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Lee IHT, Nong W, So WL, Cheung CKH, Xie Y, Baril T, Yip HY, Swale T, Chan SKF, Wei Y, Lo N, Hayward A, Chan TF, Lam HM, Hui JHL. The genome and sex-dependent responses to temperature in the common yellow butterfly, Eurema hecabe. BMC Biol 2023; 21:200. [PMID: 37749565 PMCID: PMC10521528 DOI: 10.1186/s12915-023-01703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 09/13/2023] [Indexed: 09/27/2023] Open
Abstract
BACKGROUND Lepidoptera (butterflies and moths) is one of the most geographically widespread insect orders in the world, and its species play important and diverse ecological and applied roles. Climate change is one of the biggest challenges to biodiversity this century, and lepidopterans are vulnerable to climate change. Temperature-dependent gene expression differences are of relevance under the ongoing climate crisis. However, little is known about how climate affects gene expression in lepidopterans and the ecological consequences of this, particularly with respect to genes with biased expression in one of the sexes. The common yellow butterfly, Eurema hecabe (Family Pieridae), is one of the most geographically widespread lepidopterans that can be found in Asia, Africa, and Australia. Nevertheless, what temperature-dependent effects there may be and whether the effects differ between the sexes remain largely unexplored. RESULTS Here, we generated high-quality genomic resources for E. hecabe along with transcriptomes from eight developmental stages. Male and female butterflies were subjected to varying temperatures to assess sex-specific gene expression responses through mRNA and microRNA transcriptomics. We find that there are more temperature-dependent sex-biased genes in females than males, including genes that are involved in a range of biologically important functions, highlighting potential ecological impacts of increased temperatures. Further, by considering available butterfly data on sex-biased gene expression in a comparative genomic framework, we find that the pattern of sex-biased gene expression identified in E. hecabe is highly species-specific, rather than conserved across butterfly species, suggesting that sex-biased gene expression responses to climate change are complex in butterflies. CONCLUSIONS Our study lays the foundation for further understanding of differential responses to environmental stress in a widespread lepidopteran model and demonstrates the potential complexity of sex-specific responses of lepidopterans to climate change.
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Affiliation(s)
- Ivy H T Lee
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wenyan Nong
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Wai Lok So
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Chris K H Cheung
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Yichun Xie
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Ho Yin Yip
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | | | - Simon K F Chan
- Agriculture, Fisheries and Conservation Department, Hong Kong, China
| | - Yingying Wei
- Department of Statistics, The Chinese University of Hong Kong, Hong Kong, China
| | - Nathan Lo
- School of Life and Environmental Sciences, University of Sydney, Sydney, Australia
| | | | - Ting Fung Chan
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China
| | - Jerome H L Hui
- School of Life Sciences, Simon F.S. Li Marine Science Laboratory, State Key Laboratory of Agrobiotechnology, Institute of Environment, Energy and Sustainability, The Chinese University of Hong Kong, Hong Kong, China.
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2
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Abbas MN, Kausar S, Asma B, Ran W, Li J, Lin Z, Li T, Cui H. MicroRNAs reshape the immunity of insects in response to bacterial infection. Front Immunol 2023; 14:1176966. [PMID: 37153604 PMCID: PMC10161253 DOI: 10.3389/fimmu.2023.1176966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
The interaction between bacteria and insects can significantly impact a wide range of different areas because bacteria and insects are widely distributed around the globe. The bacterial-insect interactions have the potential to directly affect human health since insects are vectors for disease transmission, and their interactions can also have economic consequences. In addition, they have been linked to high mortality rates in economically important insects, resulting in substantial economic losses. MicroRNAs (miRNAs) are types of non-coding RNAs involved in regulating gene expression post-transcriptionally. The length of miRNAs ranges from 19 to 22 nucleotides. MiRNAs, in addition to their ability to exhibit dynamic expression patterns, have a diverse range of targets. This enables them to govern various physiological activities in insects, like innate immune responses. Increasing evidence suggests that miRNAs have a crucial biological role in bacterial infection by influencing immune responses and other mechanisms for resistance. This review focuses on some of the most recent and exciting discoveries made in recent years, including the correlation between the dysregulation of miRNA expression in the context of bacterial infection and the progression of the infection. Furthermore, it describes how they profoundly impact the immune responses of the host by targeting the Toll, IMD, and JNK signaling pathways. It also emphasizes the biological function of miRNAs in regulating immune responses in insects. Finally, it also discusses current knowledge gaps about the function of miRNAs in insect immunity, in addition to areas that require more research in the future.
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Affiliation(s)
- Muhammad Nadeem Abbas
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Saima Kausar
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Bibi Asma
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
| | - Wenhao Ran
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
| | - Jingui Li
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
| | - Zini Lin
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
| | - Tiejun Li
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Gastrointestinal Vascular Surgery, The Chongqing Ninth People’s Hospital, Chongqing, China
- *Correspondence: Tiejun Li, ; Hongjuan Cui,
| | - Hongjuan Cui
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, China
- Cancer Center, Medical Research Institute, Southwest University, Chongqing, China
- Jinfeng Laboratory, Chongqing, China
- *Correspondence: Tiejun Li, ; Hongjuan Cui,
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3
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Lu MY, Chtarbanova S. The role of micro RNAs (miRNAs) in the regulation of Drosophila melanogaster's innate immunity. Fly (Austin) 2022; 16:382-396. [PMID: 36412256 PMCID: PMC9683055 DOI: 10.1080/19336934.2022.2149204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of small non-coding RNAs ~19-22 nt long which post-transcriptionally regulate gene expression. Their ability to exhibit dynamic expression patterns coupled with their wide variety of targets allows miRNAs to regulate many processes, including the innate immune response of Drosophila melanogaster. Recent studies have identified miRNAs in Drosophila which are differentially expressed during infection with different pathogens as well as miRNAs that may affect immune signalling when differentially expressed. This review provides an overview of miRNAswhich have been identified to play a role in the immune response of Drosophila through targeting of the Toll and IMD signalling pathways and other immune processes. It will also explore the role of miRNAs in fine-tuning the immune response in Drosophila and highlight current gaps in knowledge regarding the role of miRNAs in immunity and areas for further research.
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Affiliation(s)
- Max Yang Lu
- Department of Biological Sciences, the University of Alabama, Tuscaloosa, AL, USA
| | - Stanislava Chtarbanova
- Department of Biological Sciences, the University of Alabama, Tuscaloosa, AL, USA,Center for Convergent Bioscience & Medicine, University of Alabama, Tuscaloosa, AL, USA,Alabama Life Research Institute, University of Alabama, Tuscaloosa, AL, USA,CONTACT Stanislava Chtarbanova Department of Biological Sciences, the University of Alabama, 300, Hackberry Ln, Tuscaloosa, AL-35487, USA
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Gartland S, Zeng B, Marr MT. The small RNA landscape is stable with age and resistant to loss of dFOXO signaling in Drosophila. PLoS One 2022; 17:e0273590. [PMCID: PMC9668163 DOI: 10.1371/journal.pone.0273590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 11/17/2022] Open
Abstract
Aging can be defined as the progressive loss of physiological homeostasis that leads to a decline in cellular and organismal function. In recent years, it has become clear that small RNA pathways play a role in aging and aging related phenotypes. Small RNA pathways regulate many important processes including development, cellular physiology, and innate immunity. The pathways illicit a form of posttranscriptional gene regulation that relies on small RNAs bound by the protein components of the RNA-induced silencing complexes (RISCs), which inhibit the expression of complementary RNAs. In Drosophila melanogaster, Argonaute 1 (Ago1) is the core RISC component in microRNA (miRNA) silencing, while Argonaute 2 (Ago2) is the core RISC component in small interfering RNA (siRNA) silencing. The expression of Ago1 and Ago2 is regulated by stress response transcription factor Forkhead box O (dFOXO) increasing siRNA silencing efficiency. dFOXO plays a role in multiple stress responses and regulates pathways important for longevity. Here we use a next-generation sequencing approach to determine the effects of aging on small RNA abundance and RISC loading in male and female Drosophila. In addition, we examine the impact of the loss of dFOXO on these processes. We find that the relative abundance of the majority of small RNAs does not change with age. Additionally, under normal growth conditions, the loss of dFOXO has little effect on the small RNA landscape. However, we observed that age affects loading into RISC for a small number of miRNAs.
