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Dikmen F, Dabak T, Özgişi BD, Özenirler Ç, Kuralay SC, Çay SB, Çınar YU, Obut O, Balcı MA, Akbaba P, Aksel EG, Zararsız G, Solares E, Eldem V. Transcriptome-wide analysis uncovers regulatory elements of the antennal transcriptome repertoire of bumblebee at different life stages. INSECT MOLECULAR BIOLOGY 2024. [PMID: 38676460 DOI: 10.1111/imb.12914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 04/09/2024] [Indexed: 04/29/2024]
Abstract
Bumblebees are crucial pollinators, providing essential ecosystem services and global food production. The success of pollination services relies on the interaction between sensory organs and the environment. The antenna functions as a versatile multi-sensory organ, pivotal in mediating chemosensory/olfactory information, and governs adaptive responses to environmental changes. Despite an increasing number of RNA-sequencing studies on insect antenna, comprehensive antennal transcriptome studies at the different life stages were not elucidated systematically. Here, we quantified the expression profile and dynamics of coding/microRNA genes of larval head and antennal tissues from early- and late-stage pupa to the adult of Bombus terrestris as suitable model organism among pollinators. We further performed Pearson correlation analyses on the gene expression profiles of the antennal transcriptome from larval head tissue to adult stages, exploring both positive and negative expression trends. The positively correlated coding genes were primarily enriched in sensory perception of chemical stimuli, ion transport, transmembrane transport processes and olfactory receptor activity. Negatively correlated genes were mainly enriched in organic substance biosynthesis and regulatory mechanisms underlying larval body patterning and the formation of juvenile antennal structures. As post-transcriptional regulators, miR-1000-5p, miR-13b-3p, miR-263-5p and miR-252-5p showed positive correlations, whereas miR-315-5p, miR-92b-3p, miR-137-3p, miR-11-3p and miR-10-3p exhibited negative correlations in antennal tissue. Notably, based on the inverse expression relationship, positively and negatively correlated microRNA (miRNA)-mRNA target pairs revealed that differentially expressed miRNAs predictively targeted genes involved in antennal development, shaping antennal structures and regulating antenna-specific functions. Our data serve as a foundation for understanding stage-specific antennal transcriptomes and large-scale comparative analysis of transcriptomes in different insects.
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Affiliation(s)
- Fatih Dikmen
- Department of Biology, Istanbul University, İstanbul, Turkey
| | - Tunç Dabak
- Department of Biology, The Pennsylvania State University, State College, Pennsylvania, USA
| | | | | | | | | | | | - Onur Obut
- Department of Biology, Istanbul University, İstanbul, Turkey
| | | | - Pınar Akbaba
- Department of Biology, Istanbul University, İstanbul, Turkey
| | - Esma Gamze Aksel
- Faculty of Veterinary Medicine, Department of Genetics, Erciyes University, Kayseri, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University, Kayseri, Turkey
- Drug Application and Research Center (ERFARMA), Erciyes University, Kayseri, Turkey
| | - Edwin Solares
- Computer Science & Engineering Department, University of California, San Diego, California, USA
| | - Vahap Eldem
- Department of Biology, Istanbul University, İstanbul, Turkey
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Wang Z, Tang F, Xu M, Shen T. Exploring miRNA-mRNA regulatory modules responding to tannic acid stress in Micromelalopha troglodyta (Graeser) (Lepidoptera: Notodontidae) via small RNA sequencing. BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:86-97. [PMID: 35817762 DOI: 10.1017/s0007485322000359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (sRNAs) that regulate gene expression by inhibiting translation or degrading mRNA. Although the functions of miRNAs in many biological processes have been reported, there is currently no research on the possible roles of miRNAs in Micromelalopha troglodyta (Graeser) involved in the response of plant allelochemicals. In this article, six sRNA libraries (three treated with tanic acid and three control) from M. troglodyta were constructed using Illumina sequencing. From the results, 312 known and 43 novel miRNAs were differentially expressed. Notably, some of the most abundant miRNAs, such as miR-432, miR-541-3p, and miR-4448, involved in important physiological processes were also identified. To better understand the function of the targeted genes, we performed Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. The results indicated that differentially expressed miRNA targets were involved in metabolism, development, hormone biosynthesis, and immunity. Finally, we visualized a miRNA-mRNA regulatory module that supports the role of miRNAs in host-allelochemical interactions. To our knowledge, this is the first report on miRNAs responding to tannic acid in M. troglodyta. This study provides indispensable information for understanding the potential roles of miRNAs in M. troglodyta and the applications of these miRNAs in M. troglodyta management.
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Affiliation(s)
- Zhiqiang Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People's Republic of China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Fang Tang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People's Republic of China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Meng Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People's Republic of China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Tengfei Shen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, People's Republic of China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, People's Republic of China
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Soares MPM, Pinheiro DG, de Paula Freitas FC, Simões ZLP, Bitondi MMG. Transcriptome dynamics during metamorphosis of imaginal discs into wings and thoracic dorsum in Apis mellifera castes. BMC Genomics 2021; 22:756. [PMID: 34674639 PMCID: PMC8532292 DOI: 10.1186/s12864-021-08040-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 09/20/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Much of the complex anatomy of a holometabolous insect is built from disc-shaped epithelial structures found inside the larva, i.e., the imaginal discs, which undergo a rapid differentiation during metamorphosis. Imaginal discs-derived structures, like wings, are built through the action of genes under precise regulation. RESULTS We analyzed 30 honeybee transcriptomes in the search for the gene expression needed for wings and thoracic dorsum construction from the larval wing discs primordia. Analyses were carried out before, during, and after the metamorphic molt and using worker and queen castes. Our RNA-seq libraries revealed 13,202 genes, representing 86.2% of the honeybee annotated genes. Gene Ontology analysis revealed functional terms that were caste-specific or shared by workers and queens. Genes expressed in wing discs and descendant structures showed differential expression profiles dynamics in premetamorphic, metamorphic and postmetamorphic developmental phases, and also between castes. At the metamorphic molt, when ecdysteroids peak, the wing buds of workers showed maximal gene upregulation comparatively to queens, thus underscoring differences in gene expression between castes at the height of the larval-pupal transition. Analysis of small RNA libraries of wing buds allowed us to build miRNA-mRNA interaction networks to predict the regulation of genes expressed during wing discs development. CONCLUSION Together, these data reveal gene expression dynamics leading to wings and thoracic dorsum formation from the wing discs, besides highlighting caste-specific differences during wing discs metamorphosis.
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Affiliation(s)
- Michelle Prioli Miranda Soares
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14049-900, Ribeirão Preto, SP, Brazil
| | - Daniel Guariz Pinheiro
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, SP, Brazil
| | | | - Zilá Luz Paulino Simões
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14040-901, Ribeirão Preto, SP, Brazil
| | - Márcia Maria Gentile Bitondi
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, 14040-901, Ribeirão Preto, SP, Brazil.
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miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta. Sci Rep 2021; 11:10706. [PMID: 34021209 PMCID: PMC8139948 DOI: 10.1038/s41598-021-90095-9] [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: 09/14/2020] [Accepted: 04/05/2021] [Indexed: 11/08/2022] Open
Abstract
Aedes aegypti L. is the most important vector of arboviruses such as dengue, Zika, chikungunya, Mayaro, and yellow fever, which impact millions of people's health per year. MicroRNA profile has been described in some mosquito species as being important for biological processes such as digestion of blood, oviposition, sexual differentiation, insecticide resistance, and pathogens dissemination. We identified the miRNAs of Ae. aegypti females, males and eggs of a reference insecticide susceptible strain New Orleans and compared them with those other insects to determine miRNA fingerprint by new-generation sequencing. The sequences were analyzed using data mining tools and categorization, followed by differential expression analysis and conservation with other insects. A total of 55 conserved miRNAs were identified, of which 34 were of holometabolous insects and 21 shared with hemimetabolous insects. Of these miRNAs, 32 had differential expression within the stages analyzed. Three predominant functions of miRNA were related to embryonic development regulation, metamorphosis, and basal functions. The findings of this research describe new information on Ae. aegypti physiology which could be useful for the development of new control strategies, particularly in mosquito development and metamorphosis processes.
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Ylla G, Liu T, Conesa A. MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants. Bioinformatics 2020; 36:i618-i624. [PMID: 33381847 DOI: 10.1093/bioinformatics/btaa889] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
MOTIVATION microRNAs (miRNAs) are essential components of gene expression regulation at the post-transcriptional level. miRNAs have a well-defined molecular structure and this has facilitated the development of computational and high-throughput approaches to predict miRNAs genes. However, due to their short size, miRNAs have often been incorrectly annotated in both plants and animals. Consequently, published miRNA annotations and miRNA databases are enriched for false miRNAs, jeopardizing their utility as molecular information resources. To address this problem, we developed MirCure, a new software for quality control, filtering and curation of miRNA candidates. MirCure is an easy-to-use tool with a graphical interface that allows both scoring of miRNA reliability and browsing of supporting evidence by manual curators. RESULTS Given a list of miRNA candidates, MirCure evaluates a number of miRNA-specific features based on gene expression, biogenesis and conservation data, and generates a score that can be used to discard poorly supported miRNA annotations. MirCure can also curate and adjust the annotation of the 5p and 3p arms based on user-provided small RNA-seq data. We evaluated MirCure on a set of manually curated animal and plant miRNAs and demonstrated great accuracy. Moreover, we show that MirCure can be used to revisit previous bona fide miRNAs annotations to improve miRNA databases. AVAILABILITY AND IMPLEMENTATION The MirCure software and all the additional scripts used in this project are publicly available at https://github.com/ConesaLab/MirCure. A Docker image of MirCure is available at https://hub.docker.com/r/conesalab/mircure. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Guillem Ylla
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Tianyuan Liu
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Ana Conesa
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Chen EH, Tao YX, Song W, Shen F, Yuan ML, Tang PA. Transcriptome-Wide Identification of MicroRNAs and Analysis of Their Potential Roles in Development of Indian Meal Moth (Lepidoptera:Pyralidae). JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:1535-1546. [PMID: 32108881 DOI: 10.1093/jee/toaa030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) have been reported to play indispensable roles in regulating various developmental processes via the posttranscriptional repression of target genes in insect species. In the present paper, we studied the miRNAs in Indian meal moth (Plodia interpunctella (Hübener)), one of the most economically important stored grains pests around the world. In total, 12 small RNA libraries from four developmental stages of P. interpunctella were constructed, and 178 known and 23 novel miRNAs were identified. In addition, the expression profiles of these miRNAs were assessed across different developmental stages and miRNAs that were highly expressed in eggs, larvae, pupae, and adults were identified. Specifically, 100, 61, and 52 miRNAs were differentially expressed between eggs and larvae, larvae and pupae, and pupae and adults, respectively. The KEGG and GO analysis of the predicted target genes suggested the essential roles of miRNAs in the regulation of complex development of P. interpunctella. Importantly, we also found a set of miRNAs might be involved in the larval metamorphic molting process, with their expressions increasing and then decreasing during the larva-pupa-adult stages of P. interpunctella. In conclusion, the current paper has discovered numerous miRNAs, and some key miRNAs that might be responsible for regulating development in P. interpunctella. To our knowledge, this is the first study to document miRNAs and their expression patterns in interpunctella, and those findings would lay an important molecular foundation for future functional analysis of these miRNAs in P. interpunctella.
