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Sun Y, Liu X, Shan X, Wang Y, Zhong C, Lu C, Guan B, Yao S, Huo Y, Sun R, Wei M, Dong Z. Comprehensive investigation of differentially expressed ncRNAs, mRNAs, and their ceRNA networks in the regulation of shell color formation in clam, Cyclina sinensis. Gene 2024; 911:148346. [PMID: 38452877 DOI: 10.1016/j.gene.2024.148346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/29/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Noncoding RNAs (ncRNAs) have gained significant attention in recent years due to their crucial roles in various biological processes. However, our understanding of the expression and functions of ncRNAs in Cyclina sinensis, an economically important marine bivalve, remains limited. This study aimed to address this knowledge gap by systematically identifying ncRNAs in the mantles of C. sinensis with purple and white shells. Through our analysis, we identified a differential expression of 1244 mRNAs, 196 lncRNAs, 49 circRNAs, and 23 miRNAs between purple- and white-shell clams. Functional enrichment analysis revealed the involvement of these differentially expressed ncRNAs in biomineralization and pigmentation processes. To gain further insights into the regulatory mechanisms underlying shell color formation, we established competitive endogenous RNA (ceRNA) networks. These networks allowed us to identify targeted differentially expressed miRNAs (DEMis) and genes associated with shell color formation. Based on the ceRNA networks, we obtained an up-down-up lncRNA-miRNA-mRNA network consisting of 13 upregulated lncRNAs and a circRNA-miRNA-mRNA network comprising three upregulated circRNAs (novel_circ_0004787, novel_circ_0001165, novel_circ_0000245). Through these networks, we identified and selected an upregulated novel gene (evm.TU.Hic_asm_7.988) and a downregulated sponge miRNA (hru-miR-1985) as potential contributors to shell color regulation. In summary, the present investigation offers a comprehensive analysis of ncRNA catalogs expressed in the clam mantle of C. sinensis. The findings enhance our comprehension of the molecular mechanisms governing shell coloration and offer new perspectives for selective breeding of C. sinensis in the future.
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Affiliation(s)
- Yuyan Sun
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Xuxiao Liu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Xin Shan
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Yiwo Wang
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Chongyu Zhong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Chaofa Lu
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China
| | - Bin Guan
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Shun Yao
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Yujia Huo
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Runkai Sun
- Jiangsu Marine Resources Development Institute, Lianyungang 222000, China
| | - Min Wei
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
| | - Zhiguo Dong
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, Lianyungang 222000, China; Jiangsu Marine Resources Development Institute, Lianyungang 222000, China; Jiangsu Key Laboratory of Marine Biotechnology, Jiangsu Ocean University, Lianyungang 222000, China; Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Jiangsu Ocean University, Lianyungang 222000, China.
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2
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Lafuente E, Duneau D, Beldade P. Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation. Mol Ecol 2024; 33:e17294. [PMID: 38366327 DOI: 10.1111/mec.17294] [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: 09/13/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.
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Affiliation(s)
- E Lafuente
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - D Duneau
- UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - P Beldade
- cE3c (Center for Ecology, Evolution and Environmental Changes) & CHANGE (Global Change and Sustainability Institute), FCUL, Lisboa, Portugal
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3
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Wang S, Yang H, Hu Y, Zhang C, Fan D. Multi-Omics Reveals the Effect of Population Density on the Phenotype, Transcriptome and Metabolome of Mythimna separata. INSECTS 2023; 14:68. [PMID: 36661996 PMCID: PMC9861010 DOI: 10.3390/insects14010068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Population-density-dependent polymorphism is important in the biology of some agricultural pests. The oriental armyworm (Mythimna separata) is a lepidopteran pest (family Noctuidae). As the population density increases, its body color becomes darker, and the insect eats more and causes greater damage to crops. The molecular mechanisms underlying this phase change are not fully clear. Here, we used transcriptomic and metabolomic methods to study the effect of population density on the differentiation of second-day sixth instar M. separata larvae. The transcriptomic analysis identified 1148 differentially expressed genes (DEGs) in gregarious-type (i.e., high-population-density) armyworms compared with solitary-type (low-population-density) armyworms; 481 and 667 genes were up- and downregulated, respectively. The metabolomic analysis identified 137 differentially accumulated metabolites (DAMs), including 59 upregulated and 78 downregulated. The analysis of DEGs and DAMs showed that activation of the insulin-like signaling pathway promotes the melanization of gregarious armyworms and accelerates the decomposition of saccharides, which promotes the gregarious type to take in more food. The gregarious type is more capable of digesting and absorbing proteins and decreases energy consumption by inhibiting transcription and translation processes. The phase change traits of the armyworm are thus attributable to plasticity of its energy metabolism. These data broaden our understanding of the molecular mechanisms of insect-density-dependent polymorphism.
