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Zakharenko LP, Bobrovskikh MA, Gruntenko NE, Petrovskii DV, Verevkin EG, Putilov AA. Two Old Wild-Type Strains of Drosophila melanogaster Can Serve as an Animal Model of Faster and Slower Aging Processes. INSECTS 2024; 15:329. [PMID: 38786885 PMCID: PMC11122303 DOI: 10.3390/insects15050329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND Drosophila melanogaster provides a powerful platform to study the physiology and genetics of aging, i.e., the mechanisms underpinnings healthy aging, age-associated disorders, and acceleration of the aging process under adverse environmental conditions. Here, we tested the responses of daily rhythms to age-accelerated factors in two wild-type laboratory-adapted strains, Canton-S and Harwich. METHODS On the example of the 24 h patterns of locomotor activity and sleep, we documented the responses of these two strains to such factors as aging, high temperature, carbohydrate diet, and diet with different doses of caffeine-benzoate sodium. RESULTS The strains demonstrated differential responses to these factors. Moreover, compared to Canton-S, Harwich showed a reduced locomotor activity, larger amount of sleep, faster rate of development, smaller body weight, lower concentrations of main sugars, lower fecundity, and shorter lifespan. CONCLUSIONS It might be recommended to use at least two strains, one with a relatively fast and another with a relatively slow aging process, for the experimental elaboration of relationships between genes, environment, behavior, physiology, and health.
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Affiliation(s)
| | | | | | | | | | - Arcady A. Putilov
- Department of Insect Genetics, Institute of Cytology and Genetics of the Siberian Branch, The Russian Academy of Sciences, Novosibirsk 630090, Russia; (L.P.Z.); (M.A.B.); (N.E.G.); (D.V.P.); (E.G.V.)
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Zakharenko LP, Petrovskii DV, Bykov RA. The P-Element Has Not Significant Effect on the Drosophila simulans Viability. Mol Biol 2023. [DOI: 10.1134/s0026893323020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Lama J, Srivastav S, Tasnim S, Hubbard D, Hadjipanteli S, Smith BR, Macdonald SJ, Green L, Kelleher ES. Genetic variation in P-element dysgenic sterility is associated with double-strand break repair and alternative splicing of TE transcripts. PLoS Genet 2022; 18:e1010080. [PMID: 36477699 PMCID: PMC9762592 DOI: 10.1371/journal.pgen.1010080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 12/19/2022] [Accepted: 11/02/2022] [Indexed: 12/12/2022] Open
Abstract
The germline mobilization of transposable elements (TEs) by small RNA mediated silencing pathways is conserved across eukaryotes and critical for ensuring the integrity of gamete genomes. However, genomes are recurrently invaded by novel TEs through horizontal transfer. These invading TEs are not targeted by host small RNAs, and their unregulated activity can cause DNA damage in germline cells and ultimately lead to sterility. Here we use hybrid dysgenesis-a sterility syndrome of Drosophila caused by transposition of invading P-element DNA transposons-to uncover host genetic variants that modulate dysgenic sterility. Using a panel of highly recombinant inbred lines of Drosophila melanogaster, we identified two linked quantitative trait loci (QTL) that determine the severity of dysgenic sterility in young and old females, respectively. We show that ovaries of fertile genotypes exhibit increased expression of splicing factors that suppress the production of transposase encoding transcripts, which likely reduces the transposition rate and associated DNA damage. We also show that fertile alleles are associated with decreased sensitivity to double-stranded breaks and enhanced DNA repair, explaining their ability to withstand high germline transposition rates. Together, our work reveals a diversity of mechanisms whereby host genotype modulates the cost of an invading TE, and points to genetic variants that were likely beneficial during the P-element invasion.
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Affiliation(s)
- Jyoti Lama
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Satyam Srivastav
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Sadia Tasnim
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Donald Hubbard
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Savana Hadjipanteli
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Brittny R. Smith
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Stuart J. Macdonald
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, United States of America
| | - Llewellyn Green
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
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4
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Association between the Effects of High Temperature on Fertility and Sleep in Female Intra-Specific Hybrids of Drosophila melanogaster. INSECTS 2021; 12:insects12040336. [PMID: 33918720 PMCID: PMC8069354 DOI: 10.3390/insects12040336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/25/2021] [Accepted: 04/08/2021] [Indexed: 11/16/2022]
Abstract
Humans and fruit flies demonstrate similarity in sleep-wake behavior, e.g., in the pattern of sleep disturbances caused by an exposure to high temperature. Although research has provided evidence for a clear connection between sleeping problems and infertility in women, very little is known regarding the mechanisms underlying this connection. Studies of dysgenic crosses of fruit flies revealed that an exposure to elevated temperature induces sterility in female intra-specific hybrids exclusively in one of two cross directions (progeny of Canton-S females crossed with Harwich males). Given the complexity and limitations of human studies, this fruit flies' model of temperature-sensitive sterility might be used for testing whether the effects of high temperature on fertility and on 24-h sleep pattern are inter-related. To document this pattern, 315 hybrids were kept for at least five days in constant darkness at 20 °C and 29 °C. No evidence was found for a causal link between sterility and sleep disturbance. However, a diminished thermal responsiveness of sleep was shown by females with temperature-induced sterility, while significant responses to high temperature were still observed in fertile females obtained by crossing in the opposite direction (i.e., Canton-S males with Harwich females) and in fertile males from either cross.