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Affiliation(s)
- Er-Hu Chen
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Ye-Xin Tao
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Wei Song
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Fei Shen
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
| | - Ming-Long Yuan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Pei-An Tang
- Collaborative Innovation Center for Modern Grain Circulation and Safety, College of Food Science and Engineering, Nanjing University of Finance and Economics, Nanjing, Jiangsu, China
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Yang Q, Bao Z, Yang M, Shen Y, Zhang X, Yue B, Meng Y, Fan Z. Identification and characterization of microRNAs in American cockroach (Periplaneta americana). Gene 2020; 743:144610. [DOI: 10.1016/j.gene.2020.144610] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 12/23/2022]
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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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Rahimpour H, Moharramipour S, Asgari S, Mehrabadi M. The microRNA pathway core genes are differentially expressed during the development of Helicoverpa armigera and contribute in the insect's development. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 110:121-127. [PMID: 31121322 DOI: 10.1016/j.ibmb.2019.05.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/01/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs (18-25 nt) that are produced by all animals and plants as well as some viruses. Their roles have been revealed in many physiological processes including development, cancer, immunity, apoptosis and, host-microbe interactions through post-transcriptional regulation of gene expression. In this study, we predicted, characterized and transcriptionally analyzed the core miRNA pathway genes in Helicoverpa armigera. Our results showed that the canonical miRNA biogenesis pathway genes including Pasha, Drosha, Loquacious, Exportin-5, Dicer-1 and Argonaute-1 are differentially expressed in different tissues and during the development of this insect. Considering the essential role of Dicer-1 in this pathway, we used RNA interference to silence the expression of this gene in H. armigera. Silencing of Dicer-1 decreased the levels of cellular miRNAs, let-7 and miR-184. Together, our results showed that the miRNA pathway functions during the development of H. armigera, and silencing of Dicer-1 resulted in the miRNA pathway blockage and depletion of the miRNA contents leading to mortalities in the immature stage and abnormalities in the mature stage. Blockage of this pathway can therefore be considered in future attempts for interrupting/suppressing populations of this important crop pest.
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Affiliation(s)
- Hamed Rahimpour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Saeid Moharramipour
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Mohammad Mehrabadi
- Department of Entomology, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
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Li S, Xu X, Zheng Z, Zheng J, Shakeel M, Jin F. MicroRNA expression profiling of Plutella xylostella after challenge with B. thuringiensis. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 93:115-124. [PMID: 30582949 DOI: 10.1016/j.dci.2018.12.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/15/2018] [Accepted: 12/19/2018] [Indexed: 06/09/2023]
Abstract
The diamondback moth, Plutella xylostella, the main pest of brassica crops, has developed resistance to almost all major classes of insecticides as the farmers rely on insecticides to control this pest. An extensive use of broad-spectrum insecticides against P. xylostella promotes the selection of insecticide resistance, destroy natural enemies, and pollute the environment. In this scenario, it is imperative to use genetic methods such as gene silencing technology as an alternate approach against this pest. Evidence shows that microRNAs play pivotal roles in the regulation of target genes at the post-transcription level and show differential expression under various biological processes. However, the knowledge of their role in insect immunity is still in its infancy. In the present study, we aimed at exploring the response of P. xylostella miRNAs against B. thuringiensis at different time courses (6, 12, 18, 24, and 36 h) by using small RNA sequencing. After data filtration, a combined set of 149 miRNAs was identified from all the libraries. Interestingly, a couple of conserved miRNAs such as miR-1, Let-7, miR-275, miR-184, and miR-10 were listed as abundantly expressed miRNAs after exposure to B. thuringiensis. It is worth mentioning that the differential expression analysis revealed that miR-2, a conserved miRNA, was up-regulated following infection. Furthermore, we experimentally validated the involvement of miR-2b-3p in the regulation of corresponding target trypsin. Our luciferase assay results revealed that miR-2b-3p mimic significantly down-regulated the target gene trypsin indicating that it might play a crucial role in the defense mechanism of P. xylostella against B. thuringiensis infection. On the whole, our findings provide insights into the possible regulatory role of miRNAs in insect immunity in response to microorganisms.
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Affiliation(s)
- Shuzhong Li
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou, PR China
| | - Xiaoxia Xu
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou, PR China
| | - Zhihua Zheng
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou, PR China
| | - Jinlong Zheng
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou, PR China
| | - Muhammad Shakeel
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou, PR China.
| | - Fengliang Jin
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Innovation and Application of Guangdong Province, Guangzhou, PR China.
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11
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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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Ding BY, Yang L, Peng YY, Chang TY, Ye C, Shang F, Niu J, Wang JJ. RNA-sequencing of a citrus bud-feeder, Podagricomela weisei (Coleoptera: Chrysomelidae), reveals xenobiotic metabolism/core RNAi machinery-associated genes and conserved miRNAs. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 29:339-350. [PMID: 30682656 DOI: 10.1016/j.cbd.2019.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 11/15/2022]
Abstract
The citrus leaf-mining beetle, Podagricomela weisei Heikertinger, is an important citrus pest that ingests the mesophyll and new shoots. The mechanism underlying the xenobiotic metabolism of P. weisei is not well understood, in part because of a lack of available genomic and transcriptomic data, which has hampered the development of novel pest management approaches [e.g., RNA interference (RNAi)]. In this study, we completed the deep sequencing of the P. weisei transcriptome to identify factors potentially involved in xenobiotic metabolism and the core RNAi machinery. The sequencing of the P. weisei transcriptome generated >27 million clean reads, ultimately yielding 90,410 unigenes with an N50 of 1065 bp. The unigenes were used as queries to search the Nr database, which revealed that 21,847 unigenes were homologous to known genes in various species. Transcripts encoding genes involved in xenobiotic metabolism were identified, including genes encoding cytochrome P450 monooxygenase (P450, 47 unigenes), glutathione S-transferase (GST, 12 unigenes), esterase (EST, 25 unigenes), and the ATP-binding cassette transporter (ABC transporter, 32 unigenes). A parallel sequencing of small RNAs detected 30 conserved miRNAs, with the most abundant being Pwe-miR-1-3p, with an expression level reaching 517,996 reads in the prepared library, followed by Pwe-miR-8-3p (149,402 reads). Genes encoding components of the miRNA, siRNA, and piRNA pathways were also identified, and the results indicated that P. weisei possesses only one of each gene in all three pathways. In summary, this is the first detailed analysis of the transcriptome and small RNAs of P. weisei. The datasets presented herein may form the basis for future molecular characterizations of P. weisei as well as the development of enhanced pest control strategies.
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Affiliation(s)
- Bi-Yue Ding
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Li Yang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Yuan-Yuan Peng
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Teng-Yu Chang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Chao Ye
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Feng Shang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jinzhi Niu
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China
| | - Jin-Jun Wang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400716, China; Academy of Agricultural Sciences, Southwest University, Chongqing 400716, China.
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Yang H, Li X, Ji J, Yuan C, Gao X, Zhang Y, Lu C, Li F, Zhang X. Changes of microRNAs expression profiles from red swamp crayfish (Procambarus clarkia) hemolymph exosomes in response to WSSV infection. FISH & SHELLFISH IMMUNOLOGY 2019; 84:169-177. [PMID: 30291984 DOI: 10.1016/j.fsi.2018.10.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/28/2018] [Accepted: 10/03/2018] [Indexed: 06/08/2023]
Abstract
MicroRNAs (miRNAs) as short noncoding RNAs play important regulatory roles in diverse biological processes by degrading the target mRNAs, and could be delivered by exosomes. WSSV is a highly pathogenic and prevalent virus, and has brought high mortality of P. clarkia. Till present, no studies focus on the miRNAs changes in exosomes during WSSV infection. To understand the different virulence of WSSV on miRNAs expression in P. clarkia hemolymph exosome, the deep sequencing was performed to compare the small RNA libraries from the hemolymph exosome of P. clarkia individuals with or without WSSV infections. From the TEM observations, NTA and Western Blot analysis, the extracted exosomes were well identified with classic characteristics. The 209 conserved miRNAs and 250 novel miRNAs were identified from the small RNA libraries. In response to WSSV infection, there were about 98 miRNAs significantly up-regulated and 59 miRNAs significantly down-regulated. The target genes prediction, GO and KEGG enrichment analysis revealed that some target genes of P. clarkia miRNAs were grouped mainly into the categories of biological regulation, immune system process, signal pathway and other more functions. This is the first report of comprehensive identification of P. clarkia hemolymph exosome miRNAs being differentially regulated in response to WSSV infection. These results will help to understand the hemolymph exosome miRNAs response to different virulence WSSV infection.
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Affiliation(s)
- Hui Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Xixi Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jiaojun Ji
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Chunyou Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xiaojian Gao
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Yingying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Cheng Lu
- Aquaculture Technical Guidance Station, Taizhou, 225300, China
| | - Fenggang Li
- Yellow River Fisheries Research Institute, Chinese Academy of Fishery Science, Xi'an, Shaanxi, 710086, China
| | - Xiaojun Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
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14
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Qu Z, Bendena WG, Tobe SS, Hui JHL. Juvenile hormone and sesquiterpenoids in arthropods: Biosynthesis, signaling, and role of MicroRNA. J Steroid Biochem Mol Biol 2018; 184:69-76. [PMID: 29355708 DOI: 10.1016/j.jsbmb.2018.01.013] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 01/03/2018] [Accepted: 01/16/2018] [Indexed: 12/21/2022]
Abstract
Arthropod molting and reproduction are precisely controlled by the levels of sesquiterpenoids, a class of C15 hormones derived from three isoprene units. The two major functional arthropod sesquiterpenoids are juvenile hormone (JH) and methyl farnesoate (MF). In hemimetabolous insects (such as the aphids, bugs, and cockroaches) and holometabolous insects (such as beetles, bees, butterflies, and flies), dramatic decrease in the titers of JH and/or MF promote metamorphosis from larvae to adults either directly or through an intermediate pupal stage, respectively. JH is absent in crustaceans (lobster, shrimp, crab) and other arthropods (chelicerates such as ticks, mites, spiders, scorpions and myriapods such as millipede and centipedes). In some crustaceans, molting and reproduction is dependent on changing levels of MF. The regulation of sesquiterpenoid production is thus crucial in the life cycle of arthropods. Dynamic and complex mechanisms have evolved to regulate sesquiterpenoid production. Noncoding RNAs such as the microRNAs are primary regulators. This article provides an overview of microRNAs that are known to regulate sesquiterpenoid production in arthropods.
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Affiliation(s)
- Zhe Qu
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong
| | | | - Stephen S Tobe
- Department of Cell and Systems Biology, University of Toronto, Canada.
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, Partner State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong.
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15
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Chang ZX, Akinyemi IA, Guo DY, Wu Q. Characterization and comparative analysis of microRNAs in the rice pest Sogatella furcifera. PLoS One 2018; 13:e0204517. [PMID: 30248141 PMCID: PMC6152972 DOI: 10.1371/journal.pone.0204517] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous regulatory RNA molecules 21-24 nucleotides in length that act as functional regulators of post-transcriptional repression of messenger RNA. We report the identification and characterization of a conserved miRNA and 171 novel miRNAs in the migratory rice pest Sogatella furcifera by deep sequencing, which were observed to be biased towards female adults of the insect, modulating the functionality and targets of the miRNAs in sex differentiation. A switch in arm usage was also observed in 9 miRNA when compared to the insect ancestor during insect evolution. The miRNA loci showed high 5’ fidelity in both miRNA and star species and about 93.4% of WBPH miRNAs conserved within non-planthopper species were homologous with planthopper species. The novel miRNAs identified in this study provide a better understanding of the sRNA and the regulatory role of miRNA in sexual dimorphism and alteration in the expression or function of miRNAs in the rice pest.