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Affiliation(s)
- Siobhan Gartland
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
| | - Baosheng Zeng
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Michael T. Marr
- Department of Biology, Brandeis University, Waltham, Massachusetts, United States of America
- * E-mail:
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5
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Marco A. The chromosomal distribution of sex-biased microRNAs in Drosophila is non-adaptive. Genome Biol Evol 2022; 14:6637416. [PMID: 35809037 PMCID: PMC9290354 DOI: 10.1093/gbe/evac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2022] [Indexed: 11/24/2022] Open
Abstract
Genes are often differentially expressed between males and females. In Drosophila melanogaster, the analysis of sex-biased microRNAs (short noncoding regulatory molecules) has revealed striking differences with protein-coding genes. Mainly, the X chromosome is enriched in male-biased microRNA genes, although it is depleted of male-biased protein-coding genes. The paucity of male-biased genes in the X chromosome is generally explained by an evolutionary process called demasculinization. I suggest that the excess of male-biased microRNAs in the X chromosome is due to high rates of de novo emergence of microRNAs (mostly in other neighboring microRNAs), a tendency of novel microRNAs in the X chromosome to be expressed in testis, and to a lack of a demasculinization process. To test this hypothesis, I analyzed the expression profile of microRNAs in males, females, and gonads in D. pseudoobscura, in which an autosome translocated into the X chromosome effectively becoming part of a sex chromosome (neo-X). I found that the pattern of sex-biased expression is generally conserved between D. melanogaster and D. pseudoobscura. Also, orthologous microRNAs in both species conserve their chromosomal location, indicating that there is no evidence of demasculinization or other interchromosomal movement of microRNAs. Drosophila pseudoobscura-specific microRNAs in the neo-X chromosome tend to be male-biased and particularly expressed in testis. In summary, the apparent paradox resulting from male-biased protein-coding genes depleted in the X chromosome and an enrichment in male-biased microRNAs is consistent with different evolutionary dynamics between coding genes and short RNAs.
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Affiliation(s)
- Antonio Marco
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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6
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Naitore C, Villinger J, Kibet CK, Kalayou S, Bargul JL, Christoffels A, Masiga DK. The developmentally dynamic microRNA transcriptome of Glossina pallidipes tsetse flies, vectors of animal trypanosomiasis. BIOINFORMATICS ADVANCES 2021; 2:vbab047. [PMID: 36699416 PMCID: PMC9710702 DOI: 10.1093/bioadv/vbab047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/25/2021] [Accepted: 12/24/2021] [Indexed: 01/28/2023]
Abstract
Summary MicroRNAs (miRNAs) are single stranded gene regulators of 18-25 bp in length. They play a crucial role in regulating several biological processes in insects. However, the functions of miRNA in Glossina pallidipes, one of the biological vectors of African animal trypanosomosis in sub-Saharan Africa, remain poorly characterized. We used a combination of both molecular biology and bioinformatics techniques to identify miRNA genes at different developmental stages (larvae, pupae, teneral and reproductive unmated adults, gravid females) and sexes of G. pallidipes. We identified 157 mature miRNA genes, including 12 novel miRNAs unique to G. pallidipes. Moreover, we identified 93 miRNA genes that were differentially expressed by sex and/or in specific developmental stages. By combining both miRanda and RNAhybrid algorithms, we identified 5550 of their target genes. Further analyses with the Gene Ontology term and KEGG pathways for these predicted target genes suggested that the miRNAs may be involved in key developmental biological processes. Our results provide the first repository of G. pallidipes miRNAs across developmental stages, some of which appear to play crucial roles in tsetse fly development. Hence, our findings provide a better understanding of tsetse biology and a baseline for exploring miRNA genes in tsetse flies. Availability and implementation Raw sequence data are available from NCBI Sequence Read Archives (SRA) under Bioproject accession number PRJNA590626. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Careen Naitore
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi 00100, Kenya,Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000, Nairobi 00200, Kenya
| | - Jandouwe Villinger
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi 00100, Kenya,To whom correspondence should be addressed. or
| | - Caleb K Kibet
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi 00100, Kenya
| | - Shewit Kalayou
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi 00100, Kenya
| | - Joel L Bargul
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi 00100, Kenya,Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology (JKUAT), P.O. Box 62000, Nairobi 00200, Kenya
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute (SANBI), University of the Western Cape, Bellville 7530, South Africa
| | - Daniel K Masiga
- International Centre of Insect Physiology and Ecology (icipe), P.O. Box 30772, Nairobi 00100, Kenya,To whom correspondence should be addressed. or
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Hotzy C, Fowler E, Kiehl B, Francis R, Mason J, Moxon S, Rostant W, Chapman T, Immler S. Evolutionary history of sexual selection affects microRNA profiles in Drosophila sperm. Evolution 2021; 76:310-319. [PMID: 34874067 DOI: 10.1111/evo.14411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 11/28/2022]
Abstract
The presence of small RNAs in sperm is a relatively recent discovery and little is currently known about their importance and functions. Environmental changes including social conditions and dietary manipulations are known to affect the composition and expression of some small RNAs in sperm and may elicit a physiological stress response resulting in an associated change in gamete miRNA profiles. Here, we tested how microRNA profiles in sperm are affected by variation in both sexual selection and dietary regimes in Drosophila melanogaster selection lines. The selection lines were exposed to standard versus low yeast diet treatments and three different population sex ratios (male-biased, female-biased or equal sex) in a full-factorial design. After 38 generations of selection, all males were maintained on their selected diet and in a common garden male-only environment prior to sperm sampling. We performed transcriptome analyses on miRNAs in purified sperm samples. We found 11 differentially expressed miRNAs with the majority showing differences between male- and female-biased lines. Dietary treatment only had a significant effect on miRNA expression levels in interaction with sex ratio. Our findings suggest that long-term adaptation may affect miRNA profiles in sperm and that these may show varied interactions with short-term environmental changes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Cosima Hotzy
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Emily Fowler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Berrit Kiehl
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Roy Francis
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, 752 36, Sweden
| | - Janet Mason
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Wayne Rostant
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Tracey Chapman
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Simone Immler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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Lyu Y, Liufu Z, Xiao J, Tang T. A Rapid Evolving microRNA Cluster Rewires Its Target Regulatory Networks in Drosophila. Front Genet 2021; 12:760530. [PMID: 34777478 PMCID: PMC8581666 DOI: 10.3389/fgene.2021.760530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 10/11/2021] [Indexed: 11/13/2022] Open
Abstract
New miRNAs are evolutionarily important but their functional evolution remains unclear. Here we report that the evolution of a microRNA cluster, mir-972C rewires its downstream regulatory networks in Drosophila. Genomic analysis reveals that mir-972C originated in the common ancestor of Drosophila where it comprises six old miRNAs. It has subsequently recruited six new members in the melanogaster subgroup after evolving for at least 50 million years. Both the young and the old mir-972C members evolved rapidly in seed and non-seed regions. Combining target prediction and cell transfection experiments, we found that the seed and non-seed changes in individual mir-972C members cause extensive target divergence among D. melanogaster, D. simulans, and D. virilis, consistent with the functional evolution of mir-972C reported recently. Intriguingly, the target pool of the cluster as a whole remains relatively conserved. Our results suggest that clustering of young and old miRNAs broadens the target repertoires by acquiring new targets without losing many old ones. This may facilitate the establishment of new miRNAs in existing regulatory networks.