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Chen J, Zhu H, Wang R, Su X, Ruan Z, Pan Y, Peng Q. Functional Dissection of Protein Kinases in Sexual Development and Female Receptivity of Drosophila. Front Cell Dev Biol 2022; 10:923171. [PMID: 35757001 PMCID: PMC9220291 DOI: 10.3389/fcell.2022.923171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
Protein phosphorylation is crucial for a variety of biological functions, but how it is involved in sexual development and behavior is rarely known. In this study, we performed a screen of RNA interference targeting 177 protein kinases in Drosophila and identified 13 kinases involved in sexual development in one or both sexes. We further identified that PKA and CASK promote female sexual behavior while not affecting female differentiation. Knocking down PKA or CASK in about five pairs of pC1 neurons in the central brain affects the fine projection but not cell number of these pC1 neurons and reduces virgin female receptivity. We also found that PKA and CASK signaling is required acutely during adulthood to promote female sexual behavior. These results reveal candidate kinases required for sexual development and behaviors and provide insights into how kinases would regulate neuronal development and physiology to fine tune the robustness of sexual behaviors.
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Affiliation(s)
- Jiangtao Chen
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Huan Zhu
- School of Biological and Medical Engineering, Southeast University, Nanjing, China
| | - Rong Wang
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xiangbin Su
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Zongcai Ruan
- School of Biological and Medical Engineering, Southeast University, Nanjing, China
| | - Yufeng Pan
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Qionglin Peng
- The Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
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5
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Lafuente E, Alves F, King JG, Peralta CM, Beldade P. Many ways to make darker flies: Intra- and interspecific variation in Drosophila body pigmentation components. Ecol Evol 2021; 11:8136-8155. [PMID: 34188876 PMCID: PMC8216949 DOI: 10.1002/ece3.7646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 04/14/2021] [Accepted: 04/18/2021] [Indexed: 12/13/2022] Open
Abstract
Body pigmentation is an evolutionarily diversified and ecologically relevant trait with substantial variation within and between species, and important roles in animal survival and reproduction. Insect pigmentation, in particular, provides some of the most compelling examples of adaptive evolution, including its ecological significance and genetic bases. Pigmentation includes multiple aspects of color and color pattern that may vary more or less independently, and can be under different selective pressures. We decompose Drosophila thorax and abdominal pigmentation, a valuable eco-evo-devo model, into distinct measurable traits related to color and color pattern. We investigate intra- and interspecific variation for those traits and assess its different sources. For each body part, we measured overall darkness, as well as four other pigmentation properties distinguishing between background color and color of the darker pattern elements that decorate each body part. By focusing on two standard D. melanogaster laboratory populations, we show that pigmentation components vary and covary in distinct manners depending on sex, genetic background, and temperature during development. Studying three natural populations of D. melanogaster along a latitudinal cline and five other Drosophila species, we then show that evolution of lighter or darker bodies can be achieved by changing distinct component traits. Our results paint a much more complex picture of body pigmentation variation than previous studies could uncover, including patterns of sexual dimorphism, thermal plasticity, and interspecific diversity. These findings underscore the value of detailed quantitative phenotyping and analysis of different sources of variation for a better understanding of phenotypic variation and diversification, and the ecological pressures and genetic mechanisms underlying them.
