulting in substantial economic losses. MicroRNAs (miRNAs) are types of non-coding RNAs involved in regulating gene expression post-transcriptionally. The length of miRNAs ranges from 19 to 22 nucleotides. MiRNAs, in addition to their ability to exhibit dynamic expression patterns, have a diverse range of targets. This enables them to govern various physiological activities in insects, like innate immune responses. Increasing evidence suggests that miRNAs have a crucial biological role in bacterial infection by influencing immune responses and other mechanisms for resistance. This review focuses on some of the most recent and exciting discoveries made in recent years, including the correlation between the dysregulation of miRNA expression in the context of bacterial infection and the progression of the infection. Furthermore, it describes how they profoundly impact the immune responses of the host by targeting the Toll, IMD, and JNK signaling pathways. It also emphasizes the biological function of miRNAs in regulating immune responses in insects. Finally, it also discusses current knowledge gaps about the function of miRNAs in insect immunity, in addition to areas that require more research in the future.
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Affiliation(s)
- Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Saima Kausar
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Bibi Asma
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Wenhao Ran
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
| | - Jingui Li
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
| | - Zini Lin
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
| | - Tiejun Li
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
- *Correspondence: Tiejun Li, ; Hongjuan Cui,
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
- *Correspondence: Tiejun Li, ; Hongjuan Cui,
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13
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Lewkowski O, Poehlein A, Daniel R, Erler S. In the battle of the disease: a transcriptomic analysis of European foulbrood-diseased larvae of the Western honey bee (Apis mellifera). BMC Genomics 2022; 23:837. [PMID: 36536278 PMCID: PMC9764631 DOI: 10.1186/s12864-022-09075-6] [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: 08/12/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND European foulbrood is a significant bacterial brood disease of Apis sp. and can cause severe and devastating damages in beekeeping operations. Nevertheless, the epidemiology of its causative agent Melissococcus plutonius has been begun to uncover but the underlying mechanisms of infection and cause of disease still is not well understood. Here, we sought to provide insight into the infection mechanism of EFB employing RNAseq in in vitro reared Apis mellifera larvae of two developmental stages to trace transcriptional changes in the course of the disease, including Paenibacillus alvei secondary infected individuals. RESULTS In consideration of the progressing development of the larva, we show that infected individuals incur a shift in metabolic and structural protein-encoding genes, which are involved in metabolism of crucial compounds including all branches of macronutrient metabolism, transport protein genes and most strikingly chitin and cuticle associated genes. These changes underpin the frequently observed developmental retardation in EFB disease. Further, sets of expressed genes markedly differ in different stages of infection with almost no overlap. In an earlier stage of infection, a group of regulators of the melanization response cascade and complement component-like genes, predominantly C-type lectin genes, are up-regulated while a differential expression of immune effector genes is completely missing. In contrast, late-stage infected larvae up-regulated the expression of antimicrobial peptides, lysozymes and prominent bacteria-binding haemocyte receptor genes compared to controls. While we clearly show a significant effect of infection on expressed genes, these changes may partly result from a shift in expression timing due to developmental alterations of infection. A secondary infection with P. alvei elicits a specific response with most of the M. plutonius associated differential immune effector gene expression missing and several immune pathway genes even down-regulated. CONCLUSION We conclude that with progressing infection diseased individuals undergo a systemic response with a change of metabolism and their activated immune defence repertoire. Moreover, larvae are capable of adjusting their response to a secondary invasion in late stage infections.
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Affiliation(s)
- Oleg Lewkowski
- grid.9018.00000 0001 0679 2801Molecular Ecology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Anja Poehlein
- grid.7450.60000 0001 2364 4210Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, 37077 Göttingen, Germany
| | - Rolf Daniel
- grid.7450.60000 0001 2364 4210Department of Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, 37077 Göttingen, Germany
| | - Silvio Erler
- grid.9018.00000 0001 0679 2801Molecular Ecology, Institute of Biology, Martin-Luther-University Halle-Wittenberg, 06099 Halle (Saale), Germany ,grid.13946.390000 0001 1089 3517Institute for Bee Protection, Julius Kühn-Institute (JKI) – Federal Research Centre for Cultivated Plants, 38104 Braunschweig, Germany ,grid.6738.a0000 0001 1090 0254Zoological Institute, Technische Universität Braunschweig, 38106 Braunschweig, Germany
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14
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Lowe R, Wojciechowski M, Ellis N, Hurd PJ. Chromatin accessibility-based characterisation of brain gene regulatory networks in three distinct honey bee polyphenisms. Nucleic Acids Res 2022; 50:11550-11562. [PMID: 36330958 PMCID: PMC9723623 DOI: 10.1093/nar/gkac992] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
The honey bee genome has the capacity to produce three phenotypically distinct organisms (two diploid female castes: queen and worker, and a haploid male drone). Previous studies have implicated metabolic flux acting via epigenetic regulation in directing nutrition-driven phenotypic plasticity in the honey bee. However, the cis-acting DNA regulatory elements that establish tissue and polyphenism -specific epigenomes and gene expression programmes, remain unclear. Using a high resolution multiomic approach including assay for transposase-accessible chromatin by sequencing (ATAC-seq), RNA-seq and ChIP-seq, we produce the first genome-wide maps of the regulatory landscape across all three adult honey bee phenotypes identifying > 5000 regulatory regions in queen, 7500 in worker and 6500 in drone, with the vast majority of these sites located within intronic regions. These regions are defined by positive enrichment of H3K27ac and depletion of H3K4me3 and show a positive correlation with gene expression. Using ATAC-seq footprinting we determine queen, worker and drone -specific transcription factor occupancy and uncover novel phenotype-specific regulatory networks identifying two key nuclear receptors that have previously been implicated in caste-determination and adult behavioural maturation in honey bees; ecdysone receptor and ultraspiracle. Collectively, this study provides novel insights into key gene regulatory networks that are associated with these distinct polyphenisms in the honey bee.
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Affiliation(s)
- Robert Lowe
- RER Consultants, 28 Worbeck Road, London SE20 7SW, UK
| | - Marek Wojciechowski
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Nancy Ellis
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Paul J Hurd
- School of Biological and Behavioural Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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15
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He XJ, Barron AB, Yang L, Chen H, He YZ, Zhang LZ, Huang Q, Wang ZL, Wu XB, Yan WY, Zeng ZJ. Extent and complexity of RNA processing in honey bee queen and worker caste development. iScience 2022; 25:104301. [PMID: 35573188 PMCID: PMC9097701 DOI: 10.1016/j.isci.2022.104301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/12/2022] [Accepted: 04/21/2022] [Indexed: 11/03/2022] Open
Abstract
The distinct honeybee (Apis mellifera) worker and queen castes have become a model for the study of genomic mechanisms of phenotypic plasticity. Here we performed a nanopore-based direct RNA sequencing with exceptionally long reads to compare the mRNA transcripts between queen and workers at three points during their larval development. We found thousands of significantly differentially expressed transcript isoforms (DEIs) between queen and worker larvae. These DEIs were formatted by a flexible splicing system. We showed that poly(A) tails participated in this caste differentiation by negatively regulating the expression of DEIs. Hundreds of isoforms uniquely expressed in either queens or workers during their larval development, and isoforms were expressed at different points in queen and worker larval development demonstrating a dynamic relationship between isoform expression and developmental mechanisms. These findings show the full complexity of RNA processing and transcript expression in honey bee phenotypic plasticity. Honeybee caste differentiation has a complexity of RNA processing Isoforms differentially express between queens and workers during larval development Isoforms are formatted by a flexible alternative splicing system Poly(A) tails are negatively correlated with isoform expression
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Affiliation(s)
- Xu Jiang He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China.,Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi 330045, P. R. of China
| | - Andrew B Barron
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Liu Yang
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, P. R. of China
| | - Hu Chen
- Wuhan Benagen Tech Solutions Company Limited, Wuhan, Hubei 430021, P. R. of China
| | - Yu Zhu He
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Li Zhen Zhang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Qiang Huang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Zi Long Wang
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Xiao Bo Wu
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Wei Yu Yan
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China
| | - Zhi Jiang Zeng
- Honeybee Research Institute, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, P. R. of China.,Jiangxi Province Honeybee Biology and Beekeeping Nanchang, Jiangxi 330045, P. R. of China
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16
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Watson OT, Buchmann G, Young P, Lo K, Remnant EJ, Yagound B, Shambrook M, Hill AF, Oldroyd BP, Ashe A. Abundant small RNAs in the reproductive tissues and eggs of the honey bee, Apis mellifera. BMC Genomics 2022; 23:257. [PMID: 35379185 PMCID: PMC8978429 DOI: 10.1186/s12864-022-08478-9] [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: 09/09/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022] Open
Abstract
Background Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Results Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in the semen of other animals. Intriguingly we also find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. Conclusions We conclude that small RNAs may play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of-origin effects on gene expression and reproductive physiology. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08478-9.