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5
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Mohamed M, Dang NTM, Ogyama Y, Burlet N, Mugat B, Boulesteix M, Mérel V, Veber P, Salces-Ortiz J, Severac D, Pélisson A, Vieira C, Sabot F, Fablet M, Chambeyron S. A Transposon Story: From TE Content to TE Dynamic Invasion of Drosophila Genomes Using the Single-Molecule Sequencing Technology from Oxford Nanopore. Cells 2020; 9:E1776. [PMID: 32722451 PMCID: PMC7465170 DOI: 10.3390/cells9081776] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/17/2020] [Accepted: 07/23/2020] [Indexed: 11/17/2022] Open
Abstract
Transposable elements (TEs) are the main components of genomes. However, due to their repetitive nature, they are very difficult to study using data obtained with short-read sequencing technologies. Here, we describe an efficient pipeline to accurately recover TE insertion (TEI) sites and sequences from long reads obtained by Oxford Nanopore Technology (ONT) sequencing. With this pipeline, we could precisely describe the landscapes of the most recent TEIs in wild-type strains of Drosophila melanogaster and Drosophila simulans. Their comparison suggests that this subset of TE sequences is more similar than previously thought in these two species. The chromosome assemblies obtained using this pipeline also allowed recovering piRNA cluster sequences, which was impossible using short-read sequencing. Finally, we used our pipeline to analyze ONT sequencing data from a D. melanogaster unstable line in which LTR transposition was derepressed for 73 successive generations. We could rely on single reads to identify new insertions with intact target site duplications. Moreover, the detailed analysis of TEIs in the wild-type strains and the unstable line did not support the trap model claiming that piRNA clusters are hotspots of TE insertions.
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Affiliation(s)
- Mourdas Mohamed
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nguyet Thi-Minh Dang
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Yuki Ogyama
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Nelly Burlet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Bruno Mugat
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Matthieu Boulesteix
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Vincent Mérel
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Philippe Veber
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Judit Salces-Ortiz
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
- Institute of Evolutionary Biology (IBE), CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Dany Severac
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, CNRS, INSERM, Université de Montpellier, 34094 Montpellier, France;
| | - Alain Pélisson
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
| | - Cristina Vieira
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - François Sabot
- IRD/UM UMR DIADE, 911 avenue Agropolis BP64501, 34394 Montpellier, France; (N.T.-M.D.); (F.S.)
| | - Marie Fablet
- Université de Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR 5558, 69622 Villeurbanne, France; (N.B.); (M.B.); (V.M.); (P.V.); (J.S.-O.); (C.V.)
| | - Séverine Chambeyron
- Institute of Human Genetics, UMR9002, CNRS and Montpellier University, 34396 Montpellier, France; (M.M.); (Y.O.); (B.M.); (A.P.)
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Serrato-Capuchina A, Wang J, Earley E, Peede D, Isbell K, Matute DR. Paternally Inherited P-Element Copy Number Affects the Magnitude of Hybrid Dysgenesis in Drosophila simulans and D. melanogaster. Genome Biol Evol 2020; 12:808-826. [PMID: 32339225 PMCID: PMC7313671 DOI: 10.1093/gbe/evaa084] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Transposable elements (TEs) are repetitive regions of DNA that are able to self-replicate and reinsert themselves throughout host genomes. Since the discovery of TEs, a prevalent question has been whether increasing TE copy number has an effect on the fitness of their hosts. P-elements (PEs) in Drosophila are a well-studied TE that has strong phenotypic effects. When a female without PEs (M) is crossed to a male with them (P), the resulting females are often sterile, a phenomenon called hybrid dysgenesis (HD). Here, we used short- and long-read sequencing to infer the number of PEs in the genomes of dozens of isofemale lines from two Drosophila species and measured whether the magnitude of HD was correlated with the number of PEs in the paternal genome. Consistent with previous reports, we find evidence for a positive correlation between the paternal PE copy number and the magnitude of HD in progeny from ♀M × ♂ P crosses for both species. Other crosses are not affected by the number of PE copies. We also find that the correlation between the strength of HD and PE copy number differs between species, which suggests that there are genetic differences that might make some genomes more resilient to the potentially deleterious effects of TEs. Our results suggest that PE copy number interacts with other factors in the genome and the environment to cause HD and that the importance of these interactions is species specific.