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Affiliation(s)
- Zhao-Xia Chang
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China
| | - Ibukun A. Akinyemi
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China
| | - Dong-Yang Guo
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China
| | - Qingfa Wu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Life Sciences, University of Science and Technology of China, Hefei, China
- * E-mail:
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16
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Upadhyay A, Gaonkar T, Upadhyay AK, Jogaiah S, Shinde MP, Kadoo NY, Gupta VS. Global transcriptome analysis of grapevine (Vitis vinifera L.) leaves under salt stress reveals differential response at early and late stages of stress in table grape cv. Thompson Seedless. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 129:168-179. [PMID: 29885601 DOI: 10.1016/j.plaphy.2018.05.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 05/30/2018] [Accepted: 05/30/2018] [Indexed: 05/08/2023]
Abstract
Among the different abiotic stresses, salt stress has a significant effect on the growth and yield of grapevine (Vitis vinifera L.). In this study, we employed RNA sequence based transcriptome analysis to study salinity stress response in grape variety Thompson Seedless. Salt stress adversely affected the growth related and physiological parameters and the effect on physiological parameters was significant within 10 days of stress imposition. A total of 343 genes were differentially expressed in response to salt stress. Among the differentially expressed genes (DEGs) only 42 genes were common at early and late stages of stress. The gene enrichment analysis revealed that GO terms related to transcription factors were over-represented. Among the DEGs, 52 were transcription factors belonging to WRKY, EREB, MYB, NAC and bHLH families. Salt stress significantly affected several pathways like metabolic pathways, biosynthesis of secondary metabolites, membrane transport development related pathways etc. 343 DEGs were distributed on all the 19 chromosomes, however clustered regions of DEGs were present on chromosomes 2, 5, 6 and 12 suggesting probable QTLs for imparting tolerance to salt and other abiotic stresses. Real-time PCR of selected genes in control and treated samples of grafted and own root vines demonstrated that rootstock influenced expression of salt stress responsive genes. Microsatellite regions were identified in ten selected salt responsive genes and highly polymorphic markers were identified using fifteen grape genotypes. This information will be useful for the identification of key genes involved in salt stress tolerance in grape. The identified DEGs could also be useful for genome wide analysis for the identification of polymorphic markers for their subsequent use in molecular breeding for developing salt tolerant grape genotypes.
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Affiliation(s)
- Anuradha Upadhyay
- ICAR-National Research Centre for Grapes, Manjari Farm Post, Solapur Road, Pune, Maharashtra, India.
| | - Tulsi Gaonkar
- ICAR-National Research Centre for Grapes, Manjari Farm Post, Solapur Road, Pune, Maharashtra, India
| | - Ajay Kumar Upadhyay
- ICAR-National Research Centre for Grapes, Manjari Farm Post, Solapur Road, Pune, Maharashtra, India
| | - Satisha Jogaiah
- ICAR-National Research Centre for Grapes, Manjari Farm Post, Solapur Road, Pune, Maharashtra, India
| | - Manisha P Shinde
- ICAR-National Research Centre for Grapes, Manjari Farm Post, Solapur Road, Pune, Maharashtra, India
| | - Narendra Y Kadoo
- CSIR - National Chemical Laboratory, Pashan, Pune, Maharashtra, India
| | - Vidya S Gupta
- CSIR - National Chemical Laboratory, Pashan, Pune, Maharashtra, India
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17
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Hu J, Lin C, Liu M, Tong Q, Xu S, Wang D, Zhao Y. Analysis of the microRNA transcriptome of Daphnia pulex during aging. Gene 2018; 664:101-110. [PMID: 29684489 DOI: 10.1016/j.gene.2018.04.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 03/13/2018] [Accepted: 04/12/2018] [Indexed: 01/30/2023]
Abstract
Daphnia pulex is an important food organism that exhibits a particular mode of reproduction known as cyclical parthenogenesis (asexual) and sexual reproduction. Regulation of the aging process by microRNAs (miRNAs) is a research hotspot in miRNA studies. To investigate a possible role of miRNAs in regulating aging and senescence, we used Illumina HiSeq to sequence two miRNA libraries from 1-day-old (1d) and 25-day-old (25d) D. pulex specimens. In total, we obtained 11,218,097 clean reads and 28,569 unique miRNAs from 1d specimens and 11,819,106 clean reads and 44,709 unique miRNAs from 25d specimens. Bioinformatic analyses was used to identify 1335 differentially expressed miRNAs from known miRNAs, including 127 miRNAs that exhibited statistically significant differences (P < 0.01); 92 miRNAs were upregulated and 35 were downregulated. Quantitative real-time (qRT)-PCR experiments were performed for nine miRNAs from five samples (1d, 5d, 10d, 15d, 20d and 25d) during the aging process, and the sequencing and qRT-PCR data were found to be consistent. Ninety-four miRNAs were predicted to correspond to 2014 target genes in known miRNAs with 4032 target gene sites. Sixteen pathways changed significantly (P < 0.05) at different developmental stages, revealing many important principles of the miRNA regulatory aging network of D. pulex. Overall, the difference in miRNA expression profile during aging of D. pulex forms a basis for further studies aimed at understanding the role of miRNAs in regulating aging, reproductive transformation, senescence, and longevity.
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Affiliation(s)
- Jiabao Hu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Chongyuan Lin
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Mengdi Liu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Qiaoqiong Tong
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Shanliang Xu
- School of Marine Sciences, Ningbo University, Ningbo 315211, China
| | - Danli Wang
- School of Marine Sciences, Ningbo University, Ningbo 315211, China.
| | - Yunlong Zhao
- School of Life Science, East China Normal University, Shanghai 200062, China.
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18
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Shakeel M, Xu X, Xu J, Li S, Yu J, Zhou X, Xu X, Hu Q, Yu X, Jin F. Genome-Wide Identification of Destruxin A-Responsive Immunity-Related MicroRNAs in Diamondback Moth, Plutella xylostella. Front Immunol 2018; 9:185. [PMID: 29472927 PMCID: PMC5809476 DOI: 10.3389/fimmu.2018.00185] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 01/22/2018] [Indexed: 12/12/2022] Open
Abstract
Plutella xylostella, a global key pest, is one of the major lepidopteran pests of cruciferous vegetables owing to its strong ability of resistance development to a wide range of insecticides. Destruxin A, a mycotoxin of the entomopathogenic fungus, Metarhizium anisopliae, has broad-spectrum insecticidal effects and has been used as an alternative control strategy to reduce harmful effects of insecticides. However, microRNA (miRNA)-regulated reactions against destruxin A have not been elucidated yet. Therefore, here, to identify immunity-related miRNAs, we constructed four small RNA libraries from destruxin A-injected larvae of P. xylostella at three different time courses (2, 4, and 6 h) with a control, and sequenced by Illumina. Our results showed that totally 187 known and 44 novel miRNAs were identified in four libraries by bioinformatic analysis. Interestingly, among differentially expressed known miRNAs, some conserved miRNAs, such as miR-263, miR-279, miR-306, miR-2a, and miR-308, predicted to be involved in regulating immunity-related genes, were also identified. Worthy to mention, miR-306 and miR-279 were also listed as common abundantly expressed miRNA in all treatments. The Kyoto Encyclopedia of Genes and Genomes pathway analysis also indicated that differentially expressed miRNAs were involved in several immunity-related signaling pathways, including toll signaling pathway, IMD signaling pathway, JAK-STAT signaling pathway, and cell adhesion molecules signaling pathway. To the best of our knowledge, this is the first comprehensive report of destruxin A-responsive immunity-related miRNAs in P. xylostella. Our findings will improve in understanding the role of destruxin A-responsive miRNAs in the host immune system and would be useful to develop biological control strategies for controlling P. xylostella.
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Affiliation(s)
- Muhammad Shakeel
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Guangzhou, China
| | - Xiaoxia Xu
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Guangzhou, China
| | - Jin Xu
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Guangzhou, China
| | - Shuzhong Li
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Guangzhou, China
| | - Jialin Yu
- Beijing Genomic Institute, Shenzhen, China
| | | | | | - Qiongbo Hu
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Guangzhou, China
| | - Xiaoqiang Yu
- School of Life Sciences, Institute of Insect Science and Technology, South China Normal University, Guangzhou, China
| | - Fengliang Jin
- College of Agriculture, South China Agricultural University, Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, Guangzhou, China
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19
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Qiang J, Cui YT, Tao FY, Bao WJ, He J, Li XH, Xu P, Sun LY. Physiological response and microRNA expression profiles in head kidney of genetically improved farmed tilapia (GIFT, Oreochromis niloticus) exposed to acute cold stress. Sci Rep 2018; 8:172. [PMID: 29317697 PMCID: PMC5760732 DOI: 10.1038/s41598-017-18512-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/08/2017] [Indexed: 12/30/2022] Open
Abstract
Cold stress has a serious impact on the overwintering survival and yield of genetically improved farmed tilapia (GIFT, Oreochromis niloticus). Understanding the physiological and molecular regulation mechanisms of low-temperature adaptation is necessary to help breed new tolerant strains. The semi-lethal low temperature of juvenile GIFT at 96 h was determined as 9.4 °C. We constructed and sequenced two small RNA libraries from head kidney tissues, one for the control (CO) group and one for the 9.4 °C-stressed (LTS) group, and identified 1736 and 1481 known microRNAs (miRNAs), and 164 and 152 novel miRNAs in the CO and LTS libraries, respectively. We verify the expression of nine up-regulated miRNAs and eight down-regulation miRNAs by qRT-PCR, and found their expression patterns were consistent with the sequencing results. We found that cold stress may have produced dysregulation of free radical and lipid metabolism, decreased superoxide dismutase activity, reduced respiratory burst and phagocytic activity of macrophages, increased malondialdehyde content, and adversely affected the physiological adaptation of GIFT, eventually leading to death. This study revealed interactions among miRNAs and signal regulated pathways in GIFT under cold stress that may help to understand the pathways involved in cold resistance.
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Affiliation(s)
- Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Yan T Cui
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Fan Y Tao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Wen J Bao
- Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Xia H Li
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China. .,Wuxi Fisheries College, Nanjing Agricultural University, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Lan Y Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Centre, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
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20
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Roy S, Saha TT, Zou Z, Raikhel AS. Regulatory Pathways Controlling Female Insect Reproduction. ANNUAL REVIEW OF ENTOMOLOGY 2018; 63:489-511. [PMID: 29058980 DOI: 10.1146/annurev-ento-020117-043258] [Citation(s) in RCA: 291] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The synthesis of vitellogenin and its uptake by maturing oocytes during egg maturation are essential for successful female reproduction. These events are regulated by the juvenile hormones and ecdysteroids and by the nutritional signaling pathway regulated by neuropeptides. Juvenile hormones act as gonadotropins, regulating vitellogenesis in most insects, but ecdysteroids control this process in Diptera and some Hymenoptera and Lepidoptera. The complex crosstalk between the juvenile hormones, ecdysteroids, and nutritional signaling pathways differs distinctly depending on the reproductive strategies adopted by various insects. Molecular studies within the past decade have revealed much about the relationships among, and the role of, these pathways with respect to regulation of insect reproduction. Here, we review the role of juvenile hormones, ecdysteroids, and nutritional signaling, along with that of microRNAs, in regulating female insect reproduction at the molecular level.