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Affiliation(s)
- Yang Lyu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Zhongqi Liufu
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Juan Xiao
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Tian Tang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
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9
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Identification and Characterization of MicroRNAs in Gonads of Helicoverpa armigera (Lepidoptera: Noctuidae). INSECTS 2021; 12:insects12080749. [PMID: 34442315 PMCID: PMC8396854 DOI: 10.3390/insects12080749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/12/2021] [Accepted: 08/17/2021] [Indexed: 11/20/2022]
Abstract
Simple Summary For most insects, the development of the testis and ovary directly determines their reproductive ability. The cotton bollworm, Helicoverpa armigera (Hübner), is a polyphagous crop pest of the Lepidoptera Noctuidae. Owing to its broad range of host plants and strong fertility, H. armigera causes huge economic losses to agricultural production. Acting as a type of post-transcriptional regulatory factor, miRNAs participate in the gonadal development and reproductive regulation of H. arimgera. Our study uses H. armigera as a research object to identify and characterize the miRNAs and study their potential functions in the testis and ovary of this destructive crop pest. A total of 7,592,150 and 8,815,237 clean reads were obtained by constructing small RNA libraries of the testis and ovary, respectively. Length distribution analysis showed that the main types of small RNAs in the testis and ovary were different. Among the 74 known miRNAs, 60 miRNAs existed in the ovary, and 72 existed in the testis. Gene Ontology (GO) and KEGG pathway analyses indicated that the 8 gonad-biased differentially expressed miRNAs (miR-989a, miR-263-5p, miR-34, miR-2763, miR-998, miR-2c, miR-2765, and miR-252a-5p) had many target transcripts involved in the reproduction process. Abstract The high fecundity of the most destructive pest Helicoverpa armigera and its great resistance risk to insecticides and Bt crops make the reproductive-destruction-based control of this pest extremely appealing. To find suitable targets for disruption of its reproduction, we observed the testis and ovary development of H. armigera and conducted deep sequencing of the ovary and testis small RNAs of H. armigera and quantitative RT-PCR (RT-qPCR) validation to identify reproduction-related micro RNAs (miRNAs). A total of 7,592,150 and 8,815,237 clean reads were obtained from the testis and ovary tissue, respectively. After further analysis, we obtained 173 novel and 74 known miRNAs from the two libraries. Among the 74 known miRNAs, 60 miRNAs existed in the ovary and 72 existed in the testis. Further RT-qPCR validation of 5 miRNAs from the ovary and 6 miRNAs from the testis confirmed 8 of them were indeed ovary- (miR-989a, miR-263-5p, miR-34) or testis-biased (miR-2763, miR-998, miR-2c, miR-2765, miR-252a-5p). The 8 ovary- or testis-biased miRNAs had a total of 30,172 putative non-redundant target transcripts, as predicted by miRanda and RNAhybrid. Many of these target transcripts are assigned to reproduction-related GO terms (e.g., oocyte maturation, vitellogenesis, spermatogenesis) and are members of multiple reproduction-related KEGG pathways, such as the JAK-STAT signaling pathway, oocyte meiosis, the insulin signaling pathway, and insect hormone biosynthesis. These results suggest that the 8 gonad-biased miRNAs play important roles in reproduction and may be used as the targets for the development of reproductive-destruction-based control of H. armigera and, possibly, other lepidopteran pests.
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10
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Fonseca PLC, Mucherino M JJ, Porto JAM, Armache JN, de Almeida JPP, da Silva FF, Olmo RP, Faria IJDS, de Carvalho DS, Góes-Neto A, Corrêa RX, Pirovani CP, Pacheco LGC, Costa MA, Aguiar ERGR. Genome-wide identification of miRNAs and target regulatory network in the invasive ectoparasitic mite Varroa destructor. Genomics 2021; 113:2290-2303. [PMID: 34044154 DOI: 10.1016/j.ygeno.2021.05.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 04/21/2021] [Accepted: 05/23/2021] [Indexed: 12/29/2022]
Abstract
Varroa destructor is an ectoparasite mite that attacks bees leading to colony disorders worldwide. microRNAs (miRNAs) are key molecules used by eukaryotes to post-transcriptional control of gene expression. Nevertheless, still lack information aboutV. destructor miRNAs and its regulatory networks. Here, we used an integrative strategy to characterize the miRNAs in the V. destructor mite. We identified 310 precursors that give rise to 500 mature miRNAs, which 257 are likely mite-specific elements. miRNAs showed canonical length ranging between 18 and 25 nucleotides and 5' uracil preference. Top 10 elements concentrated over 80% of total miRNA expression, with bantam alone representing ~50%. We also detected non-templated bases in precursor-derived small RNAs, indicative of miRNA post-transcriptional regulatory mechanisms. Finally, we note that conserved miRNAs control similar processes in different organisms, suggesting a conservative role. Altogether, our findings contribute to the better understanding of the mite biology that can assist future studies on varroosis control.
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Affiliation(s)
- Paula L C Fonseca
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Jonathan J Mucherino M
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil; Department of Forest Management, Facultad de Ciencias Forestales y Ambientales, Universidad de Los Andes, Mérida, Mérida 5101, Venezuela
| | - Joel A M Porto
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Juliana N Armache
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - João Paulo P de Almeida
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Felipe F da Silva
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Roenick P Olmo
- Université de Strasbourg, CNRS UPR9022, Inserm, Strasbourg, France
| | - Isaque J da S Faria
- Department of Biochemistry and Immunology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Daniel S de Carvalho
- Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Aristóteles Góes-Neto
- Department of Microbiology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil; Bioinformatics Program, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais CEP 30270-901, Brazil
| | - Ronan X Corrêa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Carlos P Pirovani
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Luis G C Pacheco
- Institute of Health Sciences, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Marco Antônio Costa
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil
| | - Eric R G R Aguiar
- Department of Biological Science (DCB), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus, Bahia 45662-900, Brazil.
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11
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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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12
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A comparative genomic approach using mouse and fruit fly data to discover genes involved in testis function in hymenopterans with a focus on Nasonia vitripennis. BMC Ecol Evol 2021; 21:90. [PMID: 34011283 PMCID: PMC8132408 DOI: 10.1186/s12862-021-01825-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 05/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Spermatogenesis appears to be a relatively well-conserved process even among distantly related animal taxa such as invertebrates and vertebrates. Although Hymenopterans share many characteristics with other organisms, their complex haplodiploid reproduction system is still relatively unknown. However, they serve as a complementary insect model to Drosophila for studying functional male fertility. In this study, we used a comparative method combining taxonomic, phenotypic data and gene expression to identify candidate genes that could play a significant role in spermatogenesis in hymenopterans. Results Of the 546 mouse genes predominantly or exclusively expressed in the mouse testes, 36% had at least one ortholog in the fruit fly. Of these genes, 68% had at least one ortholog in one of the six hymenopteran species we examined. Based on their gene expression profiles in fruit fly testes, 71 of these genes were hypothesized to play a marked role in testis function. Forty-three of these 71 genes had an ortholog in at least one of the six hymenopteran species examined, and their enriched GO terms were related to the G2/M transition or to cilium organization, assembly, or movement. Second, of the 379 genes putatively involved in male fertility in Drosophila, 224 had at least one ortholog in each of the six Hymenoptera species. Finally, we showed that 199 of these genes were expressed in early pupal testis in Nasonia vitripennis; 86 exhibited a high level of expression, and 54 displayed modulated expression during meiosis. Conclusions In this study combining phylogenetic and experimental approaches, we highlighted genes that may have a major role in gametogenesis in hymenopterans; an essential prerequisite for further research on functional importance of these genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01825-6.