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Affiliation(s)
| | - Jeremy Wang
- Genetics Department, University of North Carolina, Chapel Hill
| | - Eric Earley
- Genomics in Public Health and Medicine RTI International, Research Triangle Park, North Carolina
| | - David Peede
- Biology Department, University of North Carolina, Chapel Hill
| | - Kristin Isbell
- Biology Department, University of North Carolina, Chapel Hill
| | - Daniel R Matute
- Biology Department, University of North Carolina, Chapel Hill
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Kelleher ES, Jaweria J, Akoma U, Ortega L, Tang W. QTL mapping of natural variation reveals that the developmental regulator bruno reduces tolerance to P-element transposition in the Drosophila female germline. PLoS Biol 2018; 16:e2006040. [PMID: 30376574 PMCID: PMC6207299 DOI: 10.1371/journal.pbio.2006040] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/26/2018] [Indexed: 12/15/2022] Open
Abstract
Transposable elements (TEs) are obligate genetic parasites that propagate in host genomes by replicating in germline nuclei, thereby ensuring transmission to offspring. This selfish replication not only produces deleterious mutations—in extreme cases, TE mobilization induces genotoxic stress that prohibits the production of viable gametes. Host genomes could reduce these fitness effects in two ways: resistance and tolerance. Resistance to TE propagation is enacted by germline-specific small-RNA-mediated silencing pathways, such as the Piwi-interacting RNA (piRNA) pathway, and is studied extensively. However, it remains entirely unknown whether host genomes may also evolve tolerance by desensitizing gametogenesis to the harmful effects of TEs. In part, the absence of research on tolerance reflects a lack of opportunity, as small-RNA-mediated silencing evolves rapidly after a new TE invades, thereby masking existing variation in tolerance. We have exploited the recent historical invasion of the Drosophila melanogaster genome by P-element DNA transposons in order to study tolerance of TE activity. In the absence of piRNA-mediated silencing, the genotoxic stress imposed by P-elements disrupts oogenesis and, in extreme cases, leads to atrophied ovaries that completely lack germline cells. By performing quantitative trait locus (QTL) mapping on a panel of recombinant inbred lines (RILs) that lack piRNA-mediated silencing of P-elements, we uncovered multiple QTL that are associated with differences in tolerance of oogenesis to P-element transposition. We localized the most significant QTL to a small 230-kb euchromatic region, with the logarithm of the odds (LOD) peak occurring in the bruno locus, which codes for a critical and well-studied developmental regulator of oogenesis. Genetic, cytological, and expression analyses suggest that bruno dosage modulates germline stem cell (GSC) loss in the presence of P-element activity. Our observations reveal segregating variation in TE tolerance for the first time, and implicate gametogenic regulators as a source of tolerant variants in natural populations. Transposable elements (TEs), or “jumping genes,” are mobile fragments of selfish DNA that leave deleterious mutations and DNA damage in their wake as they spread through host genomes. Their harmful effects are known to select for resistance by the host, in which the propagation of TEs is regulated and reduced. Here, we study for the first time whether host cells might also exhibit tolerance to TEs, by reducing their harmful effects without directly controlling their movement. By taking advantage of a panel of wild-type Drosophila melanogaster that lack resistance to P-element DNA transposons, we identified a small region of the genome that influences tolerance of P-element activity. We further demonstrate that a gene within that region, bruno, strongly influences the negative effects of P-element mobilization on the fly. When bruno dosage is reduced, the fertility of females carrying mobile P-elements is enhanced. The bruno locus encodes a protein with no known role in TE regulation but multiple well-characterized functions in oogenesis. We propose that bruno function reduces tolerance of the developing oocyte to DNA damage that is caused by P-elements.
