DOCSLIB.ORG

Melanogaster Downloaded from by California Institute of Technology User on 01 May 2019 Alexei A

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Melanogaster Downloaded from by California Institute of Technology User on 01 May 2019 Alexei A Published online 21 February 2019 Nucleic Acids Research, 2019, Vol. 47, No. 8 4255–4271 doi: 10.1093/nar/gkz130 piRNA silencing contributes to interspecies hybrid sterility and reproductive isolation in Drosophila melanogaster Downloaded from https://academic.oup.com/nar/article-abstract/47/8/4255/5351611 by California Institute of Technology user on 01 May 2019 Alexei A. Kotov1, Vladimir E. Adashev1, Baira K. Godneeva1, Maria Ninova2, Aleksei S. Shatskikh1, Sergei S. Bazylev1,AlexeiA.Aravin1,2,* and Ludmila V. Olenina1,* 1Institute of Molecular Genetics, Russian Academy of Sciences, Kurchatov Sq. 2, Moscow, 123182 Russia and 2California Institute of Technology, Division of Biology and Biological Engineering, 147–75, 1200 E. California Blvd., Pasadena, CA 91125, USA Received October 01, 2018; Revised February 12, 2019; Editorial Decision February 14, 2019; Accepted February 16, 2019 ABSTRACT genetic information from generation to generation. Game- togenesis is often disrupted in the progeny of interspecies The piRNA pathway is an adaptive mechanism crosses. Indeed, hybrid male sterility has been proposed to that maintains genome stability by repression of be the dominant type of postzygotic interspecies isolation selfish genomic elements. In the male germline in Drosophila (1,2); however, the underlying mechanistic of Drosophila melanogaster repression of Stellate causes and factors involved are poorly understood. Germ genes by piRNAs generated from Supressor of Stel- cell proliferation and differentiation and genome integrity late (Su(Ste)) locus is required for male fertility, are under control of a number of mechanisms. One of con- but both Su(Ste) piRNAs and their targets are ab- served pathways required for gametogenesis and fertility in sent in other Drosophila species. We found that Metazoa is the Piwi-interacting RNA (piRNA) pathway; D. melanogaster genome contains multiple X-linked via this pathway small piRNAs of 23–29 nucleotides (nts) non-coding genomic repeats that have sequence guide sequence-specific recognition and repression of com- plementary RNA targets (3,4). similarity to the protein-coding host gene vasa.In In the Drosophila female germline, a diverse set of piR- the male germline, these vasa-related AT-chX repeats NAs represses the activity of mobile elements thus en- produce abundant piRNAs that are antisense to vasa; suring genome integrity. Failure of piRNA silencing that however, vasa mRNA escapes silencing due to imper- causes derepression of transposable elements and is asso- fect complementarity to AT-chX piRNAs. Unexpect- ciated with accumulation of double-stranded DNA breaks edly, we discovered AT-chX piRNAs target vasa of likely caused by transposons integrations and activation Drosophila mauritiana in the testes of interspecies of the DNA damage check-point (5,6). Even when the hybrids. In the majority of hybrid flies, the testes were DNA damage pathway is non-functional due to a muta- strongly reduced in size and germline content. A mi- tion in Chk2 kinase, females with mutations that disrupt nority of hybrids maintained wild-type array of pre- the piRNA pathway are sterile. Complex mechanisms are meiotic germ cells in the testes, but in them harm- responsible for generation of diverse piRNAs that guide repression of mobile elements. Many piRNAs are gener- ful Stellate genes were derepressed due to the ab- ated from piRNA clusters, genomic regions that contain sence of Su(Ste) piRNAs, and meiotic failures were numerous fragments of transposons. piRNA clusters are observed. Thus, the piRNA pathway contributes to transcribed––often from both genomic strands––to gener- reproductive isolation between D. melanogaster and ate long non-coding RNAs that serve as precursors for ma- closely related species, causing hybrid male sterility ture piRNAs (3,4,7). After processing of precursors by Zuc- via misregulation of two different host protein fac- chini endonuclease, mature piRNAs, which usually con- tors. tain a strong bias for uridine residue at the 5-end (1U), are loaded into Piwi proteins (8,9). The recognition of INTRODUCTION complementary targets such as transposon mRNAs by the Piwi/piRNA complex leads to cleavage of the target RNA The maintenance of gametogenesis in heterosexual organ- by the intrinsic endonuclease activity of Piwi proteins. In isms is crucial for species viability and for the transfer of *To whom correspondence should be addressed. Tel: +7 499 196 0809; Email: olenina [email protected] Correspondence may also be addressed to Alexei A. Aravin. Tel: +7 499 196 0015, +1 626 395 4297; Email: [email protected] C The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] 