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Affiliation(s)
- Sourav Roy
- Department of Entomology, Institute for Integrative Genome Biology, and Center for Disease Vector Research, University of California, Riverside, California 92521, USA; , ,
| | - Tusar T Saha
- Department of Entomology, Institute for Integrative Genome Biology, and Center for Disease Vector Research, University of California, Riverside, California 92521, USA; , ,
| | - Zhen Zou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Alexander S Raikhel
- Department of Entomology, Institute for Integrative Genome Biology, and Center for Disease Vector Research, University of California, Riverside, California 92521, USA; , ,
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21
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Xu J, Xu X, Li S, Wang S, Xu X, Zhou X, Yu J, Yu X, Shakeel M, Jin F. Genome-Wide Profiling of Plutella xylostella Immunity-Related miRNAs after Isaria fumosorosea Infection. Front Physiol 2017; 8:1054. [PMID: 29311981 PMCID: PMC5735356 DOI: 10.3389/fphys.2017.01054] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/01/2017] [Indexed: 12/19/2022] Open
Abstract
The development of resistance by Plutella xylostella to almost all insecticides is of significant concern all over the world. Entomopathogenic fungi such as Isaria fumosorosea have been used as an alternative to insecticides. However, the knowledge of miRNA-regulated reactions against entomopathogenic fungi is still in its infant stage. In the present study, P. xylostella was challenged with I. fumosorosea at four different time points (12, 18, 24, and 36 h) including a control, to build miRNA libraries by Illumina sequencing. The results of differential expression analysis exhibited that 23 miRNAs were differentially expressed, compared to control, in all treatments. It is worth mentioning, of these, some conserved miRNAs such as miR-2, miR-9a, miR-745, miR-7b, and miR-2767, known to play critical roles in host-pathogen interaction, were also identified. Furthermore, differentially expressed miRNAs were validated by RT-qPCR. Our results provide an essential information for further functional studies of the interaction between I. fumosorosea and P. xylostella at the post-transcriptional level.
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Affiliation(s)
- Jin Xu
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiaoxia Xu
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Shuzhong Li
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Shuang Wang
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | | | | | - Jialin Yu
- Beijing Genomic Institute, Shenzhen, China
| | - Xiaoqiang Yu
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Muhammad Shakeel
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Fengliang Jin
- Laboratory of Bio-Pesticide Creation and Application of Guangdong Province, College of Agriculture, South China Agricultural University, Guangzhou, China
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Ylla G, Piulachs MD, Belles X. Comparative analysis of miRNA expression during the development of insects of different metamorphosis modes and germ-band types. BMC Genomics 2017; 18:774. [PMID: 29020923 PMCID: PMC5637074 DOI: 10.1186/s12864-017-4177-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/05/2017] [Indexed: 01/08/2023] Open
Abstract
Background Do miRNAs contribute to specify the germ-band type and the body structure in the insect embryo? Our goal was to address that issue by studying the changes in miRNA expression along the ontogeny of the German cockroach Blattella germanica, which is a short germ-band and hemimetabolan species. Results We sequenced small RNA libraries representing 11 developmental stages of B. germanica ontogeny (with especial emphasis on embryogenesis) and the changes in miRNA expression were examined. Data were compared with equivalent data for two long germ-band holometabolan species Drosophila melanogaster and Drosophila virilis, and the short germ-band holometabolan species Tribolium castaneum. The identification of B. germanica embryo small RNA sequences unveiled miRNAs not detected in previous studies, such as those of the MIR-309 family and 54 novel miRNAs. Four main waves of miRNA expression were recognized (with most miRNA changes occurring during the embryonic stages): the first from day 0 to day 1 of embryogenesis, the second during mid-embryogenesis (days 0–6), the third (with an acute expression peak) on day 2 of embryonic development, and the fourth during post-embryonic development. The second wave defined the boundaries of maternal-to-zygotic transition, with maternal mRNAs being cleared, presumably by Mir-309 and associated scavenger miRNAs. Conclusion miRNAs follow well-defined patterns of expression over hemimetabolan ontogeny, patterns that are more diverse during embryonic development than during the nymphal stages. The results suggest that miRNAs play important roles in the developmental transitions between the embryonic stages of development (starting with maternal loading), during which they might influence the germ-band type and metamorphosis mode. Electronic supplementary material The online version of this article (10.1186/s12864-017-4177-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillem Ylla
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003, Barcelona, Spain
| | - Maria-Dolors Piulachs
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003, Barcelona, Spain.
| | - Xavier Belles
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Passeig Marítim 37, 08003, Barcelona, Spain.
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MicroRNA-dependent regulation of metamorphosis and identification of microRNAs in the red flour beetle, Tribolium castaneum. Genomics 2017. [DOI: 10.1016/j.ygeno.2017.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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24
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Identification and comparative analysis of the pearl oyster Pinctada fucata hemocytes microRNAs in response to Vibrio alginolyticus infection. Genes Genomics 2017. [DOI: 10.1007/s13258-017-0575-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Radhakrishnan S, Literman R, Neuwald J, Severin A, Valenzuela N. Transcriptomic responses to environmental temperature by turtles with temperature-dependent and genotypic sex determination assessed by RNAseq inform the genetic architecture of embryonic gonadal development. PLoS One 2017; 12:e0172044. [PMID: 28296881 PMCID: PMC5352168 DOI: 10.1371/journal.pone.0172044] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 01/30/2017] [Indexed: 12/24/2022] Open
Abstract
Vertebrate sexual fate is decided primarily by the individual's genotype (GSD), by the environmental temperature during development (TSD), or both. Turtles exhibit TSD and GSD, making them ideal to study the evolution of sex determination. Here we analyze temperature-specific gonadal transcriptomes (RNA-sequencing validated by qPCR) of painted turtles (Chrysemys picta TSD) before and during the thermosensitive period, and at equivalent stages in soft-shell turtles (Apalone spinifera-GSD), to test whether TSD's and GSD's transcriptional circuitry is identical but deployed differently between mechanisms. Our data show that most elements of the mammalian urogenital network are active during turtle gonadogenesis, but their transcription is generally more thermoresponsive in TSD than GSD, and concordant with their sex-specific function in mammals [e.g., upregulation of Amh, Ar, Esr1, Fog2, Gata4, Igf1r, Insr, and Lhx9 at male-producing temperature, and of β-catenin, Foxl2, Aromatase (Cyp19a1), Fst, Nf-kb, Crabp2 at female-producing temperature in Chrysemys]. Notably, antagonistic elements in gonadogenesis (e.g., β-catenin and Insr) were thermosensitive only in TSD early-embryos. Cirbp showed warm-temperature upregulation in both turtles disputing its purported key TSD role. Genes that may convert thermal inputs into sex-specific development (e.g., signaling and hormonal pathways, RNA-binding and heat-shock) were differentially regulated. Jak-Stat, Nf-κB, retinoic-acid, Wnt, and Mapk-signaling (not Akt and Ras-signaling) potentially mediate TSD thermosensitivity. Numerous species-specific ncRNAs (including Xist) were differentially-expressed, mostly upregulated at colder temperatures, as were unannotated loci that constitute novel TSD candidates. Cirbp showed warm-temperature upregulation in both turtles. Consistent transcription between turtles and alligator revealed putatively-critical reptilian TSD elements for male (Sf1, Amh, Amhr2) and female (Crabp2 and Hspb1) gonadogenesis. In conclusion, while preliminary, our data helps illuminate the regulation and evolution of vertebrate sex determination, and contribute genomic resources to guide further research into this fundamental biological process.
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Affiliation(s)
- Srihari Radhakrishnan
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA, United States of America
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Robert Literman
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
- Ecology and Evolutionary Biology Program, Iowa State University, Ames, IA, United States of America
| | - Jennifer Neuwald
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
| | - Andrew Severin
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
- Genome Informatics Facility, Iowa State University, Ames, IA, United States of America
| | - Nicole Valenzuela
- Department of Ecology, Evolution and Organismal Biology, Iowa State University, Ames, IA, United States of America
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Qiang J, Tao F, He J, Sun L, Xu P, Bao W. Effects of exposure to Streptococcus iniae on microRNA expression in the head kidney of genetically improved farmed tilapia (Oreochromis niloticus). BMC Genomics 2017; 18:190. [PMID: 28219342 PMCID: PMC5322787 DOI: 10.1186/s12864-017-3591-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Background Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are susceptible to infection by Streptococcus iniae when maintained in modern intensive culture systems. GIFT are commercially important fishes that are cultured widely in southern China. The role of microRNAs (miRNAs) in the regulatory response of GIFT to S. iniae infection has been underestimated and has not yet been well studied. Head kidney has an important immune function in teleost fishes. The main aim of this study was to determine the possible function of miRNAs in head kidney of S. iniae-infected GIFT. MiRNAs are small, non-coding RNAs that regulate gene expression by binding to the 3’-untranslated regions of their target mRNAs. MiRNAs are known to regulate immune-regulated signaling and inflammatory response pathways. Results High-throughput deep sequencing of two libraries (control group [CO] and infected group [IN]) of RNA extracted from GIFT head kidney tissues generated 12,089,630 (CO) and 12,624,975 (IN) clean reads. Bioinformatics analysis identified 1736 and 1729 conserved miRNAs and 164 and 165 novel miRNAs in the CO and IN libraries, respectively. Three miRNAs (miR-310-3p, miR-92, and miR-127) were found to be up-regulated and four miRNAs (miR-92d-3p, miR-375-5p, miR-146-3p, and miR-694) were found to be down-regulated in the S. iniae-infected GIFT. The expressions of these miRNAs were verified by quantitative real-time PCR. RNAhybrid and TargetScan were used to identify complementary miRNA and mRNA target sites, and the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases were used to annotate and predict potential downstream regulation of biological pathways. Seven target genes, which encode immune-related proteins (complement C3, cytidine deaminase, regulator of G-protein Rgs22, mitogen-activated protein kinase Mapk1, metabotropic glutamate receptorm GluR8, calcium-sensing receptor CaSR, and microtubule-associated protein Map1S) were predicted to play crucial roles in the GIFT response to S. iniae infection. Conclusions S. iniae outbreaks have hindered the development of the tilapia industry in China. Understanding the miRNA transcriptome of S. iniae-infected GIFT is important for exploring the immune responses regulated by miRNAs as well as for studying novel regulated networks to prevent and treat S. iniae infections in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3591-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Qiang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Fanyi Tao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Jie He
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Lanyi Sun
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China.
| | - Wenjin Bao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, 9 Shanshui East Road, Wuxi, Jiangsu, 214081, China
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Ma KS, Li F, Liu Y, Liang PZ, Chen XW, Gao XW. Identification of microRNAs and their response to the stress of plant allelochemicals in Aphis gossypii (Hemiptera: Aphididae). BMC Mol Biol 2017; 18:5. [PMID: 28202045 PMCID: PMC5311835 DOI: 10.1186/s12867-017-0080-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 01/17/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are a group of short non-coding RNAs involved in the inhibition of protein translation or in mRNA degradation. Although the regulatory roles of miRNAs in various biological processes have been investigated, there is as yet an absence of studies about the regulatory roles of miRNAs involved in the metabolism of plant allelochemicals in insects. RESULTS We constructed five small RNA libraries from apterous Aphis gossypii adults that had fed on an artificial diet containing various allelochemicals. Using Illumina sequencing, a total of 73.27 million clean reads was obtained, and 292 miRNAs were identified from A. gossypii. Comparative analysis of read counts indicated that both conserved and novel miRNAs were differently expressed among the five libraries, and the differential expression was validated via qRT-PCR. We found that the transcript levels of several miRNAs were increased or decreased in all of the allelochemical treatment libraries compared to the control. The putative target genes of the miRNAs were predicted using in silico tools, and the target genes of several miRNAs were presumed to be involved in the metabolism of xenobiotic compounds. Furthermore, the target prediction results were confirmed using dual luciferase reporter assay, and Ago-miR-656a-3p was demonstrated to regulate the expression of CYP6J1 post-transcriptionally through binding to the 3' UTR of CYP6J1. CONCLUSION Our research results indicate that miRNAs may be involved in the metabolism of plant allelochemicals in A. gossypii, and these results also represent an important new small RNA genomics resource for further studies on this topic.