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Affiliation(s)
- Owen T Watson
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Gabriele Buchmann
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Paul Young
- Molecular Cardiology and Biophysics Division, Victor Chang Cardiac Research Institute NSW 2010, Darlinghurst, Australia
| | - Kitty Lo
- School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Emily J Remnant
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Boris Yagound
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mitch Shambrook
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Andrew F Hill
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria, 3086, Australia.,Institute for Health and Sport, Victoria University, Footscray, VIC, Australia
| | - Benjamin P Oldroyd
- BEE Laboratory, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, 2006, Australia. .,Wissenschaftskolleg zu Berlin, Wallotstrasse 19, 14193, Berlin, Germany.
| | - Alyson Ashe
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia.
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17
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Pulliainen U, Morandin C, Bos N, Sundström L, Schultner E. Social environment affects sensory gene expression in ant larvae. INSECT MOLECULAR BIOLOGY 2022; 31:1-9. [PMID: 34418191 DOI: 10.1111/imb.12732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/08/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Social insects depend on communication to regulate social behaviour. This also applies to their larvae, which are commonly exposed to social interactions and can react to social stimulation. However, how social insect larvae sense their environment is not known. Using RNAseq, we characterized expression of sensory-related genes in larvae of the ant Formica fusca, upon exposure to two social environments: isolation without contact to other individuals, and stimulation via the presence of other developing individuals. Expression of key sensory-related genes was higher following social stimulation, and larvae expressed many of the same sensory-related genes as adult ants and larvae of other insects, including genes belonging to the major insect chemosensory gene families. Our study provides first insights into the molecular changes associated with social information perception in social insect larvae.
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Affiliation(s)
- U Pulliainen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - C Morandin
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Ecology and Evolution, Biophore, University of Lausanne, Lausanne, Switzerland
| | - N Bos
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Biology, Faculty of Sciences, University of Copenhagen, Copenhagen, Denmark
| | - L Sundström
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Tvärminne Zoological Station, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - E Schultner
- Zoology and Evolutionary Biology, University of Regensburg, Regensburg, Germany
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18
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Martin N, Hulbert AJ, Mitchell TW, Else PL. Regulation of membrane phospholipids during the adult life of worker honey bee. JOURNAL OF INSECT PHYSIOLOGY 2022; 136:104310. [PMID: 34530044 DOI: 10.1016/j.jinsphys.2021.104310] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 06/13/2023]
Abstract
Two female castes that are genetically identical are found in honey bees: workers and queens. Adult female honey bees differ in their morphology and behaviors, but the most intriguing difference between the castes is the difference in their longevity. Queens live for years while workers live generally for weeks. The mechanisms that mediate this extraordinary difference in lifespan remain mostly unknown. Both castes share similar developmental stages and are fed liquid food (i.e. a jelly) during development. However, after emergence, workers begin to feed on pollen while queens are fed the same larval food for their entire life. Pollen has a high content of polyunsaturated fatty acids (PUFA) while royal jelly has negligible amounts. The difference in food during adult life leads to drastic changes in membrane phospholipids of female honey bees, and those changes have been proposed as mechanisms that could explain the difference in lifespan. To provide further details on those mechanisms, we characterized the membrane phospholipids of adult workers at seven different ages covering all life-history stages. Our results suggest that the majority of changes in worker membranes occur in the first four days of adult life. Shortly after emergence, workers increase their level of total phospholipids by producing phospholipids that contained saturated (SFA) and monounsaturated fatty acids (MUFA). From the second day, workers start replacing fatty acid chains from those pre-synthesized molecules with PUFA acquired from pollen. After four days, worker membranes are set and appear to be maintained for the rest of adult life, suggesting that damaged PUFA are replaced effectively. Plasmalogen phospholipids increase continuously throughout worker adult life, suggesting that plasmalogen might help to reduce lipid peroxidation in worker membranes. We postulate that the diet-induced increase in PUFA in worker membranes makes them far more prone to lipid-based oxidative damage compared to queens.
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Affiliation(s)
- N Martin
- School of Medicine, University of Wollongong, NSW 2522, Australia; School of Earth, Atmospheric and Life Sciences, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW 2522, Australia
| | - A J Hulbert
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, NSW 2522, Australia
| | - T W Mitchell
- School of Medicine, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW 2522, Australia
| | - P L Else
- School of Medicine, University of Wollongong, NSW 2522, Australia; Illawarra Health and Medical Research Institute (IHMRI), Wollongong, NSW 2522, Australia.
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19
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Wedd L, Kucharski R, Maleszka R. DNA Methylation in Honey Bees and the Unresolved Questions in Insect Methylomics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:159-176. [DOI: 10.1007/978-3-031-11454-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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Tönges S, Venkatesh G, Andriantsoa R, Hanna K, Gatzmann F, Raddatz G, Carneiro VC, Lyko F. Location-Dependent DNA Methylation Signatures in a Clonal Invasive Crayfish. Front Cell Dev Biol 2021; 9:794506. [PMID: 34957121 PMCID: PMC8695926 DOI: 10.3389/fcell.2021.794506] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/22/2021] [Indexed: 01/16/2023] Open
Abstract
DNA methylation is an important epigenetic modification that has been repeatedly implied in organismal adaptation. However, many previous studies that have linked DNA methylation patterns to environmental parameters have been limited by confounding factors, such as cell-type heterogeneity and genetic variation. In this study, we analyzed DNA methylation variation in marbled crayfish, a clonal and invasive freshwater crayfish that is characterized by a largely tissue-invariant methylome and negligible genetic variation. Using a capture-based subgenome bisulfite sequencing approach that covers a small, variably methylated portion of the marbled crayfish genome, we identified specific and highly localized DNA methylation signatures for specimens from geographically and ecologically distinct wild populations. These results were replicated both biologically and technically by re-sampling at different time points and by using independent methodology. Finally, we show specific methylation signatures for laboratory animals and for laboratory animals that were reared at a lower temperature. Our results thus demonstrate the existence of context-dependent DNA methylation signatures in a clonal animal.
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Affiliation(s)
| | | | | | | | | | | | | | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center (DKFZ), Heidelberg, Germany
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21
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Dogantzis KA, Tiwari T, Conflitti IM, Dey A, Patch HM, Muli EM, Garnery L, Whitfield CW, Stolle E, Alqarni AS, Allsopp MH, Zayed A. Thrice out of Asia and the adaptive radiation of the western honey bee. SCIENCE ADVANCES 2021; 7:eabj2151. [PMID: 34860547 PMCID: PMC8641936 DOI: 10.1126/sciadv.abj2151] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The origin of the western honey bee Apis mellifera has been intensely debated. Addressing this knowledge gap is essential for understanding the evolution and genetics of one of the world’s most important pollinators. By analyzing 251 genomes from 18 native subspecies, we found support for an Asian origin of honey bees with at least three expansions leading to African and European lineages. The adaptive radiation of honey bees involved selection on a few genomic “hotspots.” We found 145 genes with independent signatures of selection across all bee lineages, and these genes were highly associated with worker traits. Our results indicate that a core set of genes associated with worker and colony traits facilitated the adaptive radiation of honey bees across their vast distribution.
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Affiliation(s)
- Kathleen A. Dogantzis
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Tanushree Tiwari
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Ida M. Conflitti
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Alivia Dey
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
| | - Harland M. Patch
- Department of Entomology, The Pennsylvania State University, State College, PA, USA
| | - Elliud M. Muli
- Department of Life Science, South Eastern Kenya University (SEKU), P.O. Box 170-90200, Kitui, Kenya
| | - Lionel Garnery
- Laboratoire Evolution Génome Comportement Ecologie (EGCE) UMR 9191, Gif sur-Yvette, France
| | - Charles W. Whitfield
- Department of Entomology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eckart Stolle
- LIB–Leibniz Institute for the Analysis of Biodiversity Change Museum Koenig, Center of Molecular Biodiversity Research Adenauerallee 160, 53113 Bonn, Germany
| | - Abdulaziz S. Alqarni
- Department of Plant Protection, College of Food and Agriculture Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Michael H. Allsopp
- Plant Protection Research Institute, Agricultural Research Council, Stellenbosch, South Africa
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele Street, Toronto, M3J 1P3 Ontario, Canada
- Corresponding author.