4256 Nucleic Acids Research, 2019, Vol. 47, No. 8 addition to the RNAi pathway, which causes complete tar- melanogaster but that are absent from the genomes of get degradation, the ping-pong mechanism generates new, closely related Drosophila species. The AT-chX repeats have so-called secondary, piRNAs from processed target. Sec- homology to the fourth and fifth exons of vasa, they are ex- ondary piRNAs generated through ping-pong have a strong pressed from both genomic strands in developing sperma- bias for adenine at position 10, 10A (7,10). Thus, generation tocytes, and they produce abundant piRNAs. However, we of secondary piRNAs provides a clear sign of RNAs tar- found no evidence that AT-chX piRNAs, which have ∼76% vasa vasa geted by piRNA pathway. The feed-forward mechanism of identity to sequence, are able to repress expres- Downloaded from https://academic.oup.com/nar/article-abstract/47/8/4255/5351611 by California Institute of Technology user on 01 May 2019 the ping-pong cycle is believed to amplify piRNAs that tar- sion in the testes of D. melanogaster. In contrast, AT-chX get active transposons thus fine-tuning piRNA populations piRNAs produced from the D. melanogaster genome have to meet cellular needs. ∼90% identify with the vasa allele of D. mauritiana and se- Several studies have reported that in Drosophila, piR- lectively silence its expression in the testes of interspecies NAs can also control the expression of host protein-coding hybrids. The majority of hybrid testes maintain a few germ genes. For example, piRNAs derived from the 3 untrans- cells and are strongly reduced in size compared to parent lated region (3-UTR)ofthetj gene repress the fasciclin III flies. We also found a strong derepression of Stellate genes gene in follicle cells of the Drosophila ovary (11), while piR- in the minor cohort of hybrid testes with perfect germline NAs from the AT-chX locus target vasa mRNA in germ content that lacks the Su(Ste) locus. Overall, our results cells of the testes (12,13). The piRNA-dependent decay of suggest that piRNA and mRNA sequences are fine-tuned numerous maternal mRNAs occurs during the maternal- to each other in each species to ensure silencing of proper to-zygotic transition in early embryos (14), and piRNA- targets and to avoid inappropriate repression. Accordingly, mediated repression of differentiation factor Cbl is involved the piRNA pathway contributes to the reproductive isola- in the self-renewal of germline stem cells (15). The piRNA tion of D. melanogaster from closely related species via dys- pathway is also reported to control the maintenance and regulation of at least two different protein factors. differentiation of germline stem cells through regulation of c-Fos mRNA in somatic niche cells (16). In most of these MATERIALS AND METHODS cases, piRNAs are reported to have only a partial comple- mentarity to the proposed targets. The rules that govern Fly stocks the recognition of proper targets and discriminate against Germinal tissues of adult Drosophila males and females off-target effects are not clearly understood. Importantly, raised at 23◦C were used, unless otherwise indicated. The one study suggested that piRNA/Piwi complexes are able to Df(1)w67c23(2)y (designated as yw), Oregon R, Canton S target numerous cellular mRNAs in a nonsequence-specific and Batumi L strains were used as wild-type strains of manner (17). D. melanogaster. Strains carrying spindle-E (spn-E) mu- While the majority of studies of the piRNA pathway in tations were ru1 st1 spn-E1 e1 ca1/TM3, Sb1 es spn-E1, Drosophila were focused on the female germline, the piRNA and ru1 st1 spn-Ehls3987 e1 ca1/TM3, Sb1 es. aub mu- pathway is also active in the testes. In fact, piRNA silencing tants were aubQC42/CyO and aubHN2/CyO. We also used was first demonstrated in testes (18–20). The major source a piwi2/piwi3 heteroallelic combination. Heterozygous sib- of piRNAs in the testes is the Y-linked Supressor of Stellate lings (+/−) were used as wild-type controls because they (Su(Ste)) locus that produces piRNAs that target X-linked have closely related genetic background to flies carrying het- repetitive Stellate genes. Each Stellate repeat encodes a pro- eroallelic mutation combinations. tein with a homology to the regulatory subunit of protein ki- Drosophila sechellia, Drosophila mauritiana and nase CkII; however, Stellates are not expressed in wild-type Drosophila erecta stocks were obtained from the Gif- males (21–23). Derepression of Stellates due to deletion of sur-Yvette CNRS Center (France) collection. Drosophila the Su(Ste) locus or failure of the piRNA pathway leads simulans stock w.501 was obtained from UC San Diego to accumulation of needle-like crystals of Stellate protein in Drosophila Species Stock Center. The Hmr1strain of D. spermatocytes, severe meiotic defects and sterility (21,23– melanogaster (#2481) was obtained from Bloomington 25).