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Affiliation(s)
- Erin S. Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- * E-mail:
| | - Jaweria Jaweria
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Uchechukwu Akoma
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lily Ortega
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
| | - Wenpei Tang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United State of America
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Wakisaka KT, Ichiyanagi K, Ohno S, Itoh M. Association of zygotic piRNAs derived from paternal P elements with hybrid dysgenesis in Drosophila melanogaster. Mob DNA 2018; 9:7. [PMID: 29441132 PMCID: PMC5800288 DOI: 10.1186/s13100-018-0110-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/15/2018] [Indexed: 01/27/2023] Open
Abstract
Background P-element transposition in the genome causes P-M hybrid dysgenesis in Drosophila melanogaster. Maternally deposited piRNAs suppress P-element transposition in the progeny, linking them to P-M phenotypes; however, the role of zygotic piRNAs derived from paternal P elements is poorly understood. Results To elucidate the molecular basis of P-element suppression by zygotic factors, we investigated the genomic constitution and P-element piRNA production derived from fathers. As a result, we characterized males of naturally derived Q, M’ and P strains, which show different capacities for the P-element mobilizations introduced after hybridizations with M-strain females. The amounts of piRNAs produced in ovaries of F1 hybrids varied among the strains and were influenced by the characteristics of the piRNA clusters that harbored the P elements. Importantly, while both the Q- and M’-strain fathers restrict the P-element mobilization in ovaries of their daughters, the Q-strain fathers supported the production of the highest piRNA expression in the ovaries of their daughters, and the M’ strain carries KP elements in transcriptionally active regions directing the highest expression of KP elements in their daughters. Interestingly, the zygotic P-element piRNAs, but not the KP element mRNA, contributed to the variations in P transposition immunity in the granddaughters. Conclusions The piRNA-cluster-embedded P elements and the transcriptionally active KP elements from the paternal genome are both important suppressors of P element activities that are co-inherited by the progeny. Expression levels of the P-element piRNA and KP-element mRNA vary among F1 progeny due to the constitution of the paternal genome, and are involved in phenotypic variation in the subsequent generation. Electronic supplementary material The online version of this article (10.1186/s13100-018-0110-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Tsuji Wakisaka
- 1Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan
| | - Kenji Ichiyanagi
- 2Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Seiko Ohno
- 3Center for Epidemiologic Research in Asia, Shiga Univesity of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Masanobu Itoh
- 1Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan.,4Center for Advanced Insect Research Promotion (CAIRP), Kyoto Institute of Technology, Kyoto, 606-8585 Japan
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Zakharenko LP, Ivannikov AV, Ignatenko OM, Zakharov IK. Search for Canonical P Element in Genomes of Drosophilinae Subfamily Species. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418010131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Wakisaka KT, Ichiyanagi K, Ohno S, Itoh M. Diversity of P-element piRNA production among M' and Q strains and its association with P-M hybrid dysgenesis in Drosophila melanogaster. Mob DNA 2017; 8:13. [PMID: 29075336 PMCID: PMC5654125 DOI: 10.1186/s13100-017-0096-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/13/2017] [Indexed: 01/24/2023] Open
Abstract
Background Transposition of P elements in the genome causes P–M hybrid dysgenesis in Drosophila melanogaster. For the P strain, the P–M phenotypes are associated with the ability to express a class of small RNAs, called piwi-interacting small RNAs (piRNAs), that suppress the P elements in female gonads. However, little is known about the extent to which piRNAs are involved in the P–M hybrid dysgenesis in M′ and Q strains, which show different abilities to regulate the P elements from P strains. Results To elucidate the molecular basis of the suppression of paternally inherited P elements, we analyzed the mRNA and piRNA levels of P elements in the F1 progeny between males of a P strain and nine-line females of M′ or Q strains (M′ or Q progenies). M′ progenies showed the hybrid dysgenesis phenotype, while Q progenies did not. Consistently, the levels of P-element mRNA in both the ovaries and F1 embryos were higher in M′ progenies than in Q progenies, indicating that the M′ progenies have a weaker ability to suppress P-element expression. The level of P-element mRNA was inversely correlated to the level of piRNAs in F1 embryos. Importantly, the M′ progenies were characterized by a lower abundance of P-element piRNAs in both young ovaries and F1 embryonic bodies. The Q progenies showed various levels of piRNAs in both young ovaries and F1 embryonic bodies despite all of the Q progenies suppressing P-element transposition in their gonad. Conclusions Our results are consistent with an idea that the level of P-element piRNAs is a determinant for dividing strain types between M′ and Q and that the suppression mechanisms of transposable elements, including piRNAs, are varied between natural populations. Electronic supplementary material The online version of this article (10.1186/s13100-017-0096-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Keiko Tsuji Wakisaka
- Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo, Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan