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Affiliation(s)
- Elvira Lafuente
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Present address:
Swiss Federal Institute of Aquatic Science and TechnologyDepartment of Aquatic EcologyDübendorfSwitzerland
| | | | - Jessica G. King
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Present address:
Institute of Evolutionary BiologySchool of Biological SciencesUniversity of EdinburghEdinburghUK
| | - Carolina M. Peralta
- Instituto Gulbenkian de CiênciaOeirasPortugal
- Present address:
Max Planck Institute for Evolutionary BiologyPlönGermany
| | - Patrícia Beldade
- Instituto Gulbenkian de CiênciaOeirasPortugal
- CE3C: Centre for Ecology, Evolution, and Environmental Changes, Faculty of SciencesUniversity of LisbonLisbonPortugal
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Clerbaux LA, Schultz H, Roman-Holba S, Ruan DF, Yu R, Lamb AM, Bommer GT, Kennell JA. The microRNA miR-33 is a pleiotropic regulator of metabolic and developmental processes in Drosophila melanogaster. Dev Dyn 2021; 250:1634-1650. [PMID: 33840153 DOI: 10.1002/dvdy.344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 03/31/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND miR-33 family members are well characterized regulators of cellular lipid levels in mammals. Previous studies have shown that overexpression of miR-33 in Drosophila melanogaster leads to elevated triacylglycerol (TAG) levels in certain contexts. Although loss of miR-33 in flies causes subtle defects in larval and adult ovaries, the effects of miR-33 deficiency on lipid metabolism and other phenotypes impacted by metabolic state have not yet been characterized. RESULTS We found that loss of miR-33 predisposes flies to elevated TAG levels, and we identified genes involved in TAG synthesis as direct targets of miR-33, including atpcl, midway, and Akt1. miR-33 mutants survived longer upon starvation but showed greater sensitivity to an oxidative stressor. We also found evidence that miR-33 is a negative regulator of cuticle pigmentation and that miR-33 mutants show a reduction in interfollicular stalk cells during oogenesis. CONCLUSION Our data suggest that miR-33 is a conserved regulator of lipid homeostasis, and its targets are involved in both degradation and synthesis of fatty acids and TAG. The constellation of phenotypes involving tissues that are highly sensitive to metabolic state suggests that miR-33 serves to prevent extreme fluctuations in metabolically sensitive tissues.
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Affiliation(s)
- Laure-Alix Clerbaux
- Laboratory of Physiological Chemistry, de Duve Institute, Université Catholique de Louvain, Bruxelles, Belgium.,Department of Biology and Program in Biochemistry, Vassar College, Poughkeepsie, New York, USA
| | - Hayley Schultz
- Department of Biology and Program in Biochemistry, Vassar College, Poughkeepsie, New York, USA
| | - Samara Roman-Holba
- Department of Biology and Program in Biochemistry, Vassar College, Poughkeepsie, New York, USA
| | - Dan Fu Ruan
- Department of Biology and Program in Biochemistry, Vassar College, Poughkeepsie, New York, USA
| | - Ronald Yu
- Department of Biology and Program in Biochemistry, Vassar College, Poughkeepsie, New York, USA
| | - Abigail M Lamb
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Guido T Bommer
- Laboratory of Physiological Chemistry, de Duve Institute, Université Catholique de Louvain, Bruxelles, Belgium
| | - Jennifer A Kennell
- Department of Biology and Program in Biochemistry, Vassar College, Poughkeepsie, New York, USA
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Vásquez-Procopio J, Rajpurohit S, Missirlis F. Cuticle darkening correlates with increased body copper content in Drosophila melanogaster. Biometals 2020; 33:293-303. [PMID: 33026606 PMCID: PMC7538679 DOI: 10.1007/s10534-020-00245-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/29/2020] [Indexed: 12/18/2022]
Abstract
Insect epidermal cells secrete a cuticle that serves as an exoskeleton providing mechanical rigidity to each individual, but also insulation, camouflage or communication within their environment. Cuticle deposition and hardening (sclerotization) and pigment synthesis are parallel processes requiring tyrosinase activity, which depends on an unidentified copper-dependent enzyme component in Drosophila melanogaster. We determined the metallomes of fly strains selected for lighter or darker cuticles in a laboratory evolution experiment, asking whether any specific element changed in abundance in concert with pigment deposition. The results showed a correlation between total iron content and strength of pigmentation, which was further corroborated by ferritin iron quantification. To ask if the observed increase in iron body content along with increased pigment deposition could be generalizable, we crossed yellow and ebony alleles causing light and dark pigmentation, respectively, into similar genetic backgrounds and measured their metallomes. Iron remained unaffected in the various mutants providing no support for a causative link between pigmentation and iron content. In contrast, the combined analysis of both experiments suggested instead a correlation between pigment deposition and total copper body content, possibly due to increased demand for epidermal tyrosinase activity.