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Affiliation(s)
| | - Fen Li
- China Agricultural University, Beijing, China
| | - Ying Liu
- China Agricultural University, Beijing, China
| | | | | | - Xi-Wu Gao
- China Agricultural University, Beijing, China.
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Paulo DF, Azeredo-Espin AML, Canesin LEC, Vicentini R, Junqueira ACM. Identification and characterization of microRNAs in the screwworm flies Cochliomyia hominivorax and Cochliomyia macellaria (Diptera: Calliphoridae). INSECT MOLECULAR BIOLOGY 2017; 26:46-57. [PMID: 27775856 DOI: 10.1111/imb.12270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs that modulate gene expression through post-transcriptional regulation. Here, we report the identification and characterization of miRNAs in two closely related screwworm flies with different feeding habits: Cochliomyia hominivorax and Cochliomyia macellaria. The New World screwworm, C. hominivorax, is an obligatory parasite of warm-blooded vertebrates, whereas the secondary screwworm, C. macellaria, is a free-living organism that feeds on decaying organic matter. Here, the small RNA transcriptomes of adults and third-instar larvae of both species were sequenced. A total of 110 evolutionarily conserved miRNAs were identified, and 10 putative precursor miRNAs (pre-miRNAs) were predicted. The relative expression of six selected miRNAs was further investigated, including miRNAs that are related to reproduction and neural processes in other insects. Mature miRNAs were also characterized across an evolutionary time scale, suggesting that the majority of them have been conserved since the emergence of the Arthropoda [540 million years ago (Ma)], Hexapoda (488 Ma) and Brachycera (195 Ma) lineages. This study is the first report of miRNAs for screwworm flies. We also performed a comparative analysis with the hereby predicted miRNAs from the sheep blowfly, Lucilia cuprina. The results presented may advance our understanding of parasitic habits within Calliphoridae and assist further functional studies in blowflies.
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Affiliation(s)
- D F Paulo
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - A M L Azeredo-Espin
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - L E C Canesin
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - R Vicentini
- Centre for Molecular Biology and Genetic Engineering, Department of Genetics, Evolution and Bioagents, Institute of Biology, University of Campinas, Campinas, SP, Brazil
| | - A C M Junqueira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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MicroRNA-34 directly targets pair-rule genes and cytoskeleton component in the honey bee. Sci Rep 2017; 7:40884. [PMID: 28098233 PMCID: PMC5241629 DOI: 10.1038/srep40884] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/12/2016] [Indexed: 01/06/2023] Open
Abstract
MicroRNAs (miRNAs) are key regulators of developmental processes, such as cell fate determination and differentiation. Previous studies showed Dicer knockdown in honeybee embryos disrupt the processing of functional mature miRNAs and impairs embryo patterning. Here we investigated the expression profiles of miRNAs in honeybee embryogenesis and the role of the highly conserved miR-34-5p in the regulation of genes involved in insect segmentation. A total of 221 miRNAs were expressed in honey bee embryogenesis among which 97 mature miRNA sequences have not been observed before. Interestingly, we observed a switch in dominance between the 5-prime and 3-prime arm of some miRNAs in different embryonic stages; however, most miRNAs present one dominant arm across all stages of embryogenesis. Our genome-wide analysis of putative miRNA-target networks and functional pathways indicates miR-34-5p is one of the most conserved and connected miRNAs associated with the regulation of genes involved in embryonic patterning and development. In addition, we experimentally validated that miR-34-5p directly interacts to regulatory elements in the 3'-untranslated regions of pair-rule (even-skipped, hairy, fushi-tarazu transcription factor 1) and cytoskeleton (actin5C) genes. Our study suggests that miR-34-5p may regulate the expression of pair-rule and cytoskeleton genes during early development and control insect segmentation.
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Qiao Y, Mao Y, Wang J, Chen R, Libing Z, Su YQ, Chen J, Zheng WQ. Analysis of liver and gill miRNAs of Larimichthys crocea against Cryptocryon irritans challenge. FISH & SHELLFISH IMMUNOLOGY 2016; 59:484-491. [PMID: 27765701 DOI: 10.1016/j.fsi.2016.10.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 10/12/2016] [Accepted: 10/15/2016] [Indexed: 06/06/2023]
Abstract
The white-spot disease caused by marine ciliate Cryptocryon irritans hindered the sustainable development of large yellow croaker Larimichthys crocea industry. Better understandings about the parasite-host interactions in the molecular level will facilitate the prevention of mass mortality of the L. crocea caused by white-spot disease. MicroRNAs (miRNAs) are a class of small RNA molecules about 20-22 nucleotides which post-transcriptionally regulated many protein-coding genes and involved in many biological processes, especially in host-pathogen responses. In this study, we identified known and novel miRNAs in the gill and liver of L. crocea challenged by C. irritans by high throughput sequencing using Solexa technology. The data were further studied to screen differentially expressed miRNAs, and predict their target genes. The differential expression (p < 0.05) between libraries was observed in 103 miRNAs in liver tissue, among which 65 and 38 were conserved and novel miRNAs, 67 and 36 were up- and down-regulated miRNAs. While in gill tissue, 122 significant differentially expressed miRNAs were identified, among which 83 and 39 were conserved and novel miRNAs, 79 and 43 were up- and down-regulated miRNAs. In addition, these differentially expressed miRNAs target a series of genes which involved in many important biological processes including immune response. Here via deep sequencing, we for the first time characterize L. crocea miRNAs in response to C. irritans challenge, the results should help for better understandings about the immune response of the L. crocea under C. irritans challenge.
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Affiliation(s)
- Ying Qiao
- State Key Laboratory of Large Yellow Croaker Breeding, Fujian Fuding Seagull Fishing Food Co., Ltd, 352103, Fujian, China; College of Ocean and Earth Science, Xiamen University, 361005, China
| | - Yong Mao
- State Key Laboratory of Large Yellow Croaker Breeding, Fujian Fuding Seagull Fishing Food Co., Ltd, 352103, Fujian, China; College of Ocean and Earth Science, Xiamen University, 361005, China
| | - Jun Wang
- College of Ocean and Earth Science, Xiamen University, 361005, China
| | - Ruanni Chen
- College of Ocean and Earth Science, Xiamen University, 361005, China
| | - Zheng Libing
- College of Ocean and Earth Science, Xiamen University, 361005, China
| | - Yong-Quan Su
- State Key Laboratory of Large Yellow Croaker Breeding, Fujian Fuding Seagull Fishing Food Co., Ltd, 352103, Fujian, China; College of Ocean and Earth Science, Xiamen University, 361005, China.
| | - Jia Chen
- State Key Laboratory of Large Yellow Croaker Breeding, Fujian Fuding Seagull Fishing Food Co., Ltd, 352103, Fujian, China
| | - Wei-Qiang Zheng
- State Key Laboratory of Large Yellow Croaker Breeding, Fujian Fuding Seagull Fishing Food Co., Ltd, 352103, Fujian, China
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31
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Yang S, Zhang J, Wang S, Zhang X, Liu Y, Xi J. Identification and profiling of miRNAs in overwintering Lissorhoptrus oryzophilus via next-generation sequencing. Cryobiology 2016; 74:68-76. [PMID: 27908684 DOI: 10.1016/j.cryobiol.2016.11.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 09/28/2016] [Accepted: 11/27/2016] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of various biological processes in organisms. Insects subjected to abiotic stress can regulate gene expression post-transcriptionally through the use of microRNAs. However, the role of miRNAs in response to cold stress in Lissorhoptrus oryzophilus Kuschel remains unknown. The rice water weevil, L. oryzophilus, is an invasive insect that is able to survive cold winters. To characterize changes in miRNAs in response to overwintering in L. oryzophilus, a comprehensive comparative analysis of microRNAs was performed involving an overwintering and a normal adult. High-throughput Illumina sequencing and bioinformatics analyses revealed 121 conserved and 14 potential novel microRNAs in two small libraries. The novel miRNAs exhibit low expression levels in both libraries. After the expression profiles of the miRNAs in the two libraries were normalized, 36 miRNAs in L. oryzophilus were found to be differentially expressed in response to overwintering. In particular, 14 conserved miRNAs and 6 novel miRNAs were up-regulated, while 15 conserved miRNAs and 1 novel miRNA were down-regulated. In addition, the expression patterns of 11 conserved and potentially novel miRNAs were confirmed by quantitative RT-PCR analysis. Most importantly, this work provides a unique resource of characterized miRNAs for overwintering L. oryzophilus and contributes to studies of the functions of cold-related and other L. oryzophilus miRNAs.
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Affiliation(s)
- Shuang Yang
- College of Plant Science, Jilin University, Changchun 130062, PR China.
| | - Juhong Zhang
- College of Plant Science, Jilin University, Changchun 130062, PR China.
| | - Shang Wang
- College of Plant Science, Jilin University, Changchun 130062, PR China.
| | - Xinxin Zhang
- College of Plant Science, Jilin University, Changchun 130062, PR China.
| | - Yan Liu
- College of Plant Science, Jilin University, Changchun 130062, PR China.
| | - Jinghui Xi
- College of Plant Science, Jilin University, Changchun 130062, PR China.
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Abstract
Is there a correlation between miRNA diversity and levels of organismic complexity? Exhibiting extraordinary levels of morphological and developmental complexity, insects are the most diverse animal class on earth. Their evolutionary success was in particular shaped by the innovation of holometabolan metamorphosis in endopterygotes. Previously, miRNA evolution had been linked to morphological complexity, but astonishing variation in the currently available miRNA complements of insects made this link unclear. To address this issue, we sequenced the miRNA complement of the hemimetabolan Blattella germanica and reannotated that of two other hemimetabolan species, Locusta migratoria and Acyrthosiphon pisum, and of four holometabolan species, Apis mellifera, Tribolium castaneum, Bombyx mori and Drosophila melanogaster. Our analyses show that the variation of insect miRNAs is an artefact mainly resulting from poor sampling and inaccurate miRNA annotation, and that insects share a conserved microRNA toolkit of 65 families exhibiting very low variation. For example, the evolutionary shift toward a complete metamorphosis was accompanied only by the acquisition of three and the loss of one miRNA families.