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22
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Bataglia L, Simões ZLP, Nunes FMF. Active genic machinery for epigenetic RNA modifications in bees. INSECT MOLECULAR BIOLOGY 2021; 30:566-579. [PMID: 34291855 DOI: 10.1111/imb.12726] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 05/06/2023]
Abstract
Epitranscriptomics is an emerging field of investigation dedicated to the study of post-transcriptional RNA modifications. RNA methylations regulate RNA metabolism and processing, including changes in response to environmental cues. Although RNA modifications are conserved from bacteria to eukaryotes, there is little evidence of an epitranscriptomic pathway in insects. Here we identified genes related to RNA m6 A (N6-methyladenine) and m5 C (5-methylcytosine) methylation machinery in seven bee genomes (Apis mellifera, Melipona quadrifasciata, Frieseomelitta varia, Eufriesea mexicana, Bombus terrestris, Megachile rotundata and Dufourea novaeangliae). In A. mellifera, we validated the expression of methyltransferase genes and found that the global levels of m6 A and m5 C measured in the fat body and brain of adult workers differ significantly. Also, m6 A levels were differed significantly mainly between the fourth larval instar of queens and workers. Moreover, we found a conserved m5 C site in the honeybee 28S rRNA. Taken together, we confirm the existence of epitranscriptomic machinery acting in bees and open avenues for future investigations on RNA epigenetics in a wide spectrum of hymenopteran species.
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Affiliation(s)
- L Bataglia
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Z L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil
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23
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Vieira J, Freitas FCP, Cristino AS, Moda LMR, Martins JR, Bitondi MMG, Simões ZLP, Barchuk AR. miRNA-34 and miRNA-210 target hexamerin genes enhancing their differential expression during early brain development of honeybee (Apis mellifera) castes. INSECT MOLECULAR BIOLOGY 2021; 30:594-604. [PMID: 34309096 DOI: 10.1111/imb.12728] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
During the honeybee larval stage, queens develop larger brains than workers, with morphological differentiation appearing at the fourth larval phase (L4), just after a boost in nutritional difference both prospective females experience. The molecular promoters of this caste-specific brain development are already ongoing in previous larval phases. Transcriptomic analyses revealed a set of differentially expressed genes in the L3 brains of queens and workers, which represents the early molecular response to differential feeding females receive during larval development. Three genes of this set, hex70b, hex70c and hex110, are more highly transcribed in the brain of workers than in queens. The microRNAs miR-34, miR-210 and miR-317 are in higher levels in the queens' brain at the same phase of larval development. Here, we tested the hypothesis that the brain of workers expresses higher levels of hexamerins than that of queens during key phases of larval development and that this differential hexamerin genes expression is further enhanced by the repressing activity of miR-34, miR-210 and miR-317. Our transcriptional analyses showed that hex70b, hex70c and hex110 genes are differentially expressed in the brain of L3 and L4 larval phases of honeybee queens and workers. In silico reconstructed miRNA-mRNA interaction networks were validated using luciferase assays, which showed miR-34 and miR-210 negatively regulate hex70b and hex110 genes by directly and redundantly binding their 3'UTR (untranslated region) sequences. Taken together, our results suggest that miR-34 and miR-210 act together promoting differential brain development in honeybee castes by downregulating the expression of the putative antineurogenic hexamerin genes hex70b and hex110.
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Affiliation(s)
- J Vieira
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - F C P Freitas
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A S Cristino
- Griffith Institute for Drug Discovery, Griffith University, Queensland, Australia
| | - L M R Moda
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - J R Martins
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
| | - M M G Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Z L P Simões
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - A R Barchuk
- Departamento de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal de Alfenas, UNIFAL-MG, Alfenas, Minas Gerais, Brazil
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24
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Karouta C, Kucharski R, Hardy K, Thomson K, Maleszka R, Morgan I, Ashby R. Transcriptome-based insights into gene networks controlling myopia prevention. FASEB J 2021; 35:e21846. [PMID: 34405458 DOI: 10.1096/fj.202100350rr] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/11/2022]
Abstract
Myopia (short-sightedness), usually caused by excessive elongation of the eye during development, has reached epidemic proportions worldwide. In animal systems including the chicken model, several treatments have been shown to inhibit ocular elongation and experimental myopia. Although diverse in their apparent mechanism of action, each one leads to a reduction in the rate of ocular growth. We hypothesize that a defined set of retinal molecular changes may underlie growth inhibition, irrespective of the treatment agent used. Accordingly, across five well-established but diverse methods of inhibiting myopia, significant overlap is seen in the retinal transcriptome profile (transcript levels and alternative splicing events) in chicks when analyzed by RNA-seq. Within the two major pathway networks enriched during growth inhibition, that of cell signaling and circadian entrainment, transcription factors form the largest functional grouping. Importantly, a large percentage of those genes forming the defined retinal response are downstream targets of the transcription factor EGR1 which itself shows a universal response to all five growth-inhibitory treatments. This supports EGR1's previously implicated role in ocular growth regulation. Finally, by contrasting our data with human linkage and GWAS studies on refractive error, we confirm the applicability of our study to the human condition. Together, these findings suggest that a universal set of transcriptome changes, which sit within a well-defined retinal network that cannot be bypassed, is fundamental to growth regulation, thus paving a way for designing novel targets for myopia therapies.
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Affiliation(s)
- Cindy Karouta
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Robert Kucharski
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Kristine Hardy
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Kate Thomson
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia
| | - Ryszard Maleszka
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Ian Morgan
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Regan Ashby
- Centre for Research in Therapeutic Solutions, Biomedical Sciences, Faculty of Science and Technology, University of Canberra, Canberra, ACT, Australia.,Research School of Biology, Australian National University, Canberra, ACT, Australia
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25
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Gharehdaghi L, Bakhtiarizadeh MR, He K, Harkinezhad T, Tahmasbi G, Li F. Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut. BMC Genomics 2021; 22:587. [PMID: 34344297 PMCID: PMC8336336 DOI: 10.1186/s12864-021-07916-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
Background MicroRNA (miRNA) is a class of small noncoding RNAs, which targets on thousands of mRNA and thus plays important roles in many biological processes. It has been reported that miRNA has cross-species regulation functions between parasitoid-host, or plant-animal, etc. For example, several plant miRNAs enter into the honey bees and regulate gene expression. However, whether cross-species regulation function of miRNAs is a universal mechanism remains a debate question. Results We have evaluated transmission of miRNAs from sunflower and sedr plants into the midgut of honey bee using RNA-Seq analyses complemented with confirmation by RT-qPCR. The results showed that at least 11 plant miRNAs were found in the midgut of honey bee feeding by sunflower and sedr pollen. Among which, nine miRNAs, including miR-30d, miR-143, miR-148a, miR-21, let-7 g, miR-26a, miR-126, miR-27a, and miR-203, were shared between the sunflower- and sedr-fed honey bees, suggesting they might have essential roles in plant-insect interactions. Moreover, existence of these co-shared miRNAs presents a strong evidence to support the successful transmission of miRNAs into the midgut of the insect. In total, 121 honeybee mRNAs were predicted to be the target of these 11 plant-derived miRNAs. Interestingly, a sedr-derived miRNA, miR-206, targets on 53 honeybee genes. Kyoto Encyclopedia of Genes and Genome (KEGG) analyses showed that these target genes are significantly involved in hippo signaling pathway-fly, Wnt signaling pathway, and N-Glycan biosynthesis. Conclusions In summary, these results provide evidence of cross-species regulation function of miRNA between honeybee and flowering host plants, extending our understanding of the molecular interactions between plants and animals. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07916-4.
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Affiliation(s)
- Leila Gharehdaghi
- Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | | | - Kang He
- Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China
| | - Taher Harkinezhad
- Department of Animal Science, Faculty of Agriculture, University of Zanjan, Zanjan, Iran
| | - Gholamhosein Tahmasbi
- Department of Honeybee, Agricultural Research, Education and Extension Organization (AREEO), Animal Science Research Institute of Iran, Karaj, Iran
| | - Fei Li
- Ministry of Agriculture and Rural Affairs Key Lab of Molecular Biology of Crop Pathogens and Insects/Institute of Insect Sciences, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China.