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13
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Xiao S, Wang B, Li K, Xiong S, Ye X, Wang J, Zhang J, Yan Z, Wang F, Song Q, Stanley DW, Ye G, Fang Q. Identification and characterization of miRNAs in an endoparasitoid wasp, Pteromalus puparum. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2020; 103:e21633. [PMID: 31587364 DOI: 10.1002/arch.21633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/17/2019] [Accepted: 09/19/2019] [Indexed: 06/10/2023]
Abstract
MicroRNAs (miRNAs) are a form of endogenous small noncoding RNAs that regulate protein-coding gene expression at the posttranscriptional level. So far, knowledge of miRNAs in parasitoids remains rudimentary. We investigated miRNAs in Pteromalus puparum, a pupal endoparasitoid wasp with genome and transcriptome sequences completed. In this study, we constructed eight small RNA libraries from selected developmental stages and genders: male embryos, male larvae, male pupae, male adults, mixed-sex embryos, mixed-sex larvae, mixed-sex pupae, and female adults. We identified 254 mature miRNAs with 5p/3p arm features originated from 75 known and 119 novel miRNA genes in P. puparum, 88 of which reside in 26 clusters. The miRNAs in more than half of the clusters exhibit a consistent expression pattern, indicating they were co-transcribed from a long transcript. Comparing miRNA expression in the eight libraries, we found that 84 mature miRNAs were differentially expressed between embryos and larvae, 20 between larvae and pupae, and 26 between pupae and adults. We found some miRNAs were differentially expressed between sexes in embryos (10), larvae (29), pupae (8), and adults (14). Target predictions resulted in 211,571 miRNA-mRNA interactions for 254 different mature miRNAs. These miRNAs may be involved in sexual and developmental regulation of gene expression.
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Affiliation(s)
- Shan Xiao
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Beibei Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Kai Li
- Institute of Biological Sciences and Biotechnology, Donghua University, Shanghai, China
| | - Shijiao Xiong
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xinhai Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jiale Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Jiao Zhang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Zhichao Yan
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Fang Wang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qisheng Song
- Division of Plant Sciences, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, Missouri
| | - David W Stanley
- USDA Agricultural Research Service, Biological Control of Insects Research Laboratory, Columbia, Missouri
| | - Gongyin Ye
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Qi Fang
- State Key Laboratory of Rice Biology & Ministry of Agriculture and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Insect Sciences, Zhejiang University, Hangzhou, China
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14
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Divergence in Transcriptional and Regulatory Responses to Mating in Male and Female Fruitflies. Sci Rep 2019; 9:16100. [PMID: 31695054 PMCID: PMC6834580 DOI: 10.1038/s41598-019-51141-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 09/24/2019] [Indexed: 11/21/2022] Open
Abstract
Mating induces extensive physiological, biochemical and behavioural changes in female animals of many taxa. In contrast, the overall phenotypic and transcriptomic consequences of mating for males, hence how they might differ from those of females, are poorly described. Post mating responses in each sex are rapidly initiated, predicting the existence of regulatory mechanisms in addition to transcriptional responses involving de novo gene expression. That post mating responses appear different for each sex also predicts that the genome-wide signatures of mating should show evidence of sex-specific specialisation. In this study, we used high resolution RNA sequencing to provide the first direct comparisons of the transcriptomic responses of male and female Drosophila to mating, and the first comparison of mating-responsive miRNAs in both sexes in any species. As predicted, the results revealed the existence of sex- and body part-specific mRNA and miRNA expression profiles. More genes were differentially expressed in the female head-thorax than the abdomen following mating, whereas the opposite was true in males. Indeed, the transcriptional profile of male head-thorax tissue was largely unaffected by mating, and no differentially expressed genes were detected at the most stringent significance threshold. A subset of ribosomal genes in females were differentially expressed in both body parts, but in opposite directions, consistent with the existence of body part-specific resource allocation switching. Novel, mating-responsive miRNAs in each sex were also identified, and a miRNA-mRNA interactions analysis revealed putative targets among mating-responsive genes. We show that the structure of genome-wide responses by each sex to mating is strongly divergent, and provide new insights into how shared genomes can achieve characteristic distinctiveness.
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15
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Abstract
Proteins and RNA molecules are deposited into the developing egg by the mother. These gene products will drive the first stages of development and are coded by maternal genes. Maternal genes are essential, yet, despite their importance, their evolutionary dynamics is largely unknown. Here I review the current knowledge of maternal gene evolution. The evolutionary origin of maternal genes tends to be more recent than that of zygotic genes. Some studies support the theoretical prediction that maternal genes evolve faster than zygotic genes. However, most studies were done on a limited set of species and genes. I also discuss the way forward to understand the evolution of maternal genes by combining high-throughput genomics and theoretical evolutionary approaches.
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16
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Waiho K, Fazhan H, Zhang Y, Zhang Y, Li S, Zheng H, Liu W, Ikhwanuddin M, Ma H. Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:320-334. [PMID: 30835008 DOI: 10.1007/s10126-019-09882-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 02/18/2019] [Indexed: 06/09/2023]
Abstract
Although the sexual dimorphism in terms of gonadal development and gametogenesis of mud crab has been described, the internal regulating mechanism and sex differentiation process remain unclear. A comparative gonadal miRNA transcriptomic study was conducted to identify miRNAs that are differentially expressed between testes and ovaries, and potentially uncover miRNAs that might be involved in sex differentiation and gonadal maturation mechanisms of mud crabs (Scylla paramamosain). A total of 10 known miRNAs and 130 novel miRNAs were identified, among which 54 were differentially expressed. Target gene prediction revealed a significant enrichment in 30 KEGG pathways, including some reproduction-related pathways, e.g. phosphatidylinositol signalling system and inositol phosphate metabolism pathways. Further analysis on six differentially expressed known miRNAs, six differentially expressed novel miRNAs and their reproduction-related putative target genes shows that both miRNAs and putative target genes showed stage-specific expression during gonadal maturation, suggesting their potential regulatory roles in sex differentiation and reproductive development. This study reveals the sex-biased miRNA profile and establishes a solid foundation for understanding the sex differentiation and gonadal maturation mechanisms of S. paramamosain.
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Affiliation(s)
- Khor Waiho
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - Hanafiah Fazhan
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yin Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Shengkang Li
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Huaiping Zheng
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Wenhua Liu
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Mhd Ikhwanuddin
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
- Institute of Tropical Aquaculture, Universiti Malaysia Terengganu, 21030, Kuala Terengganu, Malaysia.
| | - Hongyu Ma
- Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China.
- STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China.
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Núñez-Acuña G, Gallardo-Escárate C. Characterization of the salmon louse Lepeophtheirus salmonis miRNome: Sex-biased differences related to the coding and non-coding RNA interplay. Mar Genomics 2019; 45:38-47. [PMID: 30772247 DOI: 10.1016/j.margen.2019.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 12/12/2022]
Abstract
The salmon louse Lepeophtheirus salmonis is a marine ectoparasite that has a detrimental impact on salmon farms. Genomic knowledge of adult stages is critical to understand the reproductive success and lifecycle completion of this species. Here, we report a comprehensive characterization of the L. salmonis miRNome with emphasis on the sex-differences of the parasite. Small-RNA sequencing was conducted on males and females, and mRNA-sequencing was also conducted to identify miRNA-targets at these stages. Based on bioinformatics analyses, 3101 putative miRNAs were found in L. salmonis, including precursors and variants. The most abundant and over-expressed miRNAs belonged to the bantam, mir-100, mir-1, mir-263a and mir-276 families, while the most differentially expressed mRNAs corresponded to genes related to reproduction and other biological processes involved in cell-differentiation. Target analyses revealed that the most up-regulated miRNAs in males can act by inhibiting the expression of genes related to female differentiation such as vitellogenin genes. Target prediction and expression patterns suggested a pivotal role of miRNAs in the reproductive development of L. salmonis.
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Affiliation(s)
- Gustavo Núñez-Acuña
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile
| | - Cristian Gallardo-Escárate
- Laboratory of Biotechnology and Aquatic Genomics, Interdisciplinary Center for Aquaculture Research (INCAR), University of Concepción, Concepción, Chile.