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Sun X, Liu QH, Yang B, Huang J. Differential expression of microRNAs of Litopenaeus vannamei in response to different virulence WSSV infection. FISH & SHELLFISH IMMUNOLOGY 2016; 58:18-23. [PMID: 27620817 DOI: 10.1016/j.fsi.2016.08.062] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 06/06/2023]
Abstract
WSSV is one of the most harmful pathogeny in the pacific white shrimp, and genetic variations caused the strains of different virulence. MicroRNAs (miRNAs) involved in the regulation of virus defense. To understand the different virulence of WSSV on miRNA expression in Litopeneaus vannamei, the deep sequencing was performed to compare two small RNA libraries prepared from hepatopancreas of Litopeneaus vannamei infected with normal-virulence or low-virulence WSSV. Approximately 29,398,623 raw reads from normal-virulence library and 35,291,803 raw reads from low-virulence library were obtained. There were about 37 miRNAs homologs identified. Sixteen miRNAs were significantly up-regulated and twenty-one miRNAs were significantly down-regulated in normal-virulence infection library compared with low-virulence infection library. Of these, Igi-miR-1175-3p was the most significant different miRNA, followed by bmo-miR-1175-3p and ipu-miR-26b, respectively. The putative target genes for differentially expressed miRNAs were concerned with biological processes, signal meditated, cell differentiation and apoptosis, immune recognition and other more functions. The results will help to understand the miRNAs response to different virulence WSSV infection.
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Affiliation(s)
- Xinying Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Qing-Hui Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Bing Yang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jie Huang
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Characterization and comparative profiling of the small RNA transcriptomes in the Hemipteran insect Nilaparvata lugens. Gene 2016; 595:83-91. [PMID: 27693372 DOI: 10.1016/j.gene.2016.09.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 09/12/2016] [Accepted: 09/26/2016] [Indexed: 12/26/2022]
Abstract
MicroRNAs (miRNAs) are a group of small RNAs involved in various biological processes through negative regulation of mRNAs at the post-transcriptional level. The brown planthopper (BPH), Nilaparvata lugens (Stål), is one of the most serious and destructive insect pests of rice. In the present study, two small RNA libraries of virulent N. lugens populations (Biotype I survives on susceptive rice variety TN1 and Biotype Y survives on moderately resistant rice variety YHY15) were constructed and sequenced using the high-throughput sequencing technology in order to identify the relationship between miRNAs of N.lugens and adaptation of BPH pests to rice resistance. In total 15,758,632 and 11,442,592 reads, corresponding to 3,144,026 and 2,550,049 unique sequences, were obtained in the two libraries (BPH-TN1 and BPH-YHY15 libraries), respectively. A total of 41 potential novel miRNAs were predicted in the two libraries, and 26 miRNAs showed significantly differential expression between two libraries. All miRNAs were significantly up-regulated in the BPH-TN1 library. Target genes likely regulated by these differentially expressed miRNAs were predicted using computational prediction. The functional annotation of target genes performed by Gene Ontology enrichment (GO) and Kyoto Encyclopedia of Genes and Genomes pathway analysis (KEGG) indicated that a majority of differential miRNAs were involved in "Metabolism" pathway. These results provided an understanding of the role of miRNAs in BPH to adaptability of BPH on rice resistance, and will be useful in developing new control strategies for host defense against BPH.
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Macedo LMF, Nunes FMF, Freitas FCP, Pires CV, Tanaka ED, Martins JR, Piulachs MD, Cristino AS, Pinheiro DG, Simões ZLP. MicroRNA signatures characterizing caste-independent ovarian activity in queen and worker honeybees (Apis mellifera L.). INSECT MOLECULAR BIOLOGY 2016; 25:216-26. [PMID: 26853694 DOI: 10.1111/imb.12214] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Queen and worker honeybees differ profoundly in reproductive capacity. The queen of this complex society, with 200 highly active ovarioles in each ovary, is the fertile caste, whereas the workers have approximately 20 ovarioles as a result of receiving a different diet during larval development. In a regular queenright colony, the workers have inactive ovaries and do not reproduce. However, if the queen is sensed to be absent, some of the workers activate their ovaries, producing viable haploid eggs that develop into males. Here, a deep-sequenced ovary transcriptome library of reproductive workers was used as supporting data to assess the dynamic expression of the regulatory molecules and microRNAs (miRNAs) of reproductive and nonreproductive honeybee females. In this library, most of the differentially expressed miRNAs are related to ovary physiology or oogenesis. When we quantified the dynamic expression of 19 miRNAs in the active and inactive worker ovaries and compared their expression in the ovaries of virgin and mated queens, we noted that some miRNAs (miR-1, miR-31a, miR-13b, miR-125, let-7 RNA, miR-100, miR-276, miR-12, miR-263a, miR-306, miR-317, miR-92a and miR-9a) could be used to identify reproductive and nonreproductive statuses independent of caste. Furthermore, integrative gene networks suggested that some candidate miRNAs function in the process of ovary activation in worker bees.
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Affiliation(s)
- L M F Macedo
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - F M F Nunes
- Departamento De Genética E Evolução, Centro De Ciências Biológicas E Da Saúde, Universidade Federal De São Carlos, São Carlos, Brazil
| | - F C P Freitas
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - C V Pires
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - E D Tanaka
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - J R Martins
- Departamento De Genética, Faculdade De Medicina De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
| | - M-D Piulachs
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - A S Cristino
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
| | - D G Pinheiro
- Departamento De Tecnologia, Faculdade De Ciências Agrárias E Veterinárias, Universidade Estadual Paulista, Jaboticabal, Brazil
| | - Z L P Simões
- Departamento De Biologia, Faculdade De Filosofia, Ciências E Letras De Ribeirão Preto, Universidade De São Paulo, Ribeirão Preto, Brazil
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Xu G, Han J, Xu T. Comparative analysis of the small RNA transcriptomes of miiuy croaker revealed microRNA-mediated regulation of TLR signaling pathway response to Vibrio anguillarum infection. FISH & SHELLFISH IMMUNOLOGY 2016; 52:248-257. [PMID: 26980609 DOI: 10.1016/j.fsi.2016.03.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Revised: 03/01/2016] [Accepted: 03/10/2016] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are an abundant class of endogenous noncoding small RNAs (sRNAs) that are partially complementary to their target messenger RNA (mRNA), which post-transcriptionally regulate various biological processes by repressing mRNA translation or inducing mRNA degradation. MiRNAs have been demonstrated to play crucial roles in the host response to infection by diverse pathogens. As an important bacterial pathogen, Vibrio anguillarum has been caused great economic losses in miiuy croaker aquaculture. To identify immune-related miRNAs of miiuy croaker in response to V. anguillarum infection, we constructed two sRNA libraries with or without bacterial infection. High-throughput deep sequencing and subsequent bioinformatic analysis identified 241 conserved and 137 novel miRNA precursors in miiuy croaker based on its whole genome sequences, encoding 293 and 124 mature miRNAs, respectively. Then we compared the expression patterns of miRNAs in the two libraries. There were significant differences in the expression of 12 miRNAs between the infection group (IG) and control group (CG). Further, the expressions of six miRNAs were validated by real-time quantitative PCR. The target gene prediction and function analysis were conducted for the 12 differential miRNAs. This analysis revealed that these miRNAs participated in the regulation multiple immune-related signaling pathways. Transcription factors in TLR signaling, such as AP-1, IRF5, NF-κB and IRF3, were activated by these miRNAs via post-transcriptionally regulating the expression of TLRs and TLR-associated signaling proteins, inducing effective host immune response to eradicate infectious pathogens. This is the first study of the identification and characterization of miiuy croaker miRNAs in response to V. anguillarum infection. The comprehensive analysis of the expression of miRNAs and the target gene and function prediction of differently expressed miRNAs may help to understand the regulatory mechanisms of miRNA in fish during the interaction between host and bacterial pathogens.
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Affiliation(s)
- Guoliang Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Jingjing Han
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China
| | - Tianjun Xu
- Laboratory of Fish Biogenetics & Immune Evolution, College of Marine Science, Zhejiang Ocean University, Zhoushan, 316022, China.
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Altered microRNA expression and pre-mRNA splicing events reveal new mechanisms associated with early stage Mycobacterium avium subspecies paratuberculosis infection. Sci Rep 2016; 6:24964. [PMID: 27102525 PMCID: PMC4840452 DOI: 10.1038/srep24964] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 04/08/2016] [Indexed: 12/19/2022] Open
Abstract
The molecular regulatory mechanisms of host responses to Mycobacterium avium subsp. paratuberculosis (MAP) infection during the early subclinical stage are still not clear. In this study, surgically isolated ileal segments in newborn calves (n = 5) were used to establish in vivo MAP infection adjacent to an uninfected control intestinal compartment. RNA-Seq was used to profile the whole transcriptome (mRNAs) and the microRNAome (miRNAs) of ileal tissues collected at one-month post-infection. The most related function of the differentially expressed mRNAs between infected and uninfected tissues was “proliferation of endothelial cells”, indicating that MAP infection may lead to the over-proliferation of endothelial cells. In addition, 46.2% of detected mRNAs displayed alternative splicing events. The pre-mRNA of two genes related to macrophage maturation (monocyte to macrophage differentiation-associated) and lysosome function (adenosine deaminase) showed differential alternative splicing events, suggesting that specific changes in the pre-mRNA splicing sites may be a mechanism by which MAP escapes host immune responses. Moreover, 9 miRNAs were differentially expressed after MAP infection. The integrated analysis of microRNAome and transcriptome revealed that these miRNAs might regulate host responses to MAP infection, such as “proliferation of endothelial cells” (bta-miR-196 b), “bacteria recognition” (bta-miR-146 b), and “regulation of the inflammatory response” (bta-miR-146 b).
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38
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Li R, Jiang GF, Ren QP, Wang YT, Zhou XM, Zhou CF, Qin DZ. MicroRNAs of the mesothorax in Qinlingacris elaeodes, an alpine grasshopper showing a wing polymorphism with unilateral wing form. BULLETIN OF ENTOMOLOGICAL RESEARCH 2016; 106:225-232. [PMID: 26693589 DOI: 10.1017/s0007485315000991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
MicroRNAs (miRNAs) are now recognized as key post-transcriptional regulators in regulation of phenotypic diversity. Qinlingacris elaeodes is a species of the alpine grasshopper, which is endemic to China. Adult individuals have three wing forms: wingless, unilateral-winged and short-winged. This is an ideal species to investigate the phenotypic plasticity, development and evolution of insect wings because of its case of unilateral wing form in both the sexes. We sequenced a small RNA library prepared from mesothoraxes of the adult grasshoppers using the Illumina deep sequencing technology. Approximately 12,792,458 raw reads were generated, of which the 854,580 high-quality reads were used only for miRNA identification. In this study, we identified 49 conserved miRNAs belonging to 41 families and 69 species-specific miRNAs. Moreover, seven miRNA*s were detected both for conserved miRNAs and species-specific miRNAs, which were supported by hairpin forming precursors based on polymerase chain reaction. This is the first description of miRNAs in alpine grasshoppers. The results provide a useful resource for further studies on molecular regulation and evolution of miRNAs in grasshoppers. These findings not only enrich the miRNAs for insects but also lay the groundwork for the study of post-transcriptional regulation of wing forms.