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26
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Shan S, Wang SN, Song X, Khashaveh A, Lu ZY, Dhiloo KH, Li RJ, Gao XW, Zhang YJ. Characterization and target gene analysis of microRNAs in the antennae of the parasitoid wasp Microplitis mediator. INSECT SCIENCE 2021; 28:1033-1048. [PMID: 32496619 DOI: 10.1111/1744-7917.12832] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/14/2020] [Accepted: 05/26/2020] [Indexed: 06/11/2023]
Abstract
MicroRNAs (miRNAs), a class of non-coding single-strand RNA molecules encoded by endogenous genes, are about 21-24 nucleotides long and are involved in the post-transcriptional regulation of gene expression in plants and animals. Generally, the types and quantities of miRNAs in the different tissues of an organism are diverse, and these divergences may be related to their specific functions. Here we have identified 296 known miRNAs and 46 novel miRNAs in the antennae of the parasitoid wasp Microplitis mediator by high-throughput sequencing. Thirty-three miRNAs were predicted to target olfactory-associated genes, including odorant binding proteins (OBPs), chemosensory proteins, odorant receptors (ORs), ionotropic receptors (IRs) and gustatory receptors. Among these, 17 miRNAs were significantly highly expressed in the antennae, four miRNAs were highly expressed both in the antennae and head or wings, while the remaining 12 miRNAs were mainly expressed in the head, thorax, abdomen, legs and wings. Notably, miR-9a-5p and miR-2525-3p were highly expressed in male antennae, whereas miR-1000-5p and novel-miR-13 were enriched in female antennae. The 17 miRNAs highly expressed in antennae are likely to be associated with olfaction, and were predicted to target one OBP (targeted by miR-3751-3p), one IR (targeted by miR-7-5p) and 14 ORs (targeted by 15 miRNAs including miR-6-3p, miR-9a-5p, miR-9b-5p, miR-29-5p, miR-71-5p, miR-275-3p, miR-1000-5p, miR-1000-3p, miR-2525-3p, miR-6012-3p, miR-9719-3p, novel-miR-10, novel-miR-13, novel-miR-14 and novel-miR-28). These candidate olfactory-associated miRNAs are all likely to be involved in chemoreception through the regulation of chemosensory gene expression in the antennae of M. mediator.
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Affiliation(s)
- Shuang Shan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Ning Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Plant and Environment Protection, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Xuan Song
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Adel Khashaveh
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zi-Yun Lu
- IPM Center of Hebei Province, Key Laboratory of Integrated Pest Management on Crops in Northern Region of North China, Ministry of Agriculture, Plant Protection Institute, Hebei Academy of Agricultural and Forestry Sciences, Baoding, Hebei, China
| | - Khalid Hussain Dhiloo
- Department of Entomology, Faculty of Crop Protection, Sindh Agriculture University, Tandojam, Pakistan
| | - Rui-Jun Li
- College of Plant Protection, Agricultural University of Hebei, Baoding, Hebei, China
| | - Xi-Wu Gao
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Yong-Jun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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27
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Molecular underpinnings of the early brain developmental response to differential feeding in the honey bee Apis mellifera. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2021; 1864:194732. [PMID: 34242825 DOI: 10.1016/j.bbagrm.2021.194732] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/14/2022]
Abstract
Brain differential morphogenesis in females is one of the major phenotypic manifestations of caste development in honey bees. Brain diphenism appears at the fourth larval phase as a result of the differential feeding regime developing females are submitted during early phases of larval development. Here, we used a forward genetics approach to test the early brain molecular response to differential feeding leading to the brain diphenism observed at later developmental phases. Using RNA sequencing analysis, we identified 53 differentially expressed genes (DEGs) between the brains of queens and workers at the third larval phase. Since miRNAs have been suggested to play a role in caste differentiation after horizontal and vertical transmission, we tested their potential participation in regulating the DEGs. The miRNA-mRNA interaction network, including the DEGs and the royal- and worker-jelly enriched miRNA populations, revealed a subset of miRNAs potentially involved in regulating the expression of DEGs. The interaction of miR-34, miR-210, and miR-317 with Takeout, Neurotrophin-1, Forked, and Masquerade genes was experimentally confirmed using a luciferase reporter system. Taken together, our results reconstruct the regulatory network that governs the development of the early brain diphenism in honey bees.
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28
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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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29
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Kang I, Kim W, Lim JY, Lee Y, Shin C. Organ-specific transcriptome analysis reveals differential gene expression in different castes under natural conditions in Apis cerana. Sci Rep 2021; 11:11267. [PMID: 34050219 PMCID: PMC8163739 DOI: 10.1038/s41598-021-90635-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/12/2021] [Indexed: 02/04/2023] Open
Abstract
Honeybees are one of the most environmentally important insects, as their pollination of various plant species contributes to the balance among different ecosystems. It has been studied extensively for their unique attribute of forming a caste society. Unlike other insects, honeybees communicate socially by secreting pheromones or by exhibiting specific patterns of motion. In the honeybee industry, the Asian honeybees (Apis cerana) and the Western honeybees (Apis mellifera) are dominant species. However, molecular research on the transcriptomes of A. cerana has not been studied as extensively as those of A. mellifera. Therefore, in this study, caste-specific transcriptional differences were analyzed, which provides a comprehensive analysis of A. cerana. In our dataset, we analyzed gene expression profiles using organs from worker, drone, and queen bees. This gene-expression profile helped us obtain more detailed information related to organ-specific genes, immune response, detoxification mechanisms, venom-specific genes, and ovary development. From our result, we found 4096 transcripts representing different gene-expression pattern in each organ. Our results suggest that caste-specific transcripts of each organ were expressed differently even under natural conditions. These transcriptome-wide analyses provide new insights into A. cerana and that promote honeybee research and conservation.
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Affiliation(s)
- Igojo Kang
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Woojin Kim
- grid.411545.00000 0004 0470 4320Department of Agricultural Biology, Jeonbuk National University, Jeonju, 54896 Republic of Korea
| | - Jae Yun Lim
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea
| | - Yun Lee
- grid.31501.360000 0004 0470 5905Department of Applied Biology and Chemistry, Seoul National University, Seoul, 08826 Republic of Korea
| | - Chanseok Shin
- grid.31501.360000 0004 0470 5905Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 08826 Republic of Korea ,grid.31501.360000 0004 0470 5905Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826 Republic of Korea
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30
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Fonseca PLC, Mucherino M JJ, Porto JAM, Armache JN, de Almeida JPP, da Silva FF, Olmo RP, Faria IJDS, de Carvalho DS, Góes-Neto A, Corrêa RX, Pirovani CP, Pacheco LGC, Costa MA, Aguiar ERGR. Genome-wide identification of miRNAs and target regulatory network in the invasive ectoparasitic mite Varroa destructor. Genomics 2021; 113:2290-2303. [PMID: 34044154 DOI: 10.1016/j.ygeno.2021.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 12/29/2022]
Abstract
Varroa destructor is an ectoparasite mite that attacks bees leading to colony disorders worldwide. microRNAs (miRNAs) are key molecules used by eukaryotes to post-transcriptional control of gene expression. Nevertheless, still lack information aboutV. destructor miRNAs and its regulatory networks. Here, we used an integrative strategy to characterize the miRNAs in the V. destructor mite. We identified 310 precursors that give rise to 500 mature miRNAs, which 257 are likely mite-specific elements. miRNAs showed canonical length ranging between 18 and 25 nucleotides and 5' uracil preference. Top 10 elements concentrated over 80% of total miRNA expression, with bantam alone representing ~50%. We also detected non-templated bases in precursor-derived small RNAs, indicative of miRNA post-transcriptional regulatory mechanisms. Finally, we note that conserved miRNAs control similar processes in different organisms, suggesting a conservative role. Altogether, our findings contribute to the better understanding of the mite biology that can assist future studies on varroosis control.
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Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Jonathan J Mucherino M
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil; Department of Forest Management, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Mérida 5101, Venezuela
| | - Joel A M Porto
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Juliana N Armache
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - João Paulo P de Almeida
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Felipe F da Silva
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Roenick P Olmo
- Université de Strasbourg, CNRS UPR9022, Inserm, Strasbourg, France
| | - Isaque J da S Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Daniel S de Carvalho
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil; Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Ronan X Corrêa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Carlos P Pirovani
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Marco Antônio Costa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil.