Load more

Recommended publications
  • Evaluating the Role of Natural Selection in the Evolution of Gene Regulation
    Heredity (2008) 100, 191–199 & 2008 Nature Publishing Group All rights reserved 0018-067X/08 $30.00 www.nature.com/hdy SHORT REVIEW Evaluating the role of natural selection in the evolution of gene regulation JC Fay1 and PJ Wittkopp2 1Department of Genetics, Washington University School of Medicine, St Louis, MO, USA and 2Department of Ecology and Evolutionary Biology and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA Surveys of gene expression reveal extensive variability both also discuss properties of regulatory systems relevant to within and between a wide range of species. Compelling neutral models of gene expression. Despite some potential cases have been made for adaptive changes in gene caveats, published studies provide considerable evidence for regulation, but the proportion of expression divergence adaptive changes in gene expression. Future challenges for attributable to natural selection remains unclear. Distinguish- studies of regulatory evolution will be to quantify the ing adaptive changes driven by positive selection from frequency of adaptive changes, identify the genetic basis of neutral divergence resulting from mutation and genetic drift expression divergence and associate changes in gene is critical for understanding the evolution of gene expression. expression with specific organismal phenotypes. Here, we review the various methods that have been used to Heredity (2008) 100, 191–199; doi:10.1038/sj.hdy.6801000; test for signs of selection in genomic expression
    [Show full text]
  • Interspecific Y Chromosome Introgressions Disrupt Testis-Specific Gene Expression and Male Reproductive Phenotypes in Drosophila
    Interspecific Y chromosome introgressions disrupt testis-specific gene expression and male reproductive phenotypes in Drosophila Timothy B. Sackton1, Horacio Montenegro, Daniel L. Hartl1, and Bernardo Lemos1,2 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 Contributed by Daniel L. Hartl, September 7, 2011 (sent for review August 22, 2011) The Drosophila Y chromosome is a degenerated, heterochromatic latory variation (YRV). Collectively, these genes are more likely chromosome with few functional genes. Nonetheless, natural var- to be male-biased in expression and to diverge in expression iation on the Y chromosome in Drosophila melanogaster has sub- between species (25), and are likely mediated at least in part by stantial trans-acting effects on the regulation of X-linked and variation in rDNA sequence on the Y chromosome (28). autosomal genes. However, the contribution of Y chromosome Over longer time scales, empirical results suggest the Y chro- divergence to gene expression divergence between species is un- mosome is evolutionarily dynamic. Gene content on the Y chro- known. In this study, we constructed a series of Y chromosome mosome has changed dramatically during the course of Drosophila introgression lines, in which Y chromosomes from either Drosoph- evolution: only 3 of the 12 Y-linked genes in D. melanogaster that ila sechellia or Drosophila simulans are introgressed into a common have been studied carefully are Y-linked in all 10 sequenced D. simulans genetic background. Using these lines, we compared Drosophila genomes with homologous Y chromosomes (3). Ad- genome-wide gene expression and male reproductive phenotypes ditionally, at least part of the Y-linked gene kl-2 appears to have between heterospecific and conspecific Y chromosomes.
    [Show full text]
  • Hybridization Occurs Between Drosophila Simulans and D
    doi: 10.1111/jeb.12391 Hybridization occurs between Drosophila simulans and D. sechellia in the Seychelles archipelago D. R. MATUTE* & J. F. AYROLES†‡ *Department of Human Genetics, University of Chicago, Chicago, IL, USA †Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA ‡Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA Keywords: Abstract adaptation; Drosophila simulans and D. sechellia are sister species that serve as a model to Drosophila; study the evolution of reproductive isolation. While D. simulans is a human reproductive isolation; commensal that has spread all over the world, D. sechellia is restricted to the speciation. Seychelles archipelago and is found to breed exclusively on the toxic fruit of Morinda citrifolia. We surveyed the relative frequency of males from these two species in a variety of substrates found on five islands of the Seychelles archipelago. We sampled different fruits and found that putative D. simulans can be found in a variety of substrates, including, surprisingly, M. citrifolia. Putative D. sechellia was found preferentially on M. citrifolia fruits, but a small proportion was found in other substrates. Our survey also shows the existence of putative hybrid males in areas where D. simulans is present in Seychelles. The results from this field survey support the hypothesis of cur- rent interbreeding between these species in the central islands of Seychelles and open the possibility for fine measurements of admixture between these two Drosophila species to be made. interspecific gene flow. In this case, it is likely the two Introduction populations will eventually fuse into a single species.