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Affiliation(s)
- R Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University,Nanjing,China
| | - G F Jiang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University,Nanjing,China
| | - Q P Ren
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University,Nanjing,China
| | - Y T Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University,Nanjing,China
| | - X M Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University,Nanjing,China
| | - C F Zhou
- Jiangsu Key Laboratory for Biodiversity and Biotechnology,College of Life Sciences, Nanjing Normal University,Nanjing,China
| | - D Z Qin
- Key Laboratory of Plant Protection Resources and Pest Management of the Ministry of Education,Entomological Museum,Northwest A & F University,Yangling,China
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Kang D, Shi B, Erfe MC, Craft N, Li H. Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. Sci Transl Med 2016; 7:293ra103. [PMID: 26109103 DOI: 10.1126/scitranslmed.aab2009] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Various diseases have been linked to the human microbiota, but the underlying molecular mechanisms of the microbiota in disease pathogenesis are often poorly understood. Using acne as a disease model, we aimed to understand the molecular response of the skin microbiota to host metabolite signaling in disease pathogenesis. Metatranscriptomic analysis revealed that the transcriptional profiles of the skin microbiota separated acne patients from healthy individuals. The vitamin B12 biosynthesis pathway in the skin bacterium Propionibacterium acnes was significantly down-regulated in acne patients. We hypothesized that host vitamin B12 modulates the activities of the skin microbiota and contributes to acne pathogenesis. To test this hypothesis, we analyzed the skin microbiota in healthy subjects supplemented with vitamin B12. We found that the supplementation repressed the expression of vitamin B12 biosynthesis genes in P. acnes and altered the transcriptome of the skin microbiota. One of the 10 subjects studied developed acne 1 week after vitamin B12 supplementation. To further understand the molecular mechanism, we revealed that vitamin B12 supplementation in P. acnes cultures promoted the production of porphyrins, which have been shown to induce inflammation in acne. Our findings suggest a new bacterial pathogenesis pathway in acne and provide one molecular explanation for the long-standing clinical observation that vitamin B12 supplementation leads to acne development in a subset of individuals. Our study discovered that vitamin B12, an essential nutrient in humans, modulates the transcriptional activities of skin bacteria, and provided evidence that metabolite-mediated interactions between the host and the skin microbiota play essential roles in disease development.
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Affiliation(s)
- Dezhi Kang
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Baochen Shi
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Marie C Erfe
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Noah Craft
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Huiying Li
- Department of Molecular and Medical Pharmacology, Crump Institute for Molecular Imaging, David Geffen School of Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. UCLA-Department of Energy (DOE) Institute for Genomics and Proteomics, Los Angeles, CA 90095, USA.
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40
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Zhong L, Zhang F, Zhai Y, Cao Y, Zhang S, Chang Y. Identification and comparative analysis of complement C3-associated microRNAs in immune response of Apostichopus japonicus by high-throughput sequencing. Sci Rep 2015; 5:17763. [PMID: 26634300 PMCID: PMC4669494 DOI: 10.1038/srep17763] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 10/15/2015] [Indexed: 11/24/2022] Open
Abstract
MicroRNAs (miRNAs) are important effectors in mediating host–pathogen interaction. In this report, coelomocytes miRNA libraries of three Japanese sea cucumbers Apostichopus japonicus were built by Illumina® Hiseq2000 from different time points after lipopolysaccharide challenge (at time 0 h, 6 h and 12 h). The clean data received from high throughput sequencing were used to sequences analysis. Referenced to the Strongylocentrotus purpuratus genome, 38 conserved miRNAs were found, and three miRNA candidates were predicted by software. According to the evidence resulting from the expression of AjC3, expressing levels of spu-miR-133, spu-miR-137 and spu-miR-2004 altered along with the expression of AjC3 changing at different time points after LPS injection. Thus, we speculated that the three miRNAs may have influence on A. japonicus complement C3. The spu-miR-137 and miR-137 gene family in miRBase were analyzed by bioinformatics. There is an obvious discrepancy between invertebrates and vertebrates. The first and ninth nucleotides in invertebrate miR-137 are offset compared vertebrate miR-137. Importantly, this is the first attempt to map the stage of immune response regulome in echinoderms, which might be considered as information for elucidating the intrinsic mechanism underlying the immune system in this species.
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Affiliation(s)
- Lei Zhong
- Key Laboratory of Mariculture &Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, P.R. China
| | - Feng Zhang
- Key Laboratory of Mariculture &Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, P.R. China
| | - Yu Zhai
- Key Laboratory of Mariculture &Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, P.R. China
| | - Yanhui Cao
- Key Laboratory of Mariculture &Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, P.R. China
| | - Si Zhang
- Key Laboratory of Mariculture &Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, P.R. China
| | - Yaqing Chang
- Key Laboratory of Mariculture &Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, 116023, P.R. China
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41
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Fu X, Li T, Chen J, Dong Y, Qiu J, Kang K, Zhang W. Functional screen for microRNAs of Nilaparvata lugens reveals that targeting of glutamine synthase by miR-4868b regulates fecundity. JOURNAL OF INSECT PHYSIOLOGY 2015; 83:22-9. [PMID: 26546713 DOI: 10.1016/j.jinsphys.2015.11.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 10/08/2015] [Accepted: 11/03/2015] [Indexed: 05/14/2023]
Abstract
Insect fecundity is regulated by the interaction of genotypes and the environment. MicroRNAs (miRNAs) also act in insect development and reproduction by regulating genes involved in these physiological processes. Although hundreds of insect miRNAs have been identified, the biological roles of most remain poorly understood. Here, we used a multi-algorithm approach for miRNA target prediction in 3'UTRs of fecundity-related genes in the brown planthopper (BPH) Nilaparvata lugens and identified 38 putative miRNAs targeting 9 fecundity-related genes. High-ranked miRNAs were selected for target validation. Using a dual luciferase reporter assay in S2 cells, we experimentally verified N. lugens glutamine synthetase (NlGS) as an authentic target of microRNA-4868b (miR-4868b). In the females, NlGS protein expression was down-regulated after injection of a miR-4868b mimic but up-regulated after injection of a miR-4868b inhibitor. In addition, overexpression of miR-4868b reduced fecundity, and disrupted ovary development and Vg expression in N. lugens. These findings showed that miR-4868b is involved in regulating N. lugens fecundity by targeting NlGS. Moreover, this study may lead to better understanding of the fecundity of this important agricultural insect pest.
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Affiliation(s)
- Xian Fu
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Tengchao Li
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jie Chen
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yi Dong
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Jieqi Qiu
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Kui Kang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenqing Zhang
- State Key Laboratory of Biocontrol and School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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A Diversity of Conserved and Novel Ovarian MicroRNAs in the Speckled Wood (Pararge aegeria). PLoS One 2015; 10:e0142243. [PMID: 26556800 PMCID: PMC4640560 DOI: 10.1371/journal.pone.0142243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/18/2015] [Indexed: 02/02/2023] Open
Abstract
microRNAs (miRNAs) are important regulators of animal development and other processes, and impart robustness to living systems through post-transcriptional regulation of specific mRNA transcripts. It is postulated that newly emergent miRNAs are generally expressed at low levels and with spatiotemporally restricted expression domains, thus minimising effects of spurious targeting on animal transcriptomes. Here we present ovarian miRNA transcriptome data for two geographically distinct populations of the Speckled Wood butterfly (Pararge aegeria). A total of 74 miRNAs were identified, including 11 newly discovered and evolutionarily-young miRNAs, bringing the total of miRNA genes known from P. aegeria up to 150. We find a positive correlation between miRNA age and expression level. A common set of 55 miRNAs are expressed in both populations. From this set, we identify seven that are consistently either ovary-specific or highly upregulated in ovaries relative to other tissues. This ‘ovary set’ includes miRNAs with known contributions to ovarian function in other insect species with similar ovaries and mode of oogenesis, including miR-989 and miR-2763, plus new candidates for ovarian function. We also note that conserved miRNAs are overrepresented in the ovary relative to the whole body.
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43
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Wynant N, Santos D, Subramanyam SH, Verlinden H, Vanden Broeck J. Drosha, Dicer-1 and Argonaute-1 in the desert locust: phylogenetic analyses, transcript profiling and regulation during phase transition and feeding. JOURNAL OF INSECT PHYSIOLOGY 2015; 75:20-29. [PMID: 25746231 DOI: 10.1016/j.jinsphys.2015.02.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/18/2015] [Accepted: 02/22/2015] [Indexed: 06/04/2023]
Abstract
In this article, we identify and characterise the miRNA machinery components Drosha, Dicer-1 and Argonaute-1 of the desert locust. By means of phylogenetic analyses, we reveal important insights in the evolutionary context of these components. Our data illustrate that insect Argonaute-1 proteins form a monophyletic group with ALG-1 and ALG-2 of Caenorhabditis elegans and with the four (non-Piwi) Argonaute proteins present in humans. On the other hand, humans apparently lack clear homologues of the insect Argonaute-2 proteins. In addition, we demonstrate that drosha, dicer-1 and argonaute-1 display wide transcript tissue-distribution in adult desert locusts, and that during locust phase transition and feeding of starved locusts the expression levels of the miRNA pathway are regulated at the transcript level.
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Affiliation(s)
- Niels Wynant
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium.
| | - Dulce Santos
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium
| | - Sudheendra Hebbar Subramanyam
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium
| | - Heleen Verlinden
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium
| | - Jozef Vanden Broeck
- Molecular Developmental Physiology and Signal Transduction, KU Leuven, Naamsestraat 59, P.O. Box 02465, B-3000 Leuven, Belgium
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MiR-2 family regulates insect metamorphosis by controlling the juvenile hormone signaling pathway. Proc Natl Acad Sci U S A 2015; 112:3740-5. [PMID: 25775510 DOI: 10.1073/pnas.1418522112] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In 2009 we reported that depletion of Dicer-1, the enzyme that catalyzes the final step of miRNA biosynthesis, prevents metamorphosis in Blattella germanica. However, the precise regulatory roles of miRNAs in the process have remained elusive. In the present work, we have observed that Dicer-1 depletion results in an increase of mRNA levels of Krüppel homolog 1 (Kr-h1), a juvenile hormone-dependent transcription factor that represses metamorphosis, and that depletion of Kr-h1 expression in Dicer-1 knockdown individuals rescues metamorphosis. We have also found that the 3'UTR of Kr-h1 mRNA contains a functional binding site for miR-2 family miRNAs (for miR-2, miR-13a, and miR-13b). These data suggest that metamorphosis impairment caused by Dicer-1 and miRNA depletion is due to a deregulation of Kr-h1 expression and that this deregulation is derived from a deficiency of miR-2 miRNAs. We corroborated this by treating the last nymphal instar of B. germanica with an miR-2 inhibitor, which impaired metamorphosis, and by treating Dicer-1-depleted individuals with an miR-2 mimic to allow nymphal-to-adult metamorphosis to proceed. Taken together, the data indicate that miR-2 miRNAs scavenge Kr-h1 transcripts when the transition from nymph to adult should be taking place, thus crucially contributing to the correct culmination of metamorphosis.