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Affiliation(s)
- Johana Vásquez-Procopio
- Departamento de Fisiología, Biofísica y Neurociencias, Cinvestav, Zacatenco, Mexico City, Mexico
| | - Subhash Rajpurohit
- Division of Biological and Life Sciences, School of Arts and Sciences, Ahmedabad University, Commerce Six Road, Navrangpura, Ahmedabad, Gujarat, India
| | - Fanis Missirlis
- Departamento de Fisiología, Biofísica y Neurociencias, Cinvestav, Zacatenco, Mexico City, Mexico.
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8
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Flaven-Pouchon J, Alvarez JV, Rojas C, Ewer J. The tanning hormone, bursicon, does not act directly on the epidermis to tan the Drosophila exoskeleton. BMC Biol 2020; 18:17. [PMID: 32075655 PMCID: PMC7029472 DOI: 10.1186/s12915-020-0742-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/24/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND In insects, continuous growth requires the periodic replacement of the exoskeleton. Once the remains of the exoskeleton from the previous stage have been shed during ecdysis, the new one is rapidly sclerotized (hardened) and melanized (pigmented), a process collectively known as tanning. The rapid tanning that occurs after ecdysis is critical for insect survival, as it reduces desiccation, and gives the exoskeleton the rigidity needed to support the internal organs and to provide a solid anchor for the muscles. This rapid postecdysial tanning is triggered by the "tanning hormone", bursicon. Since bursicon is released into the hemolymph, it has naturally been assumed that it would act on the epidermal cells to cause the tanning of the overlying exoskeleton. RESULTS Here we investigated the site of bursicon action in Drosophila by examining the consequences on tanning of disabling the bursicon receptor (encoded by the rickets gene) in different tissues. To our surprise, we found that rapid tanning does not require rickets function in the epidermis but requires it instead in peptidergic neurons of the ventral nervous system (VNS). Although we were unable to identify the signal that is transmitted from the VNS to the epidermis, we show that neurons that express the Drosophila insulin-like peptide ILP7, but not the ILP7 peptide itself, are involved. In addition, we found that some of the bursicon targets involved in melanization are different from those that cause sclerotization. CONCLUSIONS Our findings show that bursicon does not act directly on the epidermis to cause the tanning of the overlying exoskeleton but instead requires an intermediary messenger produced by peptidergic neurons within the central nervous system. Thus, this work has uncovered an unexpected layer of control in a process that is critical for insect survival, which will significantly alter the direction of future research aimed at understanding how rapid postecdysial tanning occurs.
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Affiliation(s)
| | - Javier V Alvarez
- Instituto de Neurociencia, Universidad de Valparaíso, Valparaiso, Chile
| | - Candy Rojas
- Instituto de Neurociencia, Universidad de Valparaíso, Valparaiso, Chile
| | - John Ewer
- Instituto de Neurociencia, Universidad de Valparaíso, Valparaiso, Chile.
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9
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Transcriptional profiling of long non-coding RNAs in mantle of Crassostrea gigas and their association with shell pigmentation. Sci Rep 2018; 8:1436. [PMID: 29362405 PMCID: PMC5780484 DOI: 10.1038/s41598-018-19950-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 01/10/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in diverse biological processes and have drawn extensive attention in the past few years. However, lncRNAs remain poorly understood about expression and roles in Crassostrea gigas, a potential model organism for marine molluscan studies. Here, we systematically identified lncRNAs in the mantles of C. gigas from four full-sib families characterized by white, black, golden, and partially pigmented shell. Using poly(A)-independent and strand-specific RNA-seq, a total of 441,205,852 clean reads and 12,243 lncRNA transcripts were obtained. LncRNA transcripts were relatively short with few exons and low levels of expression in comparison to protein coding mRNA transcripts. A total of 427 lncRNAs and 349 mRNAs were identified to differentially express among six pairwise groups, mainly involving in biomineralization and pigmentation through functional enrichment. Furthermore, a total of 6 mRNAs and their cis-acting lncRNAs were predicted to involve in synthesis of melanin, carotenoid, tetrapyrrole, or ommochrome. Of them, chorion peroxidase and its cis-acting lincRNA TCONS_00951105 are implicated in playing an essential role in the melanin synthetic pathway. Our studies provided the first systematic characterization of lncRNAs catalog expressed in oyster mantle, which may facilitate understanding the molecular regulation of shell colour diversity and provide new insights into future selective breeding of C. gigas for aquaculture.