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31
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10-hydroxy-2E-decenoic acid (10HDA) does not promote caste differentiation in Melipona scutellaris stingless bees. Sci Rep 2021; 11:9882. [PMID: 33972627 PMCID: PMC8110752 DOI: 10.1038/s41598-021-89212-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
In bees from genus Melipona, differential feeding is not enough to fully explain female polyphenism. In these bees, there is a hypothesis that in addition to the environmental component (food), a genetic component is also involved in caste differentiation. This mechanism has not yet been fully elucidated and may involve epigenetic and metabolic regulation. Here, we verified that the genes encoding histone deacetylases HDAC1 and HDAC4 and histone acetyltransferase KAT2A were expressed at all stages of Melipona scutellaris, with fluctuations between developmental stages and castes. In larvae, the HDAC genes showed the same profile of Juvenile Hormone titers-previous reported-whereas the HAT gene exhibited the opposite profile. We also investigated the larvae and larval food metabolomes, but we did not identify the putative queen-fate inducing compounds, geraniol and 10-hydroxy-2E-decenoic acid (10HDA). Finally, we demonstrated that the histone deacetylase inhibitor 10HDA-the major lipid component of royal jelly and hence a putative regulator of honeybee caste differentiation-was unable to promote differentiation in queens in Melipona scutellaris. Our results suggest that epigenetic and hormonal regulations may act synergistically to drive caste differentiation in Melipona and that 10HDA is not a caste-differentiation factor in Melipona scutellaris.
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32
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The microRNA miR-14 Regulates Egg-Laying by Targeting EcR in Honeybees ( Apis mellifera). INSECTS 2021; 12:insects12040351. [PMID: 33919981 PMCID: PMC8071020 DOI: 10.3390/insects12040351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022]
Abstract
Honeybees (Apis mellifera) are important pollinators and are commonly used for honey production. The oviposition behavior in honeybees is complex and errors in oviposition could affect the development of the bee colony. Recent studies reported that RNA-RNA cross-talk played a critical role in several biological processes, including reproduction. Ecdysone receptor (EcR) and miR-14 were previously reported to play important roles in egg-laying. Moreover, EcR was predicted to be the target gene of miR-14 and may form miR-14-EcR cross-talk. In this study, knocking down and overexpression of miR-14 and EcR in queen model were implemented. The effect of RNA expression of miR-14 and EcR on the number of eggs laid by honeybee queens were analyzed. Further, luciferase assay was used to confirm the target relation between miR-14 and 3'UTR of EcR. The results showed that the expression of miR-14 and EcR was associated with the number of eggs laid by queens. In specific, inhibition of miR-14 expression enhanced the number of eggs laid, while overexpression of EcR enhanced the number of eggs laid. Lastly, we determined that miR-14 directly targets the mRNA of EcR. These findings suggest that the cross-talk of miR-14-EcR plays an important role in the number of eggs laid by honeybee queens.
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33
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Dyson CJ, Goodisman MAD. Gene Duplication in the Honeybee: Patterns of DNA Methylation, Gene Expression, and Genomic Environment. Mol Biol Evol 2021; 37:2322-2331. [PMID: 32243528 DOI: 10.1093/molbev/msaa088] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Accepted: 03/27/2020] [Indexed: 12/12/2022] Open
Abstract
Gene duplication serves a critical role in evolutionary adaptation by providing genetic raw material to the genome. The evolution of duplicated genes may be influenced by epigenetic processes such as DNA methylation, which affects gene function in some taxa. However, the manner in which DNA methylation affects duplicated genes is not well understood. We studied duplicated genes in the honeybee Apis mellifera, an insect with a highly sophisticated social structure, to investigate whether DNA methylation was associated with gene duplication and genic evolution. We found that levels of gene body methylation were significantly lower in duplicate genes than in single-copy genes, implicating a possible role of DNA methylation in postduplication gene maintenance. Additionally, we discovered associations of gene body methylation with the location, length, and time since divergence of paralogous genes. We also found that divergence in DNA methylation was associated with divergence in gene expression in paralogs, although the relationship was not completely consistent with a direct link between DNA methylation and gene expression. Overall, our results provide further insight into genic methylation and how its association with duplicate genes might facilitate evolutionary processes and adaptation.
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Affiliation(s)
- Carl J Dyson
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA
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34
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Huang M, Dong J, Guo H, Wang D. Effects of Dinotefuran on Brain miRNA Expression Profiles in Young Adult Honey Bees (Hymenopptera: Apidae). JOURNAL OF INSECT SCIENCE (ONLINE) 2021; 21:3. [PMID: 33400795 PMCID: PMC7785045 DOI: 10.1093/jisesa/ieaa131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Indexed: 05/05/2023]
Abstract
Honey bees are important pollinators of wild plants and crops. MicroRNAs (miRNAs) are endogenous regulators of gene expression. In this study, we initially determined that the lethal concentration 50 (LC50) of dinotefuran was 0.773 mg/l. Then, the expression profiles and differentially expressed miRNAs (DE miRNAs) in honey bee brains after 1, 5, and 10 d of treatment with the lethal concentration 10 (LC10) of dinotefuran were explored via deep small-RNA sequencing and bioinformatics. In total, 2, 23, and 27 DE miRNAs were identified after persistent exposure to the LC10 of dinotefuran for 1, 5, and 10 d, respectively. Some abundant miRNAs, such as ame-miR-375-3p, ame-miR-281-5p, ame-miR-3786-3p, ame-miR-10-5p, and ame-miR-6037-3p, were extremely significantly differentially expressed. Enrichment analysis suggested that the candidate target genes of the DE miRNAs are involved in the regulation of biological processes, cellular processes, and behaviors. These results expand our understanding of the regulatory roles of miRNAs in honey bee Apis mellifera (Hymenopptera: Apidae) responses to neonicotinoid insecticides and facilitate further studies on the functions of miRNAs in honey bees.
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Affiliation(s)
- Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haikun Guo
- Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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35
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Villagra C, Frías-Lasserre D. Epigenetic Molecular Mechanisms in Insects. NEOTROPICAL ENTOMOLOGY 2020; 49:615-642. [PMID: 32514997 DOI: 10.1007/s13744-020-00777-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/06/2020] [Indexed: 06/11/2023]
Abstract
Insects are the largest animal group on Earth both in biomass and diversity. Their outstanding success has inspired genetics and developmental research, allowing the discovery of dynamic process explaining extreme phenotypic plasticity and canalization. Epigenetic molecular mechanisms (EMMs) are vital for several housekeeping functions in multicellular organisms, regulating developmental, ontogenetic trajectories and environmental adaptations. In Insecta, EMMs are involved in the development of extreme phenotypic divergences such as polyphenisms and eusocial castes. Here, we review the history of this research field and how the main EMMs found in insects help to understand their biological processes and diversity. EMMs in insects confer them rapid response capacity allowing insect either to change with plastic divergence or to keep constant when facing different stressors or stimuli. EMMs function both at intra as well as transgenerational scales, playing important roles in insect ecology and evolution. We discuss on how EMMs pervasive influences in Insecta require not only the control of gene expression but also the dynamic interplay of EMMs with further regulatory levels, including genetic, physiological, behavioral, and environmental among others, as was earlier proposed by the Probabilistic Epigenesis model and Developmental System Theory.
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Affiliation(s)
- C Villagra
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile.
| | - D Frías-Lasserre
- Instituto de Entomología, Univ Metropolitana de Ciencias de la Educación, Santiago, Chile
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36
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Guo S, Wang X, Kang L. Special Significance of Non- Drosophila Insects in Aging. Front Cell Dev Biol 2020; 8:576571. [PMID: 33072758 PMCID: PMC7536347 DOI: 10.3389/fcell.2020.576571] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/04/2020] [Indexed: 12/30/2022] Open
Abstract
Aging is the leading risk factor of human chronic diseases. Understanding of aging process and mechanisms facilitates drug development and the prevention of aging-related diseases. Although many aging studies focus on fruit fly as a canonical insect system, minimal attention is paid to the potentially significant roles of other insects in aging research. As the most diverse group of animals, insects provide many aging types and important complementary systems for aging studies. Insect polyphenism represents a striking example of the natural variation in longevity and aging rate. The extreme intraspecific variations in the lifespan of social insects offer an opportunity to study how aging is differentially regulated by social factors. Insect flight, as an extremely high-intensity physical activity, is suitable for the investigation of the complex relationship between metabolic rate, oxidative stress, and aging. Moreover, as a "non-aging" state, insect diapause not only slows aging process during diapause phase but also affects adult longevity during/after diapause. In the past two decades, considerable progress has been made in understanding the molecular basis of aging regulation in insects. Herein, the recent research progress in non-Drosophila insect aging was reviewed, and its potential utilization in aging in the future was discussed.