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18
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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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19
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Differentially expressed microRNAs associated with changes of transcript levels in detoxification pathways and DDT-resistance in the Drosophila melanogaster strain 91-R. PLoS One 2018; 13:e0196518. [PMID: 29698530 PMCID: PMC5919617 DOI: 10.1371/journal.pone.0196518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/13/2018] [Indexed: 01/01/2023] Open
Abstract
Dichloro-diphenyl-trichloroethane (DDT) resistance among arthropod species is a model for understanding the molecular adaptations in response to insecticide exposures. Previous studies reported that DDT resistance may involve one or multiple detoxification genes, such as cytochrome P450 monooxygenases (P450s), glutathione S-transferases (GSTs), esterases, and ATP binding cassette (ABC) transporters, or changes in the voltage-sensitive sodium channel. However, the possible involvement of microRNAs (miRNAs) in the post-transcriptional regulation of genes associated with DDT resistance in the Drosophila melanogaster strain 91-R remains poorly understood. In this study, the majority of the resulting miRNAs discovered in small RNA libraries from 91-R and the susceptible control strain, 91-C, ranged from 16-25 nt, and contained 163 precursors and 256 mature forms of previously-known miRNAs along with 17 putative novel miRNAs. Quantitative analyses predicted the differential expression of ten miRNAs between 91-R and 91-C, and, based on Gene Ontology and pathway analysis, these ten miRNAs putatively target transcripts encoding proteins involved in detoxification mechanisms. RT-qPCR validated an inverse correlation between levels of differentially-expressed miRNAs and their putatively targeted transcripts, which implies a role of these miRNAs in the differential regulation of detoxification pathways in 91-R compared to 91-C. This study provides evidence associating the differential expression of miRNAs in response to multigenerational DDT selection in Drosophila melanogaster and provides important clues for understanding the possible roles of miRNAs in mediating insecticide resistance traits.
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20
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Jiang L, Wang Q, Yu J, Gowda V, Johnson G, Yang J, Kan X, Yang X. miRNAome expression profiles in the gonads of adult Melopsittacus undulatus. PeerJ 2018; 6:e4615. [PMID: 29666766 PMCID: PMC5896495 DOI: 10.7717/peerj.4615] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/22/2018] [Indexed: 01/11/2023] Open
Abstract
The budgerigar (Melopsittacus undulatus) is one of the most widely studied parrot species, serving as an excellent animal model for behavior and neuroscience research. Until recently, it was unknown how sexual differences in the behavior, physiology, and development of organisms are regulated by differential gene expression. MicroRNAs (miRNAs) are endogenous short non-coding RNA molecules that can post-transcriptionally regulate gene expression and play a critical role in gonadal differentiation as well as early development of animals. However, very little is known about the role gonadal miRNAs play in the early development of birds. Research on the sex-biased expression of miRNAs in avian gonads are limited, and little is known about M. undulatus. In the current study, we sequenced two small non-coding RNA libraries made from the gonads of adult male and female budgerigars using Illumina paired-end sequencing technology. We obtained 254 known and 141 novel miRNAs, and randomly validated five miRNAs. Of these, three miRNAs were differentially expressed miRNAs and 18 miRNAs involved in sexual differentiation as determined by functional analysis with GO annotation and KEGG pathway analysis. In conclusion, this work is the first report of sex-biased miRNAs expression in the budgerigar, and provides additional sequences to the avian miRNAome database which will foster further functional genomic research.
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Affiliation(s)
- Lan Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Qingqing Wang
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Jue Yu
- College of Foreign Studies, Anhui Normal University, Wuhu, China
| | - Vinita Gowda
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, Madhya Pradesh, India
| | - Gabriel Johnson
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, District of Columbia, USA
| | - Jianke Yang
- School of Basic Medicine, Wannan Medical College, Wuhu, China
| | - Xianzhao Kan
- The Institute of Bioinformatics, College of Life Sciences, Anhui Normal University, Wuhu, China.,The Provincial Key Laboratory of the Conservation and Exploitation Research of Biological Resources in Anhui, Wuhu, China
| | - Xiaojun Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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21
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Wei G, Sun L, Li R, Li L, Xu J, Ma F. Dynamic miRNA-mRNA regulations are essential for maintaining Drosophila immune homeostasis during Micrococcus luteus infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 81:210-224. [PMID: 29198775 DOI: 10.1016/j.dci.2017.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/15/2017] [Accepted: 11/29/2017] [Indexed: 06/07/2023]
Abstract
Pathogen bacteria infections can lead to dynamic changes of microRNA (miRNA) and mRNA expression profiles, which may control synergistically the outcome of immune responses. To reveal the role of dynamic miRNA-mRNA regulation in Drosophila innate immune responses, we have detailedly analyzed the paired miRNA and mRNA expression profiles at three time points during Drosophila adult males with Micrococcus luteus (M. luteus) infection using RNA- and small RNA-seq data. Our results demonstrate that differentially expressed miRNAs and mRNAs represent extensively dynamic changes over three time points during Drosophila with M. luteus infection. The pathway enrichment analysis indicates that differentially expressed genes are involved in diverse signaling pathways, including Toll and Imd as well as orther signaling pathways at three time points during Drosophila with M. luteus infection. Remarkably, the dynamic change of miRNA expression is delayed by compared to mRNA expression change over three time points, implying that the "time" parameter should be considered when the function of miRNA/mRNA is further studied. In particular, the dynamic miRNA-mRNA regulatory networks have shown that miRNAs may synergistically regulate gene expressions of different signaling pathways to promote or inhibit innate immune responses and maintain homeostasis in Drosophila, and some new regulators involved in Drosophila innate immune response have been identified. Our findings strongly suggest that miRNA regulation is a key mechanism involved in fine-tuning cooperatively gene expressions of diverse signaling pathways to maintain innate immune response and homeostasis in Drosophila. Taken together, the present study reveals a novel role of dynamic miRNA-mRNA regulation in immune response to bacteria infection, and provides a new insight into the underlying molecular regulatory mechanism of Drosophila innate immune responses.
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Affiliation(s)
- Guanyun Wei
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Lianjie Sun
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Ruimin Li
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Lei Li
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China; Laboratory of Intelligent Computation, School of Computer Science, Nanjing Normal University, Nanjing 210046, China
| | - Jiao Xu
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics, Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing 210046, China.
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22
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Martinez-Sanchez A, Nguyen-Tu MS, Cebola I, Yavari A, Marchetti P, Piemonti L, de Koning E, Shapiro AMJ, Johnson P, Sakamoto K, Smith DM, Leclerc I, Ashrafian H, Ferrer J, Rutter GA. MiR-184 expression is regulated by AMPK in pancreatic islets. FASEB J 2018; 32:2587-2600. [PMID: 29269398 PMCID: PMC6207280 DOI: 10.1096/fj.201701100r] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AMPK is a critical energy sensor and target for widely used antidiabetic drugs. In β cells, elevated glucose concentrations lower AMPK activity, and the ablation of both catalytic subunits [β-cell–specific AMPK double-knockout (βAMPKdKO) mice] impairs insulin secretion in vivo and β-cell identity. MicroRNAs (miRNAs) are small RNAs that silence gene expression that are essential for pancreatic β-cell function and identity and altered in diabetes. Here, we have explored the miRNAs acting downstream of AMPK in mouse and human β cells. We identified 14 down-regulated and 9 up-regulated miRNAs in βAMPKdKO vs. control islets. Gene ontology analysis of targeted transcripts revealed enrichment in pathways important for β-cell function and identity. The most down-regulated miRNA was miR-184 (miR-184-3p), an important regulator of β-cell function and compensatory expansion that is controlled by glucose and reduced in diabetes. We demonstrate that AMPK is a potent regulator and an important mediator of the negative effects of glucose on miR-184 expression. Additionally, we reveal sexual dimorphism in miR-184 expression in mouse and human islets. Collectively, these data demonstrate that glucose-mediated changes in AMPK activity are central for the regulation of miR-184 and other miRNAs in islets and provide a link between energy status and gene expression in β cells.—Martinez-Sanchez, A., Nguyen-Tu, M.-S., Cebola, I., Yavari, A., Marchetti, P., Piemonti, L., de Koning, E., Shapiro, A. M. J., Johnson, P., Sakamoto, K., Smith, D. M., Leclerc, I., Ashrafian, H., Ferrer, J., Rutter, G. A. MiR-184 expression is regulated by AMPK in pancreatic islets.