| | - Kenji Ichiyanagi
- Laboratory of Genome and Epigenome Dynamics, Department of Applied Molecular Biosciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Seiko Ohno
- Center for Epidemiologic Research in Asia, Shiga Univesity of Medical Science, Otsu, Shiga 520-2192 Japan
| | - Masanobu Itoh
- Department of Applied Biology, Kyoto Institute of Technology, Hashigamicyo, Matsugasaki, Sakyo-ku, Kyoto, 606-8585 Japan.,Center for Advanced Insect Research Promotion (CAIRP), Kyoto Institute of Technology, Kyoto, 606-8585 Japan
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11
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Bergman CM, Han S, Nelson MG, Bondarenko V, Kozeretska I. Genomic analysis of P elements in natural populations of Drosophila melanogaster. PeerJ 2017; 5:e3824. [PMID: 28929030 PMCID: PMC5602686 DOI: 10.7717/peerj.3824] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 08/29/2017] [Indexed: 11/20/2022] Open
Abstract
The Drosophila melanogaster P transposable element provides one of the best cases of horizontal transfer of a mobile DNA sequence in eukaryotes. Invasion of natural populations by the P element has led to a syndrome of phenotypes known as P-M hybrid dysgenesis that emerges when strains differing in their P element composition mate and produce offspring. Despite extensive research on many aspects of P element biology, many questions remain about the genomic basis of variation in P-M dysgenesis phenotypes across populations. Here we compare estimates of genomic P element content with gonadal dysgenesis phenotypes for isofemale strains obtained from three worldwide populations of D. melanogaster to illuminate the molecular basis of natural variation in cytotype status. We show that P element abundance estimated from genome sequences of isofemale strains is highly correlated across different bioinformatics approaches, but that abundance estimates are sensitive to method and filtering strategies as well as incomplete inbreeding of isofemale strains. We find that P element content varies significantly across populations, with strains from a North American population having fewer P elements but a higher proportion of full-length elements than strains from populations sampled in Europe or Africa. Despite these geographic differences in P element abundance and structure, neither the number of P elements nor the ratio of full-length to internally-truncated copies is strongly correlated with the degree of gonadal dysgenesis exhibited by an isofemale strain. Thus, variation in P element abundance and structure across different populations does not necessarily lead to corresponding geographic differences in gonadal dysgenesis phenotypes. Finally, we confirm that population differences in the abundance and structure of P elements that are observed from isofemale lines can also be observed in pool-seq samples from the same populations. Our work supports the view that genomic P element content alone is not sufficient to explain variation in gonadal dysgenesis across strains of D. melanogaster, and informs future efforts to decode the genomic basis of geographic and temporal differences in P element induced phenotypes.
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Affiliation(s)
- Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom.,Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Shunhua Han
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States of America
| | - Michael G Nelson
- Faculty of Life Sciences, University of Manchester, Manchester, United Kingdom
| | - Vladyslav Bondarenko
- Department of General and Molecular Genetics, Taras Shevchenko University of Kyiv, Kyiv, Ukraine
| | - Iryna Kozeretska
- Department of General and Molecular Genetics, Taras Shevchenko University of Kyiv, Kyiv, Ukraine
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12
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Paternal Induction of Hybrid Dysgenesis in Drosophila melanogaster Is Weakly Correlated with Both P-Element and hobo Element Dosage. G3-GENES GENOMES GENETICS 2017; 7:1487-1497. [PMID: 28315830 PMCID: PMC5427502 DOI: 10.1534/g3.117.040634] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Transposable elements (TEs) are virtually ubiquitous components of genomes, yet they often impose significant fitness consequences on their hosts. In addition to producing specific deleterious mutations by insertional inactivation, TEs also impose general fitness costs by inducing DNA damage and participating in ectopic recombination. These latter fitness costs are often assumed to be dosage-dependent, with stronger effects occurring in the presence of higher TE copy numbers. We test this assumption in Drosophila melanogaster by considering the relationship between the copy number of two active DNA transposons, P-element and hobo element, and the incidence of hybrid dysgenesis, a sterility syndrome associated with transposon activity in the germline. By harnessing a subset of the Drosophila Genetic Reference Panel (DGRP), a group of fully-sequenced D. melanogaster strains, we describe quantitative and structural variation in P-elements and hobo elements among wild-derived genomes and associate these factors with hybrid dysgenesis. We find that the incidence of hybrid dysgenesis is associated with both P-element and hobo element copy number in a dosage-dependent manner. However, the relationship is weak for both TEs, suggesting that dosage alone explains only a small part of TE-associated fitness costs.
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Dorogova NV, Bolobolova EU, Zakharenko LP. Cellular aspects of gonadal atrophy in Drosophila P-M hybrid dysgenesis. Dev Biol 2017; 424:105-112. [DOI: 10.1016/j.ydbio.2017.02.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 02/01/2017] [Accepted: 02/26/2017] [Indexed: 10/20/2022]
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