    [Show full text]
  • Enriched G-Quadruplexes on the Drosophila Male X Chromosome
    bioRxiv preprint doi: https://doi.org/10.1101/656538; this version posted June 2, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Enriched G-quadruplexes on the Drosophila Male X Chromosome Function as Insulators of Dosage Compensation Complex Authors: Sheng-Hu Qian, Lu Chen, Zhen-Xia Chen* Affiliations: Hubei Key Laboratory of Agricultural Bioinformatics, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, PR China *Correspondence to: [email protected] Abstract: The evolution of sex chromosomes has resulted in half X chromosome dosage in males as females. Dosage compensation, or the two-fold upregulation in males, was thus evolved to balance the gene expression between sexes. However, the step-wise evolutionary trajectory of dosage compensation during Y chromosome degeneration is still unclear. Here, we show that the specific structured elements G-quadruplexes (G4s) are enriched on the X chromosome in Drosophila melanogaster. Meanwhile, on the X chromosome, the G4s are underrepresented on the H4K16 acetylated regions and the binding sites of dosage compensation complex male-specific lethal (MSL) complex. Peaks of G4 density and potential are observed at the flanking regions of MSL binding sites, suggesting G4s act as insulators to precisely up-regulate certain regions in males. Thus, G4s may be involved in the evolution of dosage compensation process through fine-tuning one-dose proto-X chromosome regions around MSL binding sites during the gradual Y chromosome degeneration.
    [Show full text]
  • Variation in Fiber Number of a Male-Specific Muscle Between Drosophila Species: a Genetic and Developmental Analysis
    EVOLUTION & DEVELOPMENT 9:4, 368–377 (2007) Variation in fiber number of a male-specific muscle between Drosophila species: a genetic and developmental analysis Virginie Orgogozo,a,1,Ã Noelle M. Muro,a and David L. Sterna aDepartment of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA ÃAuthor for correspondence (email: [email protected]) 1Present address: Universite´ Pierre et Marie Curie, Baˆt. A, 5e`me etage, case 29, 7 Quai Saint Bernard, 75005 Paris, France SUMMARY We characterize a newly discovered comparison of MOL development indicates that the species morphological difference between species of the Drosophila difference appears during metamorphosis. We mapped the melanogaster subgroup. The muscle of Lawrence (MOL) quantitative trait loci responsible for the change in muscle fiber contains about four to five fibers in D. melanogaster and number between D. sechellia and D. simulans to two genomic Drosophila simulans and six to seven fibers in Drosophila regions on chromosome 2. Our data eliminate the possibility of mauritiana and Drosophila sechellia. The same number of evolving mutations in the fruitless gene and suggest that a nuclei per fiber is present in these species but their total change in the twist might be partly responsible for this number of MOL nuclei differs. This suggests that the number evolutionary change. of muscle precursor cells has changed during evolution. Our INTRODUCTION Elucidating the molecular mechanisms that determine the total number of fibers within a skeletal muscle is of Contractile organs filled with myofibrils of actin and myosin fundamental importance for agriculture. For more than a that slide across each other, known as muscles, are present in hundred years, cattle with greatly enlarged muscles have all Bilateria.
    [Show full text]
  • Genetic Analysis by Interspecific Crosses of the Tolerance of Drosophila Sechellia to Major Aliphatic Acids of Its Host Plant M Amlou, E Pla, B Moreteau, Jr David
    Genetic analysis by interspecific crosses of the tolerance of Drosophila sechellia to major aliphatic acids of its host plant M Amlou, E Pla, B Moreteau, Jr David To cite this version: M Amlou, E Pla, B Moreteau, Jr David. Genetic analysis by interspecific crosses of the tolerance of Drosophila sechellia to major aliphatic acids of its host plant. Genetics Selection Evolution, BioMed Central, 1997, 29 (5), pp.511-522. hal-00894184 HAL Id: hal-00894184 https://hal.archives-ouvertes.fr/hal-00894184 Submitted on 1 Jan 1997 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Original article Genetic analysis by interspecific crosses of the tolerance of Drosophila sechellia to major aliphatic acids of its host plant M Amlou, E Pla, B Moreteau JR David Laboratoire populations, génétique et évolution, Centre national de la recherche scientifique, 91198 Gif sur-Yvette cedex, France (Received 3 March 1997; accepted 11 July 1997) Summary - Toxicity of hexanoic and octanoic acid, ie, the two major aliphatic acids found in ripe fruits of Morinda citrifolia, was measured on adult flies of Drosophila sechellia, D simulans, F1 hybrids and backcrosses. With both acids, tolerance was much higher in D sechellia than in D simulans while F1 and backcross progeny exhibited intermediate characteristics.