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10
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Saleh Ziabari O, Shingleton AW. Quantifying Abdominal Pigmentation in Drosophila melanogaster. J Vis Exp 2017. [PMID: 28605370 DOI: 10.3791/55732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Pigmentation is a morphologically simple but highly variable trait that often has adaptive significance. It has served extensively as a model for understanding the development and evolution of morphological phenotypes. Abdominal pigmentation in Drosophila melanogaster has been particularly useful, allowing researchers to identify the loci that underlie inter- and intraspecific variations in morphology. Hitherto, however, D. melanogaster abdominal pigmentation has been largely assayed qualitatively, through scoring, rather than quantitatively, which limits the forms of statistical analysis that can be applied to pigmentation data. This work describes a new methodology that allows for the quantification of various aspects of the abdominal pigmentation pattern of adult D. melanogaster. The protocol includes specimen mounting, image capture, data extraction, and analysis. All the software used for image capture and analysis feature macros written for open-source image analysis. The advantage of this approach is the ability to precisely measure pigmentation traits using a methodology that is highly reproducible across different imaging systems. While the technique has been used to measure variation in the tergal pigmentation patterns of adult D. melanogaster, the methodology is flexible and broadly applicable to pigmentation patterns in myriad different organisms.
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11
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Rajpurohit S, Peterson LM, Orr AJ, Marlon AJ, Gibbs AG. An Experimental Evolution Test of the Relationship between Melanism and Desiccation Survival in Insects. PLoS One 2016; 11:e0163414. [PMID: 27658246 PMCID: PMC5033579 DOI: 10.1371/journal.pone.0163414] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 08/15/2016] [Indexed: 11/25/2022] Open
Abstract
We used experimental evolution to test the ‘melanism-desiccation’ hypothesis, which proposes that dark cuticle in several Drosophila species is an adaptation for increased desiccation tolerance. We selected for dark and light body pigmentation in replicated populations of D. melanogaster and assayed several traits related to water balance. We also scored pigmentation and desiccation tolerance in populations selected for desiccation survival. Populations in both selection regimes showed large differences in the traits directly under selection. However, after over 40 generations of pigmentation selection, dark-selected populations were not more desiccation-tolerant than light-selected and control populations, nor did we find significant changes in mass or carbohydrate amounts that could affect desiccation resistance. Body pigmentation of desiccation-selected populations did not differ from control populations after over 140 generations of selection, although selected populations lost water less rapidly. Our results do not support an important role for melanization in Drosophila water balance.