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Affiliation(s)
- Siyuan Guo
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xianhui Wang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Le Kang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
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37
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Imrit MA, Dogantzis KA, Harpur BA, Zayed A. Eusociality influences the strength of negative selection on insect genomes. Proc Biol Sci 2020; 287:20201512. [PMID: 32811314 PMCID: PMC7482261 DOI: 10.1098/rspb.2020.1512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/23/2020] [Indexed: 12/16/2022] Open
Abstract
While much of the focus of sociobiology concerns identifying genomic changes that influence social behaviour, we know little about the consequences of social behaviour on genome evolution. It has been hypothesized that social evolution can influence the strength of negative selection via two mechanisms. First, division of labour can influence the efficiency of negative selection in a caste-specific manner; indirect negative selection on worker traits is theoretically expected to be weaker than direct selection on queen traits. Second, increasing social complexity is expected to lead to relaxed negative selection because of its influence on effective population size. We tested these two hypotheses by estimating the strength of negative selection in honeybees, bumblebees, paper wasps, fire ants and six other insects that span the range of social complexity. We found no consistent evidence that negative selection was significantly stronger on queen-biased genes relative to worker-biased genes. However, we found strong evidence that increased social complexity reduced the efficiency of negative selection. Our study clearly illustrates how changes in behaviour can influence patterns of genome evolution by modulating the strength of natural selection.
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Affiliation(s)
- Mohammad A. Imrit
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada, M3 J 1P3
| | - Kathleen A. Dogantzis
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada, M3 J 1P3
| | - Brock A. Harpur
- Department of Entomology, Purdue University, 901 W State Street, West Lafayette, IN 47907, USA
| | - Amro Zayed
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada, M3 J 1P3
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38
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Kapheim KM, Jones BM, Søvik E, Stolle E, Waterhouse RM, Bloch G, Ben-Shahar Y. Brain microRNAs among social and solitary bees. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200517. [PMID: 32874647 PMCID: PMC7428247 DOI: 10.1098/rsos.200517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/15/2020] [Indexed: 05/03/2023]
Abstract
Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are unknown. We examined the relationship between social organization and lineage-specific microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologues in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are not enriched for genes with caste-biased expression or genes under positive selection in social species. Together, these results suggest that novel miRNAs may coevolve with novel genes, and thus contribute to lineage-specific patterns of evolution in bees, but do not appear to have significant influence on social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.
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Affiliation(s)
- Karen M. Kapheim
- Department of Biology, Utah State University, 5305 Old Main Hill, Logan, UT 84322, USA
- Author for correspondence: Karen M. Kapheim e-mail:
| | - Beryl M. Jones
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Eirik Søvik
- Department of Science and Mathematics, Volda University College, 6100 Volda, Norway
| | - Eckart Stolle
- Centre of Molecular Biodiversity Research, Forschungsmuseum Alexander Koenig, Adenauerallee 160, 53113 Bonn, Germany
| | - Robert M. Waterhouse
- Department of Ecology and Evolution, University of Lausanne and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Guy Bloch
- Department of Ecology, Evolution and Behavior, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yehuda Ben-Shahar
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
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39
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Exploring DNA Methylation Diversity in the Honey Bee Brain by Ultra-Deep Amplicon Sequencing. EPIGENOMES 2020; 4:epigenomes4020010. [PMID: 34968244 PMCID: PMC8594699 DOI: 10.3390/epigenomes4020010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 02/04/2023] Open
Abstract
Understanding methylation dynamics in organs or tissues containing many different cell types is a challenging task that cannot be efficiently addressed by the low-depth bisulphite sequencing of DNA extracted from such sources. Here we explored the feasibility of ultra-deep bisulphite sequencing of long amplicons to reveal the brain methylation patterns in three selected honey bee genes analysed across five distinct conditions on the Illumina MiSeq platform. By combing 15 libraries in one run we achieved a very high sequencing depth of 240,000–340,000 reads per amplicon, suggesting that most of the cell types in the honey bee brain, containing approximately 1 million neurons, are represented in this dataset. We found a small number of gene-specific patterns for each condition in individuals of different ages and performing distinct tasks with 80–90% of those were represented by no more than a dozen patterns. One possibility is that such a small number of frequent patterns is the result of differentially methylated epialleles, whereas the rare and less frequent patterns reflect activity-dependent modifications. The condition-specific methylation differences within each gene appear to be position-dependent with some CpGs showing significant changes and others remaining stable in a methylated or non-methylated state. Interestingly, no significant loss of methylation was detected in very old individuals. Our findings imply that these diverse patterns represent a special challenge in the analyses of DNA methylation in complex tissues and organs that cannot be investigated by low-depth genome-wide bisulphite sequencing. We conclude that ultra-deep sequencing of gene-specific amplicons combined with genotyping of differentially methylated epialleles is an effective way to facilitate more advanced neuro-epigenomic studies in honey bees and other insects.
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Xiao S, Wang B, Li K, Xiong S, Ye X, Wang J, Zhang J, Yan Z, Wang F, Song Q, Stanley DW, Ye G, Fang Q. Identification and characterization of miRNAs in an endoparasitoid wasp, Pteromalus puparum. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21633. [PMID: 31587364 DOI: 10.1002/arch.21633] [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: 07/29/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) are a form of endogenous small noncoding RNAs that regulate protein-coding gene expression at the posttranscriptional level. So far, knowledge of miRNAs in parasitoids remains rudimentary. We investigated miRNAs in Pteromalus puparum, a pupal endoparasitoid wasp with genome and transcriptome sequences completed. In this study, we constructed eight small RNA libraries from selected developmental stages and genders: male embryos, male larvae, male pupae, male adults, mixed-sex embryos, mixed-sex larvae, mixed-sex pupae, and female adults. We identified 254 mature miRNAs with 5p/3p arm features originated from 75 known and 119 novel miRNA genes in P. puparum, 88 of which reside in 26 clusters. The miRNAs in more than half of the clusters exhibit a consistent expression pattern, indicating they were co-transcribed from a long transcript. Comparing miRNA expression in the eight libraries, we found that 84 mature miRNAs were differentially expressed between embryos and larvae, 20 between larvae and pupae, and 26 between pupae and adults. We found some miRNAs were differentially expressed between sexes in embryos (10), larvae (29), pupae (8), and adults (14). Target predictions resulted in 211,571 miRNA-mRNA interactions for 254 different mature miRNAs. These miRNAs may be involved in sexual and developmental regulation of gene expression.
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Affiliation(s)
- Shan Xiao
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Beibei Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kai Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jiao Zhang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri
| | - David W Stanley
- USDA Agricultural Research Service, Biological Control of Insects Research Laboratory, Columbia, Missouri
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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Ledda B, Ottaggio L, Izzotti A, Sukkar SG, Miele M. Small RNAs in eucaryotes: new clues for amplifying microRNA benefits. Cell Biosci 2020; 10:1. [PMID: 31911829 PMCID: PMC6942390 DOI: 10.1186/s13578-019-0370-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022] Open
Abstract
miRNAs, the smallest nucleotide molecules able to regulate gene expression at post transcriptional level, are found in both animals and plants being involved in fundamental processes for growth and development of living organisms. The number of miRNAs has been hypothesized to increase when some organisms specialized the process of mastication and grinding of food. Further to the vertical transmission, miRNAs can undergo horizontal transmission among different species, in particular between plants and animals. In the last years, an increasing number of studies reported that miRNA passage occurs through feeding, and that in animals, plant miRNAs can survive the gastro intestinal digestion and transferred by blood into host cells, where they can exert their functions modulating gene expression. The present review reports studies on miRNAs during evolution, with particular focus on biogenesis and mechanisms regulating their stability in plants and animals. The different biogenesis and post biogenesis modifications allow to discriminate miRNAs of plant origin from those of animal origin, and make it possible to better clarify the controversial question on whether a possible cross-kingdom miRNA transfer through food does exist. The majority of human medicines and supplements derive from plants and a regular consumption of plant food is suggested for their beneficial effects in the prevention of metabolic diseases, cancers, and dietary related disorders. So far, these beneficial effects have been generally attributed to the content of secondary metabolites, whereas mechanisms regarding other components remain unclear. Therefore, in light of the above reported studies miRNAs could result another component for the medical properties of plants. miRNAs have been mainly studied in mammals characterizing their sequences and molecular targets as available in public databases. The herein presented studies provide evidences that miRNA situation is much more complex than the static situation reported in databases. Indeed, miRNAs may have redundant activities, variable sequences, different methods of biogenesis, and may be differently influenced by external and environmental factors. In-depth knowledge of mechanisms of synthesis, regulation and transfer of plant miRNAs to other species can open new frontiers in the therapy of many human diseases, including cancer.