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45
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Kakumani PK, Chinnappan M, Singh AK, Malhotra P, Mukherjee SK, Bhatnagar RK. Identification and characteristics of microRNAs from army worm, Spodoptera frugiperda cell line Sf21. PLoS One 2015; 10:e0116988. [PMID: 25693181 PMCID: PMC4333348 DOI: 10.1371/journal.pone.0116988] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Accepted: 12/17/2014] [Indexed: 02/07/2023] Open
Abstract
microRNAs play important regulatory role in all intrinsic cellular functions. Amongst lepidopteran insects, miRNAs from only Bombyx mori have been studied extensively with a little focus on Spodoptera sp. In the present study, we identified a total of 226 miRNAs from Spodoptera frugiperda cell line Sf21. Of the total, 116 miRNAs were well conserved within other insects, like B. mori, Drosophila melanogaster and Tribolium castenum while the remaining 110 miRNAs were identified as novel based on comparative analysis with the insect miRNA data set. Landscape distribution analysis based on Sf21 genome assembly revealed clustering of few novel miRNAs. A total of 5 miRNA clusters were identified and the largest one encodes 5 miRNA genes. In addition, 12 miRNAs were validated using northern blot analysis and putative functional role assignment for 6 Sf miRNAs was investigated by examining their relative abundance at different developmental stages of Spodoptera litura and body parts of 6th instar larvae. Further, we identified a total of 809 potential target genes with GO terms for selected miRNAs, involved in different metabolic and signalling pathways of the insect. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs and analysis of expression profiles reveal their involvement at various steps of biochemical pathways of the army worm.
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Affiliation(s)
- Pavan Kumar Kakumani
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mahendran Chinnappan
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashok K. Singh
- Department of Zoology, University of Delhi, Cavalry Lane, New Delhi, 110007, India
| | - Pawan Malhotra
- Malaria Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail: (PM); (SKM); (RKB)
| | - Sunil K. Mukherjee
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail: (PM); (SKM); (RKB)
| | - Raj K. Bhatnagar
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
- * E-mail: (PM); (SKM); (RKB)
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46
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Ling L, Ge X, Li Z, Zeng B, Xu J, Aslam AFM, Song Q, Shang P, Huang Y, Tan A. MicroRNA Let-7 regulates molting and metamorphosis in the silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2014; 53:13-21. [PMID: 25016132 DOI: 10.1016/j.ibmb.2014.06.011] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 05/26/2014] [Accepted: 06/27/2014] [Indexed: 06/03/2023]
Abstract
MicroRNAs (miRNAs) are a class of endogenous, non-coding, regulatory RNA molecules that post-transcriptionally regulate gene expression by binding to the 3'UTRs of mRNA targets and thus cause their degradation or translational inhibition. In insects, important roles of miRNAs in various biological processes have been demonstrated in Drosophila melanogaster. However, biological roles of miRNAs are barely unveiled in the majority of insect species due to limited genetic tools. In the present study, we introduce the transgenic miRNA sponge (miR-SP) technology combining with the binary GAL4/UAS system in the domesticated silkworm, Bombyx mori, to exploit the biological function of an evolutionally conserved miRNA, let-7. We successfully established transgenic silkworm lines in which a miRNA sponge construct targeting BmLet-7 seed region was expressed in a ubiquitous manner directed by A3-GAL4 driver. Transgenic animals showed decreased expression of BmLet-7, leading to developmental arrestment during the larval-larval and larval-pupal transition. Simultaneously, expression levels of the predicted BmLet-7 target genes, FTZ-F1 and Eip74EF (E74), key regulatory factors in the ecdysone pathway, were elevated in transgenic animals. The current study is the first report on application of the transgenic miR-SP technology in non-drosophilid insects, which will not only contribute to better understanding of let-7 biological roles, but also greatly facilitate future miRNA functional analysis in insects.
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Affiliation(s)
- Lin Ling
- Faculty of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China; Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xie Ge
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqian Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Baosheng Zeng
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xu
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Abu F M Aslam
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qisheng Song
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Peng Shang
- Faculty of Life Sciences, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yongping Huang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Anjiang Tan
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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Huang Y, Dou W, Liu B, Wei D, Liao CY, Smagghe G, Wang JJ. Deep sequencing of small RNA libraries reveals dynamic expression patterns of microRNAs in multiple developmental stages of Bactrocera dorsalis. INSECT MOLECULAR BIOLOGY 2014; 23:656-667. [PMID: 24957108 DOI: 10.1111/imb.12111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In eukaryotes, microRNAs (miRNAs) are small, conserved, noncoding RNAs that have emerged as critical regulators of gene expression. The oriental fruit fly Bactrocera dorsalis is one of the most economically important fruit fly pests in East Asia and the Pacific. Although transcriptome analyses have greatly enriched our knowledge of its structural genes, little is known about post-transcriptional regulation by miRNAs in this dipteran species. In this study, small RNA libraries corresponding to four B. dorsalis developmental stages (eggs, larvae, pupae and adults) were constructed and sequenced. Approximately 30.7 million reads of 18-30 nucleotides were obtained, with 123 known miRNAs and 60 novel miRNAs identified amongst these libraries. More than half of the miRNAs were stage-specific during the four developmental stages. A set of miRNAs was found to be up- or down-regulated during development by comparison of their reads at different developmental stages. Moreover, a small part of miRNAs owned both miR-#-3p and miR-#-5p types, with enormously variable miR-#-3p/miR-#-5p ratios in the same library and amongst different developmental stages for each miRNA. Taking these findings together, the current study has uncovered a number of miRNAs and provided insights into their possible involvement in developmental regulation by expression profiling of miRNAs. Further analyses of the expression and function of these miRNAs could increase our understanding of regulatory networks in this insect and lead to novel approaches for its control.
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Affiliation(s)
- Y Huang
- Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing, China
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Zhou X, Qian K, Tong Y, Zhu JJ, Qiu X, Zeng X. De novo transcriptome of the Hemimetabolous German cockroach (Blattella germanica). PLoS One 2014; 9:e106932. [PMID: 25265537 PMCID: PMC4180286 DOI: 10.1371/journal.pone.0106932] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 08/10/2014] [Indexed: 11/23/2022] Open
Abstract
Background The German cockroach, Blattella germanica, is an important insect pest that transmits various pathogens mechanically and causes severe allergic diseases. This insect has long served as a model system for studies of insect biology, physiology and ecology. However, the lack of genome or transcriptome information heavily hinder our further understanding about the German cockroach in every aspect at a molecular level and on a genome-wide scale. To explore the transcriptome and identify unique sequences of interest, we subjected the B. germanica transcriptome to massively parallel pyrosequencing and generated the first reference transcriptome for B. germanica. Methodology/Principal Findings A total of 1,365,609 raw reads with an average length of 529 bp were generated via pyrosequencing the mixed cDNA library from different life stages of German cockroach including maturing oothecae, nymphs, adult females and males. The raw reads were de novo assembled to 48,800 contigs and 3,961 singletons with high-quality unique sequences. These sequences were annotated and classified functionally in terms of BLAST, GO and KEGG, and the genes putatively coding detoxification enzyme systems, insecticide targets, key components in systematic RNA interference, immunity and chemoreception pathways were identified. A total of 3,601 SSRs (Simple Sequence Repeats) loci were also predicted. Conclusions/Significance The whole transcriptome pyrosequencing data from this study provides a usable genetic resource for future identification of potential functional genes involved in various biological processes.
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Affiliation(s)
- Xiaojie Zhou
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Kun Qian
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Ying Tong
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
| | - Junwei Jerry Zhu
- United States Department of Agriculture, Agricultural Research Service, Lincoln, Nebraska, United States of America
| | - Xinghui Qiu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- * E-mail: (XQ); (XPZ)
| | - Xiaopeng Zeng
- Institute of Disinfection and Vector Control, Beijing Center for Disease Control and Prevention, Beijing, China
- * E-mail: (XQ); (XPZ)
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Zhang D, Lu K, Dong Z, Jiang G, Xu W, Liu W. The effect of exposure to a high-fat diet on microRNA expression in the liver of blunt snout bream (Megalobrama amblycephala). PLoS One 2014; 9:e96132. [PMID: 24788396 PMCID: PMC4008502 DOI: 10.1371/journal.pone.0096132] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 04/02/2014] [Indexed: 12/15/2022] Open
Abstract
Blunt snout bream (Megalobrama amblycephala) are susceptible to hepatic steatosis when maintained in modern intensive culture systems. The aim of this study was to investigate the potential roles of microRNAs (miRNAs) in diet-induced hepatic steatosis in this species. MiRNAs, small non-coding RNAs that regulate gene expression at the posttranscriptional level, are involved in diverse biological processes, including lipid metabolism. Deep sequencing of hepatic small RNA libraries from blunt snout bream fed normal-fat and high-fat diets identified 202 (193 known and 9 novel) miRNAs, of which 12 were differentially expressed between the normal-fat and high-fat diet groups. Quantitative stem-loop reverse transcriptase-polymerase chain reaction analyses confirmed the upregulation of miR-30c and miR-30e-3p and the downregulation of miR-145 and miR-15a-5p in high-fat diet-fed fish. Bioinformatics tools were used to predict the targets of these verified miRNAs and to explore potential downstream gene ontology biological process categories and Kyoto Encyclopedia of Genes and Genomes pathways. Six putative lipid metabolism-related target genes (fetuin-B, Cyp7a1, NADH dehydrogenase (ubiquinone) 1 beta subcomplex subunit 2, 3-oxoacid CoA transferase 1b, stearoyl-CoA desaturase, and fatty-acid synthase) were identified as having potential important roles in the development of diet-induced hepatic steatosis in blunt snout bream. The results presented here are a foundation for future studies of miRNA-controlled lipid metabolism regulatory networks in blunt snout bream.
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Affiliation(s)
- Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Kangle Lu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
- * E-mail: (WL); (ZD)
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Weina Xu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
- * E-mail: (WL); (ZD)
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Mayoral JG, Etebari K, Hussain M, Khromykh AA, Asgari S. Wolbachia infection modifies the profile, shuttling and structure of microRNAs in a mosquito cell line. PLoS One 2014; 9:e96107. [PMID: 24759922 PMCID: PMC3997519 DOI: 10.1371/journal.pone.0096107] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/03/2014] [Indexed: 11/26/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that play important roles in many biological processes such as development, cell signaling and immune response. Small RNA deep sequencing technology provided an opportunity for a thorough survey of the miRNA profile of a mosquito cell line from Aedes aegypti. We characterized the miRNA composition of the nucleus and the cytoplasm of uninfected cells and compared it with the one of cells infected with the endosymbiotic bacterium Wolbachia strain wMelPop-CLA. We found an overall increase of small RNAs between 18 and 28 nucleotides in both cellular compartments in Wolbachia-infected cells and identified specific miRNAs induced and/or suppressed by the Wolbachia infection. We discuss the mechanisms that the cell may use to shuttle miRNAs between the cytoplasm and the nucleus. In addition, we identified piRNAs that changed their abundance in response to Wolbachia infection. The miRNAs and piRNAs identified in this study provide promising leads for investigations into the host-endosymbiont interactions and for better understanding of how Wolbachia manipulates the host miRNA machinery in order to facilitate its persistent replication in infected cells.
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Affiliation(s)
- Jaime G. Mayoral
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Kayvan Etebari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Mazhar Hussain
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Alexander A. Khromykh
- Australian Infectious Disease Research Centre, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
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