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Affiliation(s)
- Subhash Rajpurohit
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States of America
| | - Lisa Marie Peterson
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States of America
| | - Andrew J Orr
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States of America
| | - Anthony J Marlon
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States of America
| | - Allen G Gibbs
- School of Life Sciences, University of Nevada, Las Vegas, NV 89154, United States of America
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12
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Wallingford AK, Loeb GM. Developmental Acclimation of Drosophila suzukii (Diptera: Drosophilidae) and Its Effect on Diapause and Winter Stress Tolerance. ENVIRONMENTAL ENTOMOLOGY 2016; 45:1081-1089. [PMID: 27412194 DOI: 10.1093/ee/nvw088] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Accepted: 06/24/2016] [Indexed: 06/06/2023]
Abstract
We investigated the influence of developmental conditions on adult morphology, reproductive arrest, and winter stress tolerance of the invasive pest of small fruit, Drosophila suzukii (Matsumura) (Diptera: Drosophilidae). Cooler rearing temperatures (15 °C) resulted in larger, darker "winter morph" (WM) adults than "summer morph" flies reared at optimal temperatures (25 °C). Abdominal pigmentation scores and body size measurements of laboratory-reared WMs were similar to those of D. suzukii females captured in late autumn in Geneva, NY. We evaluated reproductive diapause and cold hardiness in live-captured D. suzukii WMs as well as WMs reared in the laboratory from egg to adult under four developmental conditions: static cool temperatures (SWM; 15 °C, 12:12 h L:D), fluctuating temperatures (FWM; 20 °C L: 10 °C D, 12:12 h L:D), and static cool temperatures (15 °C, 12:12 h L:D) followed by posteclosion chilling (CWM; 10 °C) under short-day (SD; 12:12 h L:D) or long-day photoperiods (LD; 16:8 h L:D). Live-captured D. suzukii WMs and CWMs had longer preoviposition times than newly eclosed summer morph adults, indicating a reproductive diapause that was not observed in SWMs or FWMs. Additionally, recovery after acute freeze stress was not different between CWM-SD females and live captured WM females. More 7-d-old CWMs survived 0, -1, or - 3 °C freeze stress than summer morph adults, and more CWM-SD adults survived -3 °C freeze stress than CWM-LD adults. Survival after -3 °C freeze stress was significantly higher in diapausing, CWMs than nondiapausing SWMs and FWMs.
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Affiliation(s)
- Anna K Wallingford
- Department of Entomology, Cornell University, 630 W. North St., Geneva, NY 14456 (; ),
| | - Gregory M Loeb
- Department of Entomology, Cornell University, 630 W. North St., Geneva, NY 14456 (; )
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13
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Regna K, Kurshan PT, Harwood BN, Jenkins AM, Lai CQ, Muskavitch MAT, Kopin AS, Draper I. A critical role for the Drosophila dopamine D1-like receptor Dop1R2 at the onset of metamorphosis. BMC DEVELOPMENTAL BIOLOGY 2016; 16:15. [PMID: 27184815 PMCID: PMC4868058 DOI: 10.1186/s12861-016-0115-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/08/2016] [Indexed: 01/26/2023]
Abstract
BACKGROUND Insect metamorphosis relies on temporal and spatial cues that are precisely controlled. Previous studies in Drosophila have shown that untimely activation of genes that are essential to metamorphosis results in growth defects, developmental delay and death. Multiple factors exist that safeguard these genes against dysregulated expression. The list of identified negative regulators that play such a role in Drosophila development continues to expand. RESULTS By using RNAi transgene-induced gene silencing coupled to spatio/temporal assessment, we have unraveled an important role for the Drosophila dopamine 1-like receptor, Dop1R2, in development. We show that Dop1R2 knockdown leads to pre-adult lethality. In adults that escape death, abnormal wing expansion and/or melanization defects occur. Furthermore we show that salivary gland expression of this GPCR during the late larval/prepupal stage is essential for the flies to survive through adulthood. In addition to RNAi-induced effects, treatment of larvae with the high affinity D1-like receptor antagonist flupenthixol, also results in developmental arrest, and in morphological defects comparable to those seen in Dop1R2 RNAi flies. To examine the basis for pupal lethality in Dop1R2 RNAi flies, we carried out transcriptome analysis. These studies revealed up-regulation of genes that respond to ecdysone, regulate morphogenesis and/or modulate defense/immunity. CONCLUSION Taken together our findings suggest a role for Dop1R2 in the repression of genes that coordinate metamorphosis. Premature release of this inhibition is not tolerated by the developing fly.
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Affiliation(s)
- Kimberly Regna
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - Peri T Kurshan
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, USA.,Present Address: Department of Biology, Stanford University, California, 94305, USA
| | - Benjamin N Harwood
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, USA
| | - Adam M Jenkins
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA
| | - Chao-Qiang Lai
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, 02111, USA
| | - Marc A T Muskavitch
- Department of Biology, Boston College, Chestnut Hill, MA, 02467, USA.,Discovery Research, Biogen Idec, Cambridge, MA, 02142, USA
| | - Alan S Kopin
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, USA
| | - Isabelle Draper
- Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA, 02111, USA.