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Affiliation(s)
- Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Marie-Sophie Nguyen-Tu
- Section of Cell Biology and Functional Genomics Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Ines Cebola
- Beta Cell Genome Regulation Laboratory, Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Arash Yavari
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Piero Marchetti
- Department of Endocrinology and Metabolism, University of Pisa, Pisa, Italy
| | - Lorenzo Piemonti
- San Raffaele Diabetes Research Institute (SR-DRI), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy.,Vita-Salute San Raffaele University, Milan, Italy
| | - Eelco de Koning
- Hubrecht Institute, Utrecht, The Netherlands.,Department of Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - A M James Shapiro
- Clinical Islet Laboratory and Clinical Islet Transplant Program, University of Alberta, Edmonton, Alberta, Canada
| | - Paul Johnson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Kei Sakamoto
- Nestle Institute of Health Sciences, Lausanne, Switzerland
| | - David M Smith
- AstraZeneca Research and Development, Innovative Medicines and Early Development, Discovery Sciences, Cambridge, United Kingdom
| | - Isabelle Leclerc
- Section of Cell Biology and Functional Genomics Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Houman Ashrafian
- Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jorge Ferrer
- Beta Cell Genome Regulation Laboratory, Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
| | - Guy A Rutter
- Section of Cell Biology and Functional Genomics Division of Diabetes, Endocrinology, and Metabolism, Department of Medicine, Imperial College London, London, United Kingdom
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23
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Sex-biased microRNA expression in mammals and birds reveals underlying regulatory mechanisms and a role in dosage compensation. Genome Res 2017; 27:1961-1973. [PMID: 29079676 PMCID: PMC5741053 DOI: 10.1101/gr.225391.117] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 09/21/2017] [Indexed: 12/14/2022]
Abstract
Sexual dimorphism depends on sex-biased gene expression, but the contributions of microRNAs (miRNAs) have not been globally assessed. We therefore produced an extensive small RNA sequencing data set to analyze male and female miRNA expression profiles in mouse, opossum, and chicken. Our analyses uncovered numerous cases of somatic sex-biased miRNA expression, with the largest proportion found in the mouse heart and liver. Sex-biased expression is explained by miRNA-specific regulation, including sex-biased chromatin accessibility at promoters, rather than piggybacking of intronic miRNAs on sex-biased protein-coding genes. In mouse, but not opossum and chicken, sex bias is coordinated across tissues such that autosomal testis-biased miRNAs tend to be somatically male-biased, whereas autosomal ovary-biased miRNAs are female-biased, possibly due to broad hormonal control. In chicken, which has a Z/W sex chromosome system, expression output of genes on the Z Chromosome is expected to be male-biased, since there is no global dosage compensation mechanism that restores expression in ZW females after almost all genes on the W Chromosome decayed. Nevertheless, we found that the dominant liver miRNA, miR-122-5p, is Z-linked but expressed in an unbiased manner, due to the unusual retention of a W-linked copy. Another Z-linked miRNA, the male-biased miR-2954-3p, shows conserved preference for dosage-sensitive genes on the Z Chromosome, based on computational and experimental data from chicken and zebra finch, and acts to equalize male-to-female expression ratios of its targets. Unexpectedly, our findings thus establish miRNA regulation as a novel gene-specific dosage compensation mechanism.
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24
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Liufu Z, Zhao Y, Guo L, Miao G, Xiao J, Lyu Y, Chen Y, Shi S, Tang T, Wu CI. Redundant and incoherent regulations of multiple phenotypes suggest microRNAs' role in stability control. Genome Res 2017; 27:1665-1673. [PMID: 28904014 PMCID: PMC5630030 DOI: 10.1101/gr.222505.117] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 08/22/2017] [Indexed: 12/11/2022]
Abstract
Each microRNA (miRNA) represses a web of target genes and, through them, controls multiple phenotypes. The difficulties inherent in such controls cast doubt on how effective miRNAs are in driving phenotypic changes. A "simple regulation" model posits "one target-one phenotype" control under which most targeting is nonfunctional. In an alternative "coordinate regulation" model, multiple targets are assumed to control the same phenotypes coherently, and most targeting is functional. Both models have some empirical support but pose different conceptual challenges. Here, we concurrently analyze multiple targets and phenotypes associated with the miRNA-310 family (miR310s) of Drosophila Phenotypic rescue in the mir310s knockout background is achieved by promoter-directed RNA interference that restores wild-type expression. For one phenotype (eggshell morphology), we observed redundant regulation, hence rejecting "simple regulation" in favor of the "coordinate regulation" model. For other phenotypes (egg-hatching and male fertility), however, one gene shows full rescue, but three other rescues aggravate the phenotype. Overall, phenotypic controls by miR310s do not support either model. Like a thermostat that controls both heating and cooling elements to regulate temperature, redundancy and incoherence in regulation generally suggest some capacity in stability control. Our results therefore support the published view that miRNAs play a role in the canalization of transcriptome and, hence, phenotypes.
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Affiliation(s)
- Zhongqi Liufu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Yixin Zhao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Li Guo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Guangxia Miao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Juan Xiao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Yang Lyu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Yuxin Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Suhua Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Tian Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
| | - Chung-I Wu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, Guangdong, China
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637, USA
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25
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Comparative profiling of microRNAs and their association with sexual dimorphism in the fig wasp Ceratosolen solmsi. Gene 2017; 633:54-60. [DOI: 10.1016/j.gene.2017.08.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/25/2017] [Accepted: 08/29/2017] [Indexed: 12/17/2022]
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26
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Leite DJ, Ninova M, Hilbrant M, Arif S, Griffiths-Jones S, Ronshaugen M, McGregor AP. Pervasive microRNA Duplication in Chelicerates: Insights from the Embryonic microRNA Repertoire of the Spider Parasteatoda tepidariorum. Genome Biol Evol 2016; 8:2133-44. [PMID: 27324919 PMCID: PMC4987109 DOI: 10.1093/gbe/evw143] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs are small (∼22 nt) noncoding RNAs that repress translation and therefore regulate the production of proteins from specific target mRNAs. microRNAs have been found to function in diverse aspects of gene regulation within animal development and many other processes. Among invertebrates, both conserved and novel, lineage specific, microRNAs have been extensively studied predominantly in holometabolous insects such as Drosophila melanogaster However little is known about microRNA repertoires in other arthropod lineages such as the chelicerates. To understand the evolution of microRNAs in this poorly sampled subphylum, we characterized the microRNA repertoire expressed during embryogenesis of the common house spider Parasteatoda tepidariorum We identified a total of 148 microRNAs in P. tepidariorum representing 66 families. Approximately half of these microRNA families are conserved in other metazoans, while the remainder are specific to this spider. Of the 35 conserved microRNAs families 15 had at least two copies in the P. tepidariorum genome. A BLAST-based approach revealed a similar pattern of duplication in other spiders and a scorpion, but not among other chelicerates and arthropods, with the exception of a horseshoe crab. Among the duplicated microRNAs we found examples of lineage-specific tandem duplications, and the duplication of entire microRNA clusters in three spiders, a scorpion, and in a horseshoe crab. Furthermore, we found that paralogs of many P. tepidariorum microRNA families exhibit arm switching, which suggests that duplication was often followed by sub- or neofunctionalization. Our work shows that understanding the evolution of microRNAs in the chelicerates has great potential to provide insights into the process of microRNA duplication and divergence and the evolution of animal development.