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Affiliation(s)
- Bernardetta Ledda
- 1Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy
| | - Laura Ottaggio
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| | - Alberto Izzotti
- 1Department of Health Sciences, University of Genoa, Via A. Pastore 1, 16132 Genoa, Italy.,Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| | - Samir G Sukkar
- UOD Dietetic and Clinical Nutrition, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
| | - Mariangela Miele
- Mutagenesis and Cancer Prevention Unit, IRCCS Ospedale Policlinico San Martino, L.Go R. Benzi, 10, Genoa, Italy
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Gualtieri C, Leonetti P, Macovei A. Plant miRNA Cross-Kingdom Transfer Targeting Parasitic and Mutualistic Organisms as a Tool to Advance Modern Agriculture. FRONTIERS IN PLANT SCIENCE 2020; 11:930. [PMID: 32655608 PMCID: PMC7325723 DOI: 10.3389/fpls.2020.00930] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/08/2020] [Indexed: 05/13/2023]
Abstract
MicroRNAs (miRNAs), defined as small non-coding RNA molecules, are fine regulators of gene expression. In plants, miRNAs are well-known for regulating processes spanning from cell development to biotic and abiotic stress responses. Recently, miRNAs have been investigated for their potential transfer to distantly related organisms where they may exert regulatory functions in a cross-kingdom fashion. Cross-kingdom miRNA transfer has been observed in host-pathogen relations as well as symbiotic or mutualistic relations. All these can have important implications as plant miRNAs can be exploited to inhibit pathogen development or aid mutualistic relations. Similarly, miRNAs from eukaryotic organisms can be transferred to plants, thus suppressing host immunity. This two-way lane could have a significant impact on understanding inter-species relations and, more importantly, could leverage miRNA-based technologies for agricultural practices. Additionally, artificial miRNAs (amiRNAs) produced by engineered plants can be transferred to plant-feeding organisms in order to specifically regulate their cross-kingdom target genes. This minireview provides a brief overview of cross-kingdom plant miRNA transfer, focusing on parasitic and mutualistic relations that can have an impact on agricultural practices and discusses some opportunities related to miRNA-based technologies. Although promising, miRNA cross-kingdom transfer remains a debated argument. Several mechanistic aspects, such as the availability, transfer, and uptake of miRNAs, as well as their potential to alter gene expression in a cross-kingdom manner, remain to be addressed.
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Affiliation(s)
- Carla Gualtieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Paola Leonetti
- Institute for Sustainable Plant Protection, National Council of Research, Research Unit of Bari, Bari, Italy
| | - Anca Macovei
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- *Correspondence: Anca Macovei,
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Liu M, Huang J, Zhang G, Liu X, An J. Analysis of miRNAs in the Heads of Different Castes of the Bumblebee Bombus lantschouensis (Hymenoptera: Apidae). INSECTS 2019; 10:E349. [PMID: 31623265 PMCID: PMC6835379 DOI: 10.3390/insects10100349] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 10/11/2019] [Accepted: 10/14/2019] [Indexed: 12/13/2022]
Abstract
Bumblebees are important insect pollinators for many wildflowers and crops. MicroRNAs (miRNAs) are endogenous non-coding small RNAs that regulate different biological functions in insects. In this study, the miRNAs in the heads of the three castes of the bumblebee Bombus lantschouensis were identified and characterized by small RNA deep sequencing. The significant differences in the expression of miRNAs and their target genes were analyzed. The results showed that the length of the small RNA reads from males, queens, and workers was distributed between 18 and 30 nt, with a peak at 22 nt. A total of 364 known and 89 novel miRNAs were identified from the heads of the three castes. The eight miRNAs with the highest expressed levels in males, queens, and workers were identical, although the order of these miRNAs based on expression differed. The male vs. queen, male vs. worker, and worker vs. queen comparisons identified nine, fourteen, and four miRNAs with significant differences in expression, respectively. The different castes were clustered based on the differentially expressed miRNAs (DE miRNAs), and the expression levels of the DE miRNAs obtained by RT-qPCR were consistent with the read counts obtained through Solexa sequencing. The putative target genes of these DE miRNAs were enriched in 29 Gene Ontology (GO) terms, and catalytic activity was the most enriched GO term, as demonstrated by its association with 2837 target genes in the male vs. queen comparison, 3535 target genes in the male vs. worker comparison, and 2185 target genes in the worker vs. queen comparison. This study highlights the characteristics of the miRNAs in the three B. lantschouensis castes and will aid further studies on the functions of miRNAs in bumblebees.
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Affiliation(s)
- Meijuan Liu
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| | - Jiaxing Huang
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| | - Guangshuo Zhang
- Key Laboratory for Insect-Pollinator Biology of the Ministry of Agriculture and Rural Affairs, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| | - Xiaofeng Liu
- School of Life Science, Peking University, Beijing 100871, China.
| | - Jiandong An
- School of Life Science, Peking University, Beijing 100871, China.
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Marshall H, Lonsdale ZN, Mallon EB. Methylation and gene expression differences between reproductive and sterile bumblebee workers. Evol Lett 2019; 3:485-499. [PMID: 31636941 PMCID: PMC6791180 DOI: 10.1002/evl3.129] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 07/09/2019] [Accepted: 07/12/2019] [Indexed: 12/18/2022] Open
Abstract
Phenotypic plasticity is the production of multiple phenotypes from a single genome and is notably observed in social insects. Multiple epigenetic mechanisms have been associated with social insect plasticity, with DNA methylation being explored to the greatest extent. DNA methylation is thought to play a role in caste determination in Apis mellifera, and other social insects, but there is limited knowledge on its role in other bee species. In this study, we analyzed whole genome bisulfite sequencing and RNA-seq data sets from head tissue of reproductive and sterile castes of the eusocial bumblebee Bombus terrestris. We found that genome-wide methylation in B. terrestris is similar to other holometabolous insects and does not differ between reproductive castes. We did, however, find differentially methylated genes between castes, which are enriched for multiple biological processes including reproduction. However, we found no relationship between differential methylation and differential gene expression or differential exon usage between castes. Our results also indicate high intercolony variation in methylation. These findings suggest that methylation is associated with caste differences but may serve an alternate function, other than direct caste determination in this species. This study provides the first insights into the nature of a bumblebee caste-specific methylome as well as its interaction with gene expression and caste-specific alternative splicing, providing greater understanding of the role of methylation in phenotypic plasticity within social bee species. Future experimental work is needed to determine the function of methylation and other epigenetic mechanisms in insects.
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Affiliation(s)
- Hollie Marshall
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
| | - Zoë N. Lonsdale
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
| | - Eamonn B. Mallon
- Department of Genetics and Genome BiologyThe University of LeicesterLeicesterUnited Kingdom
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Yagound B, Smith NMA, Buchmann G, Oldroyd BP, Remnant EJ. Unique DNA Methylation Profiles Are Associated with cis-Variation in Honey Bees. Genome Biol Evol 2019; 11:2517-2530. [PMID: 31406991 PMCID: PMC6740151 DOI: 10.1093/gbe/evz177] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation is an important epigenetic modification that mediates diverse processes such as cellular differentiation, phenotypic plasticity, and genomic imprinting. Mounting evidence suggests that local DNA sequence variation can be associated with particular DNA methylation states, indicating that the interplay between genetic and epigenetic factors may contribute synergistically to the phenotypic complexity of organisms. Social insects such as ants, bees, and wasps have extensive phenotypic plasticity manifested in their different castes, and this plasticity has been associated with variation in DNA methylation. Yet, the influence of genetic variation on DNA methylation state remains mostly unknown. Here we examine the importance of sequence-specific methylation at the genome-wide level, using whole-genome bisulfite sequencing of the semen of individual honey bee males. We find that individual males harbor unique DNA methylation patterns in their semen, and that genes that are more variable at the epigenetic level are also more likely to be variable at the genetic level. DNA sequence variation can affect DNA methylation by modifying CG sites directly, but can also be associated with local variation in cis that is not CG-site specific. We show that covariation in sequence polymorphism and DNA methylation state contributes to the individual-specificity of epigenetic marks in social insects, which likely promotes their retention across generations, and their capacity to influence evolutionary adaptation.