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14
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Sunaga S, Akiyama N, Miyagi R, Takahashi A. Factors underlying natural variation in body pigmentation of Drosophila melanogaster. Genes Genet Syst 2016; 91:127-137. [PMID: 27021917 DOI: 10.1266/ggs.15-00061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Molecular mechanisms underlying standing genetic variation of an ecologically relevant trait such as pigmentation trait variation in a model insect, Drosophila melanogaster, are relevant to our understanding of different kinds of intergenomic interactions. In this study, we focused on the association between body pigmentation and stress resistance, and on genotype-by-environment interaction, both of which are likely to contribute to the persistence of phenotypic variation in a natural population. First, we detected a significant association between pigmentation traits in females and starvation resistance (darker strains were weaker) and a weak association between pigmentation and chill coma recovery time (darker strains showed shorter recovery time) among 20 inbred strains from the Drosophila melanogaster Genetic Reference Panel (DGRP), which originated from a natural population in North America. These associations revealed a complex relationship between body pigmentation and physiological traits that may give rise to balanced selective forces acting on the traits under fluctuating environmental conditions. Second, using four of the DGRP strains, a substantial degree of genotype (strain) × environment (rearing temperature) interaction was detected among expression levels of the genes encoding effector enzymes in the melanin biosynthesis pathway. These interactions can potentially reduce the efficiency of purifying selection on the pigmentation traits over a wide range of temperature conditions. Finally, we discuss possible mechanisms that contribute to the maintenance of the standing pigmentation variation in this species.
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Affiliation(s)
- Saki Sunaga
- Department of Biological Sciences, Tokyo Metropolitan University
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15
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Garlena RA, Lennox AL, Baker LR, Parsons TE, Weinberg SM, Stronach BE. The receptor tyrosine kinase Pvr promotes tissue closure by coordinating corpse removal and epidermal zippering. Development 2015; 142:3403-15. [PMID: 26293306 DOI: 10.1242/dev.122226] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 08/10/2015] [Indexed: 12/14/2022]
Abstract
A leading cause of human birth defects is the incomplete fusion of tissues, often manifested in the palate, heart or neural tube. To investigate the molecular control of tissue fusion, embryonic dorsal closure and pupal thorax closure in Drosophila are useful experimental models. We find that Pvr mutants have defects in dorsal midline closure with incomplete amnioserosa internalization and epidermal zippering, as well as cardia bifida. These defects are relatively mild in comparison to those seen with other signaling mutants, such as in the JNK pathway, and we demonstrate that JNK signaling is not perturbed by altering Pvr receptor tyrosine kinase activity. Rather, modulation of Pvr levels in the ectoderm has an impact on PIP3 membrane accumulation, consistent with a link to PI3K signal transduction. Polarized PI3K activity influences protrusive activity from the epidermal leading edge and the protrusion area changes in accord with Pvr signaling intensity, providing a possible mechanism to explain Pvr mutant phenotypes. Tissue-specific rescue experiments indicate a partial requirement in epithelial tissue, but confirm the essential role of Pvr in hemocytes for embryonic survival. Taken together, we argue that inefficient removal of the internalizing amnioserosa tissue by mutant hemocytes coupled with impaired midline zippering of mutant epithelium creates a situation in some embryos whereby dorsal midline closure is incomplete. Based on these observations, we suggest that efferocytosis (corpse clearance) could contribute to proper tissue closure and thus might underlie some congenital birth defects.