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Affiliation(s)
- Daniel J Leite
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Maria Ninova
- Faculty of Life Sciences, University of Manchester, United Kingdom
| | - Maarten Hilbrant
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | - Saad Arif
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
| | | | | | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford, OX3 0BP, United Kingdom
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27
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Peng W, Tariq K, Xie J, Zhang H. Identification and Characterization of Sex-Biased MicroRNAs in Bactrocera dorsalis (Hendel). PLoS One 2016; 11:e0159591. [PMID: 27441641 PMCID: PMC4956098 DOI: 10.1371/journal.pone.0159591] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 07/06/2016] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs that regulate various biological processes including sexual dimorphism. The oriental fruit fly Bactrocera dorsalis is one of the most destructive agricultural insect pests in many Asian countries. However, no miRNAs have been identified from the separate sex and gonads to elucidate sex gonad differentiation in B. dorsalis. In this study, we constructed four small RNA libraries from whole body of females, males (except ovaries and testes) and ovaries, testes of B. dorsalis for deep sequencing. The data analysis revealed 183 known and 120 novel miRNAs from these libraries. 18 female-biased and 16 male-biased miRNAs that may be involved in sexual differentiation were found by comparing the miRNA expression profiles in the four libraries. Using a bioinformatic approach, we predicted doublesex (dsx) as a target gene of the female-biased miR-989-3p which is considered as the key switch gene in the sex determination of tephritid insects. This study reveals the first miRNA profile related to the sex differentiation and gives a first insight into sex differences in miRNA expression of B. dorsalis which could facilitate studies of the reproductive organ specific roles of miRNAs.
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Affiliation(s)
- Wei Peng
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology, Ministry of Education and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Kaleem Tariq
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology, Ministry of Education and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Junfei Xie
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology, Ministry of Education and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
| | - Hongyu Zhang
- State Key Laboratory of Agricultural Microbiology, Key Laboratory of Horticultural Plant Biology, Ministry of Education and Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, People’s Republic of China
- * E-mail:
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28
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Miao N, Wang X, Hou Y, Feng Y, Gong Y. Identification of male-biased microRNA-107 as a direct regulator for nuclear receptor subfamily 5 group A member 1 based on sexually dimorphic microRNA expression profiling from chicken embryonic gonads. Mol Cell Endocrinol 2016; 429:29-40. [PMID: 27036932 DOI: 10.1016/j.mce.2016.03.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 03/08/2016] [Accepted: 03/27/2016] [Indexed: 12/15/2022]
Abstract
Several studies indicate that sexual dimorphic microRNAs (miRNAs) in chicken gonads are likely to have important roles in sexual development, but a more global understanding of the roles of miRNAs in sexual differentiation is still needed. To this end, we performed miRNA expression profiling in chicken gonads at embryonic day 5.5 (E5.5). Among the sex-biased miRNAs validated by qRT-PCR, twelve male-biased and six female-biased miRNAs were consistent with the sequencing results. Bioinformatics analysis revealed that some sex-biased miRNAs were potentially involved in gonadal development. Further functional analysis found that over-expression of miR-107 directly inhibited nuclear receptor subfamily 5 group A member 1 (NR5a1), and its downstream cytochrome P450 family 19 subfamily A, polypeptide 1 (CYP19A1). However, anti-Mullerian hormone (AMH) was not directly or indirectly regulated by miR-107. Overall results indicate that miR-107 may specifically mediate avian ovary-development by post-transcriptional regulation of NR5a1 and CYP19A1 in estrogen signaling pathways.
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Affiliation(s)
- Nan Miao
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Xin Wang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yue Hou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Yanping Feng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Yanzhang Gong
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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29
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Marco A. Selection Against Maternal microRNA Target Sites in Maternal Transcripts. G3 (BETHESDA, MD.) 2015; 5:2199-207. [PMID: 26306531 PMCID: PMC4593001 DOI: 10.1534/g3.115.019497] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/19/2015] [Indexed: 12/20/2022]
Abstract
In animals, before the zygotic genome is expressed, the egg already contains gene products deposited by the mother. These maternal products are crucial during the initial steps of development. In Drosophila melanogaster, a large number of maternal products are found in the oocyte, some of which are indispensable. Many of these products are RNA molecules, such as gene transcripts and ribosomal RNAs. Recently, microRNAs (small RNA gene regulators) have been detected early during development and are important in these initial steps. The presence of some microRNAs in unfertilized eggs has been reported, but whether they have a functional impact in the egg or early embryo has not being explored. I have extracted and sequenced small RNAs from Drosophila unfertilized eggs. The unfertilized egg is rich in small RNAs and contains multiple microRNA products. Maternal microRNAs often are encoded within the intron of maternal genes, suggesting that many maternal microRNAs are the product of transcriptional hitchhiking. Comparative genomics analyses suggest that maternal transcripts tend to avoid target sites for maternal microRNAs. I also developed a microRNA target mutation model to study the functional impact of polymorphisms at microRNA target sites. The analysis of Drosophila populations suggests that there is selection against maternal microRNA target sites in maternal transcripts. A potential role of the maternal microRNA mir-9c in maternal-to-zygotic transition is also discussed. In conclusion, maternal microRNAs in Drosophila have a functional impact in maternal protein-coding transcripts.
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Affiliation(s)
- Antonio Marco
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, United Kingdom
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30
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Mueller JC, Kuhl H, Timmermann B, Kempenaers B. Characterization of the genome and transcriptome of the blue tit Cyanistes caeruleus: polymorphisms, sex-biased expression and selection signals. Mol Ecol Resour 2015. [PMID: 26220359 DOI: 10.1111/1755-0998.12450] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Decoding genomic sequences and determining their variation within populations has potential to reveal adaptive processes and unravel the genetic basis of ecologically relevant trait variation within a species. The blue tit Cyanistes caeruleus--a long-time ecological model species--has been used to investigate fitness consequences of variation in mating and reproductive behaviour. However, very little is known about the underlying genetic changes due to natural and sexual selection in the genome of this songbird. As a step to bridge this gap, we assembled the first draft genome of a single blue tit, mapped the transcriptome of five females and five males to this reference, identified genomewide variants and performed sex-differential expression analysis in the gonads, brain and other tissues. In the gonads, we found a high number of sex-biased genes, and of those, a similar proportion were sex-limited (genes only expressed in one sex) in males and females. However, in the brain, the proportion of female-limited genes within the female-biased gene category (82%) was substantially higher than the proportion of male-limited genes within the male-biased category (6%). This suggests a predominant on-off switching mechanism for the female-limited genes. In addition, most male-biased genes were located on the Z-chromosome, indicating incomplete dosage compensation for the male-biased genes. We called more than 500,000 SNPs from the RNA-seq data. Heterozygote detection in the single reference individual was highly congruent between DNA-seq and RNA-seq calling. Using information from these polymorphisms, we identified potential selection signals in the genome. We list candidate genes which can be used for further sequencing and detailed selection studies, including genes potentially related to meiotic drive evolution. A public genome browser of the blue tit with the described information is available at http://public-genomes-ngs.molgen.mpg.de.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Heiner Kuhl
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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31
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Tarver JE, Cormier A, Pinzón N, Taylor RS, Carré W, Strittmatter M, Seitz H, Coelho SM, Cock JM. microRNAs and the evolution of complex multicellularity: identification of a large, diverse complement of microRNAs in the brown alga Ectocarpus. Nucleic Acids Res 2015; 43:6384-98. [PMID: 26101255 PMCID: PMC4513859 DOI: 10.1093/nar/gkv578] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 04/19/2015] [Accepted: 05/21/2015] [Indexed: 01/02/2023] Open
Abstract
There is currently convincing evidence that microRNAs have evolved independently in at least six different eukaryotic lineages: animals, land plants, chlorophyte green algae, demosponges, slime molds and brown algae. MicroRNAs from different lineages are not homologous but some structural features are strongly conserved across the eukaryotic tree allowing the application of stringent criteria to identify novel microRNA loci. A large set of 63 microRNA families was identified in the brown alga Ectocarpus based on mapping of RNA-seq data and nine microRNAs were confirmed by northern blotting. The Ectocarpus microRNAs are highly diverse at the sequence level with few multi-gene families, and do not tend to occur in clusters but exhibit some highly conserved structural features such as the presence of a uracil at the first residue. No homologues of Ectocarpus microRNAs were found in other stramenopile genomes indicating that they emerged late in stramenopile evolution and are perhaps specific to the brown algae. The large number of microRNA loci in Ectocarpus is consistent with the developmental complexity of many brown algal species and supports a proposed link between the emergence and expansion of microRNA regulatory systems and the evolution of complex multicellularity.