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Affiliation(s)
- Boris Yagound
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Nicholas M A Smith
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Gabriele Buchmann
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Benjamin P Oldroyd
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
| | - Emily J Remnant
- Behaviour and Genetics of Social Insects Laboratory, School of Life and Environmental Sciences, University of Sydney, Australia
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Chen D, Du Y, Chen H, Fan Y, Fan X, Zhu Z, Wang J, Xiong C, Zheng Y, Hou C, Diao Q, Guo R. Comparative Identification of MicroRNAs in Apis cerana cerana Workers' Midguts in Responseto Nosema ceranae Invasion. INSECTS 2019; 10:E258. [PMID: 31438582 PMCID: PMC6780218 DOI: 10.3390/insects10090258] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/19/2019] [Accepted: 08/19/2019] [Indexed: 02/06/2023]
Abstract
Here, the expression profiles and differentially expressed miRNAs (DEmiRNAs) in the midguts of Apis cerana cerana workers at 7 d and 10 d post-inoculation (dpi) with N. ceranae were investigated via small RNA sequencing and bioinformatics. Five hundred and twenty nine (529) known miRNAs and 25 novel miRNAs were identified in this study, and the expression of 16 predicted miRNAs was confirmed by Stem-loop RT-PCR. A total of 14 DEmiRNAs were detected in the midgut at 7 dpi, including eight up-regulated and six down-regulated miRNAs, while 12 DEmiRNAs were observed in the midgut at 10 dpi, including nine up-regulated and three down-regulated ones. Additionally, five DEmiRNAs were shared, while nine and seven DEmiRNAs were specifically expressed in midguts at 7 dpi and 10 dpi. Gene ontology analysis suggested some DEmiRNAs and corresponding target mRNAs were involved in various functions including immune system processes and response to stimulus. KEGG pathway analysis shed light on the potential functions of some DEmiRNAs in regulating target mRNAs engaged in material and energy metabolisms, cellular immunity and the humoral immune system. Further investigation demonstrated a complex regulation network between DEmiRNAs and their target mRNAs, with miR-598-y, miR-252-y, miR-92-x and miR-3654-y at the center. Our results can facilitate future exploration of the regulatory roles of miRNAs in host responses to N. ceranae, and provide potential candidates for further investigation of the molecular mechanisms underlying eastern honeybee-microsporidian interactions.
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Affiliation(s)
- Dafu Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yu Du
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huazhi Chen
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuanchan Fan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xiaoxue Fan
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zhiwei Zhu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jie Wang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiling Xiong
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yanzhen Zheng
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chunsheng Hou
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Qingyun Diao
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Rui Guo
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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Chen X, Shi W, Chen C. Differential circular RNAs expression in ovary during oviposition in honey bees. Genomics 2019; 111:598-606. [DOI: 10.1016/j.ygeno.2018.03.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Revised: 03/10/2018] [Accepted: 03/19/2018] [Indexed: 02/02/2023]
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Matsunami M, Nozawa M, Suzuki R, Toga K, Masuoka Y, Yamaguchi K, Maekawa K, Shigenobu S, Miura T. Caste-specific microRNA expression in termites: insights into soldier differentiation. INSECT MOLECULAR BIOLOGY 2019; 28:86-98. [PMID: 30126008 DOI: 10.1111/imb.12530] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Eusocial insects have polyphenic caste systems in which each caste exhibits characteristic morphology and behaviour. In insects, caste systems arose independently in different lineages, such as Isoptera and Hymenoptera. Although partial molecular mechanisms for the development of eusociality in termites have been clarified by the functional analysis of genes and hormones, the contribution of microRNAs (miRNAs) to caste differentiation is unknown. To understand the role of miRNAs in termite caste polyphenism, we performed small RNA sequencing in a subterranean termite (Reticulitermes speratus) and identified the miRNAs that were specifically expressed in the soldier and worker castes. Of the 550 miRNAs annotated in the R. speratus genome, 74 were conserved in insects and 174 were conserved in other termite species. We found that eight miRNAs (mir-1, mir-125, mir-133, mir-2765, mir-87a and three termite-specific miRNAs) are differentially expressed (DE) in soldiers and workers of R. speratus. This differential expression was experimentally verified for five miRNAs by real-time quantitative PCR. Further, four of the eight DE miRNAs in soldier and worker termite castes were also differentially expressed in hymenopteran castes. The finding that Isoptera and Hymenoptera shared several DE miRNAs amongst castes suggests that these miRNAs evolved independently in these phylogenetically distinct lineages.
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Affiliation(s)
- M Matsunami
- Laboratory of Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
- Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - M Nozawa
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Japan
| | - R Suzuki
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - K Toga
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
- Department of Biosciences, College of Humanities and Sciences, Nihon University, Tokyo, Japan
| | - Y Masuoka
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - K Yamaguchi
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - K Maekawa
- Graduate School of Science and Engineering, University of Toyama, Toyama, Japan
| | - S Shigenobu
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki, Japan
| | - T Miura
- Laboratory of Ecological Genetics, Graduate School of Environmental Science, Hokkaido University, Sapporo, Japan
- Misaki Marine Biological Station, University of Tokyo, Miura, Kanagawa, Japan
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Kashani B, Hasani Bidgoli M, Motahari SA, Sedaghat N, Modarressi MH. You are what you eat: Sequence analysis reveals how plant microRNAs may regulate the human genome. Comput Biol Med 2019; 106:106-113. [PMID: 30708219 DOI: 10.1016/j.compbiomed.2019.01.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/01/2019] [Accepted: 01/21/2019] [Indexed: 01/15/2023]
Abstract
BACKGROUND Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. METHODS miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally alignment with the human CDS (41 results). The identified genes were further analyzed in-silico to find their functions and relations to human diseases. RESULTS Four common plant miRNAs were identified to match perfectly with 22 human transcripts. The identified target genes were involved in a broad range of body functions, from muscle contraction to tumor suppression. We could also indicate some connections between these findings and folk herbology and botanical medicine. CONCLUSIONS The food that we regularly eat has a great potential in affecting our genome and altering body functions. Plant miRNAs can provide means of designing drugs for a vast range of health problems including obesity and cancer, since they target genes involved in cell cycle (CCNC), digestion (GIPR) and muscular contractions (MYLK). They can also target regions of CDS for which we still have no sufficient information, to help boost our knowledge of the human genome.
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Affiliation(s)
- Bahareh Kashani
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | | | - Nafiseh Sedaghat
- Computer Engineering School, Iran University of Science and Technology, Tehran, Iran
| | - Mohammad Hossein Modarressi
- Department of Medical Genetics, Faculty of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran.
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50
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Abstract
More than 70% of eukaryotic genomes are transcribed into RNA transcripts, the majority of these transcripts are noncoding protein, and their biological functions are largely unknown. Over the last decade, the application of high-throughput sequencing technologies has led to the description of almost all cellular coding and noncoding RNA transcripts except perhaps for those transcripts that are lowly abundant or those present only in specific cells that are underrepresented in sampled tissue(s). An often underrepresented class of noncoding are long noncoding RNAs (lncRNAs), and these often play key regulatory functions for many biological processes such as cell identity and cell division. However, the purification and functional characterization in vitro are still a challenge in both animal and plant experimental systems. Here, we describe in detail methodology for purification of specific cell types, bioinformatic annotation of lncRNAs, and investigation of biological function using the reference plant Arabidopsis thaliana.
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Affiliation(s)
- Trung Do
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Zhipeng Qu
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Iain Searle
- Department of Molecular and Biomedical Sciences, School of Biological Sciences, The University of Adelaide, Adelaide, SA, Australia.
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