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Affiliation(s)
- Rebecca A Garlena
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Ashley L Lennox
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Lewis R Baker
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Trish E Parsons
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Seth M Weinberg
- Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
| | - Beth E Stronach
- Department of Microbiology and Molecular Genetics, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15219, USA
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Yamamoto-Hino M, Yoshida H, Ichimiya T, Sakamura S, Maeda M, Kimura Y, Sasaki N, Aoki-Kinoshita KF, Kinoshita-Toyoda A, Toyoda H, Ueda R, Nishihara S, Goto S. Phenotype-based clustering of glycosylation-related genes by RNAi-mediated gene silencing. Genes Cells 2015; 20:521-42. [PMID: 25940448 PMCID: PMC4682476 DOI: 10.1111/gtc.12246] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/24/2015] [Indexed: 01/16/2023]
Abstract
Glycan structures are synthesized by a series of reactions conducted by glycosylation-related (GR) proteins such as glycosyltransferases, glycan-modifying enzymes, and nucleotide-sugar transporters. For example, the common core region of glycosaminoglycans (GAGs) is sequentially synthesized by peptide-O-xylosyltransferase, β1,4-galactosyltransferase I, β1,3-galactosyltransferase II, and β1,3-glucuronyltransferase. This raises the possibility that functional impairment of GR proteins involved in synthesis of the same glycan might result in the same phenotypic abnormality. To examine this possibility, comprehensive silencing of genes encoding GR and proteoglycan core proteins was conducted in Drosophila. Drosophila GR candidate genes (125) were classified into five functional groups for synthesis of GAGs, N-linked, O-linked, Notch-related, and unknown glycans. Spatiotemporally regulated silencing caused a range of malformed phenotypes that fell into three types: extra veins, thick veins, and depigmentation. The clustered phenotypes reflected the biosynthetic pathways of GAGs, Fringe-dependent glycan on Notch, and glycans placed at or near nonreducing ends (herein termed terminal domains of glycans). Based on the phenotypic clustering, CG33145 was predicted to be involved in formation of terminal domains. Our further analysis showed that CG33145 exhibited galactosyltransferase activity in synthesis of terminal N-linked glycans. Phenotypic clustering, therefore, has potential for the functional prediction of novel GR genes.
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Affiliation(s)
- Miki Yamamoto-Hino
- Department of Life Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
| | - Hideki Yoshida
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan.,Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo, Japan.,Department of Applied Biology, Insect Biomedical Research Center, Kyoto Institute of Technology, Sakyo-ku, Kyoto, Japan
| | - Tomomi Ichimiya
- Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Sho Sakamura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Megumi Maeda
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Yoshinobu Kimura
- Department of Biofunctional Chemistry, Graduate School of Environmental and Life Science, Okayama University, Okayama, Japan
| | - Norihiko Sasaki
- Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo, Japan.,Research Team for Geriatric Medicine (Vascular Medicine), Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, Japan
| | - Kiyoko F Aoki-Kinoshita
- Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Akiko Kinoshita-Toyoda
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Hidenao Toyoda
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan
| | - Ryu Ueda
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan.,Invertebrate Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Shoko Nishihara
- Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan.,Department of Bioinformatics, Faculty of Engineering, Soka University, Hachioji, Tokyo, Japan
| | - Satoshi Goto
- Department of Life Science, Rikkyo University, Toshima-ku, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST) of Japan Science and Technology Agency (JST), Kawaguchi, Saitama, Japan
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Guo JY, Cheng L, Ye GY, Fang Q, Guo JY. Feeding on a begomovirus-infected plant enhances fecundity via increased expression of an insulin-like peptide in the whitefly, MEAM1. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2014; 85:164-79. [PMID: 24532462 DOI: 10.1002/arch.21151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The Middle East-Minor 1 cryptic species (MEAM1), Bemisia tabaci (Gennadius) is a globally invasive pest. It spreads widely due to its high fecundity and mutualistic interactions with the virus they vector. Feeding on virus (tomato yellow leaf curl China virus, TYLCCNV)-infected host plants improves their fecundity, however, the key factor regulating the signaling transduction in reproduction of whitefly remains to be identified. Here, we cloned a full length cDNA encoding an insulin-like peptide in MEAM1 (BtILP1) and investigated its expression profile, functions, and the expression induced by feeding on virus-infected tobacco plants. The full length cDNA of BtILP1 was 590 bps and encoded an open reading frame containing 149 amino acid residues. Multiple sequences alignment results showed BtILP1 contained the structural features typical of the insulin family. Expression dynamics associated with development showed the expression level of BtILP1 peaked at 5 days posteclosion (PE). During 1 to 3 days PE, BtILP1 was expressed highly in the head and abdomen of female adults and highly in the head during 5 to 7 days PE. Knockdown of the BtILP1 expression also impaired vitellogenin gene expression at both transcript and protein levels. Downregulating BtILP1 expression decreased fecundity of female adults and hatching rate of eggs. Feeding on virus-infected tobacco increased BtILP1 expression in MEAM1 female adults. We infer feeding on begomovirus-infected tobacco enhances the reproduction of MEAM1 by inducing BtILP1 expression. Our results give a new sight into the mutualistic interactions between virus and its insect vector.
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