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Affiliation(s)
- James E Tarver
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK Genome Evolution Laboratory, Department of Biology, The National University of Ireland, Maynooth, Kildare, Ireland
| | - Alexandre Cormier
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Natalia Pinzón
- Institute of Human Genetics, UPR 1142, CNRS, 34396 Montpellier Cedex 5, France
| | - Richard S Taylor
- School of Earth Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Wilfrid Carré
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Martina Strittmatter
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Hervé Seitz
- Institute of Human Genetics, UPR 1142, CNRS, 34396 Montpellier Cedex 5, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
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32
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Liu J, Luo M, Sheng Y, Hong Q, Cheng H, Zhou R. Dynamic evolution and biogenesis of small RNAs during sex reversal. Sci Rep 2015; 5:9999. [PMID: 25944477 PMCID: PMC4421800 DOI: 10.1038/srep09999] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/24/2015] [Indexed: 12/31/2022] Open
Abstract
Understanding origin, evolution and functions of small RNA (sRNA) genes has been a great challenge in the past decade. Molecular mechanisms underlying sexual reversal in vertebrates, particularly sRNAs involved in this process, are largely unknown. By deep-sequencing of small RNA transcriptomes in combination with genomic analysis, we identified a large amount of piRNAs and miRNAs including over 1,000 novel miRNAs, which were differentially expressed during gonad reversal from ovary to testis via ovotesis. Biogenesis and expressions of miRNAs were dynamically changed during the reversal. Notably, phylogenetic analysis revealed dynamic expansions of miRNAs in vertebrates and an evolutionary trajectory of conserved miR-17-92 cluster in the Eukarya. We showed that the miR-17-92 cluster in vertebrates was generated through multiple duplications from ancestor miR-92 in invertebrates Tetranychus urticae and Daphnia pulex from the Chelicerata around 580 Mya. Moreover, we identified the sexual regulator Dmrt1 as a direct target of the members miR-19a and -19b in the cluster. These data suggested dynamic biogenesis and expressions of small RNAs during sex reversal and revealed multiple expansions and evolutionary trajectory of miRNAs from invertebrates to vertebrates, which implicate small RNAs in sexual reversal and provide new insight into evolutionary and molecular mechanisms underlying sexual reversal.
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Affiliation(s)
- Jie Liu
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Majing Luo
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Yue Sheng
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Qiang Hong
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Hanhua Cheng
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
| | - Rongjia Zhou
- Department of Genetics, College of Life Sciences, Wuhan University, Wuhan 430072, P. R. China
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33
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Hu W, Criscione F, Liang S, Tu Z. MicroRNAs of two medically important mosquito species: Aedes aegypti and Anopheles stephensi. INSECT MOLECULAR BIOLOGY 2015; 24:240-52. [PMID: 25420875 PMCID: PMC4361387 DOI: 10.1111/imb.12152] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
MicroRNAs (miRNAs) are endogenous, single-stranded small RNAs that have important regulatory functions at the post-transcriptional level. In the present study, we characterize miRNAs in two divergent mosquito species, Aedes aegypti and Anopheles stephensi, through deep sequencing of small RNAs spanning all developmental stages. We discovered eight novel miRNAs in Ae. aegypti and 20 novel miRNAs in An. stephensi, which enabled the first systematic analysis of miRNA evolution in mosquitos. We traced the phylogenetic history of all miRNAs in both species and report a rate of 0.055-0.13 miRNA net gain per million years. Most novel miRNAs originate de novo. Duplications that produced miRNA clusters and families are more common in Ae. aegypti than in An. stephensi. We also identified arm-switch as a source of new miRNAs. Expression profile analysis identified mosquito-specific miRNAs that showed strong stage-specific expression in one or both lineages. For example, the aae-miR-2941/2946 family represents the most abundant maternally deposited and zygotically transcribed miRNAs in Ae. aegypti. miR-2943 is a highly expressed zygotic miRNA in both Ae. aegypti and An. stephensi. Such information provides the basis from which to study the function of these miRNAs in biology common to all mosquitos or unique to one particular lineage.
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Affiliation(s)
- W Hu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, USA; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
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Castellano L, Rizzi E, Krell J, Di Cristina M, Galizi R, Mori A, Tam J, De Bellis G, Stebbing J, Crisanti A, Nolan T. The germline of the malaria mosquito produces abundant miRNAs, endo-siRNAs, piRNAs and 29-nt small RNAs. BMC Genomics 2015; 16:100. [PMID: 25766668 PMCID: PMC4345017 DOI: 10.1186/s12864-015-1257-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 01/19/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Small RNAs include different classes essential for endogenous gene regulation and cellular defence against genomic parasites. However, a comprehensive analysis of the small RNA pathways in the germline of the mosquito Anopheles gambiae has never been performed despite their potential relevance to reproductive capacity in this malaria vector. RESULTS We performed small RNA deep sequencing during larval and adult gonadogenesis and find that they predominantly express four classes of regulatory small RNAs. We identified 45 novel miRNA precursors some of which were sex-biased and gonad-enriched , nearly doubling the number of previously known miRNA loci. We also determine multiple genomic clusters of 24-30 nt Piwi-interacting RNAs (piRNAs) that map to transposable elements (TEs) and 3'UTR of protein coding genes. Unusually, many TEs and the 3'UTR of some endogenous genes produce an abundant peak of 29-nt small RNAs with piRNA-like characteristics. Moreover, both sense and antisense piRNAs from TEs in both Anopheles gambiae and Drosophila melanogaster reveal novel features of piRNA sequence bias. We also discovered endogenous small interfering RNAs (endo-siRNAs) that map to overlapping transcripts and TEs. CONCLUSIONS This is the first description of the germline miRNome in a mosquito species and should prove a valuable resource for understanding gene regulation that underlies gametogenesis and reproductive capacity. We also provide the first evidence of a piRNA pathway that is active against transposons in the germline and our findings suggest novel piRNA sequence bias. The contribution of small RNA pathways to germline TE regulation and genome defence in general is an important finding for approaches aimed at manipulating mosquito populations through the use of selfish genetic elements.
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Affiliation(s)
- Leandro Castellano
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Ermanno Rizzi
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy.
| | - Jonathan Krell
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Manlio Di Cristina
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy.
| | - Roberto Galizi
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Ayako Mori
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Janis Tam
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
| | - Gianluca De Bellis
- Istituto di Tecnologie Biomediche, Consiglio Nazionale delle Ricerche (ITB-CNR), Segrate, Milan, Italy.
| | - Justin Stebbing
- Division of Oncology, Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College, London, UK.
| | - Andrea Crisanti
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
- Dipartimento di Medicina Sperimentale Via Gambuli, Centro di Genomica Funzionale, University of Perugia, 06132, Perugia, Italy.
| | - Tony Nolan
- Department of Life Sciences, South Kensington Campus, Imperial College London, London, SW7 2AZ, United Kingdom.
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