    [Show full text]
  • Genetics of Morphological Differences and Hybrid Sterility Between Drosophila Sechellia and Its Relatives
    Genet. Res., Camb. (1991), 57, pp. 113-122 With 2 text-figures Printed in Great Britain 113 Genetics of morphological differences and hybrid sterility between Drosophila sechellia and its relatives JERRY A. COYNE*1, JOHN RUX1 AND JEAN R. DAVID2 1 Department of Ecology and Evolution, The University of Chicago, 1103 East 57th Street, Chicago, Illinois 60637 USA 2Laboraloire de Biologie el Ge'ne'tique Evolutives, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette Cedex, France (Received 5 April 1990 and in revised form 15 June 1990) Summary We conducted classical genetic analysis of the difference in male genitalia and hybrid sterility between the island-dwelling sibling species Drosophila sechellia and D. mauritiana. At least two loci (one on each autosome) are responsible for the genital difference, with the X chromosome having no significant effect. In contrast, male hybrid sterility is caused by at least four gene loci distributed among all major chromosomes, with those on the X chromosome having the largest effect. We also show that the large difference in ovariole number between D. sechellia and its mainland relative D. simulans is due to at least two gene substitutions, one on each major autosome. The X and the left arm of the second chromosome, however, have no significant effect on the character. This implies that the evolution of reduced ovariole number involved relatively few gene substitutions. These results extend previous findings that morphological differences between Drosophila species are caused by genes distributed among all chromosomes, while hybrid sterility and inviability are due primarily to X-linked genes.
    [Show full text]
  • Regulatory Divergence in Drosophila Revealed by Mrna-Seq
    Downloaded from genome.cshlp.org on September 26, 2021 - Published by Cold Spring Harbor Laboratory Press Research Regulatory divergence in Drosophila revealed by mRNA-seq C. Joel McManus,1 Joseph D. Coolon,2 Michael O. Duff,1,3 Jodi Eipper-Mains,1 Brenton R. Graveley,1,3,4 and Patricia J. Wittkopp2,4 1Department of Genetics and Developmental Biology, University of Connecticut Stem Cell Institute, University of Connecticut Health Center, Farmington, Connecticut 06030, USA; 2Department of Ecology and Evolutionary Biology, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA; 3University of Connecticut Stem Cell Institute, University of Connecticut Health Center, Farmington, Connecticut 06030, USA The regulation of gene expression is critical for organismal function and is an important source of phenotypic diversity between species. Understanding the genetic and molecular mechanisms responsible for regulatory divergence is therefore expected to provide insight into evolutionary change. Using deep sequencing, we quantified total and allele-specific mRNA expression levels genome-wide in two closely related Drosophila species (D. melanogaster and D. sechellia) and their F1 hybrids. We show that 78% of expressed genes have divergent expression between species, and that cis- and trans-regulatory divergence affects 51% and 66% of expressed genes, respectively, with 35% of genes showing evidence of both. This is a relatively larger contribution of trans-regulatory divergence than was expected based on prior studies, and may result from the unique demographic history of D. sechellia. Genes with antagonistic cis- and trans-regulatory changes were more likely to be misexpressed in hybrids, consistent with the idea that such regulatory changes contribute to hybrid in- compatibilities.
    [Show full text]
  • Introduction
    Genetic Contributions of desatF and eloF to Courtship Mating Behavior and Cuticular Hydrocarbon Production in Drosophila simulans and D. sechellia BY Jennifer L. Hackett Submitted to the graduate degree program in Molecular Biosciences and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Master of Arts. ________________________________ Chairperson Jennifer M. Gleason ________________________________ Stuart J. Macdonald ________________________________ Robert E. Ward IV Date Defended: 26 August 2011 The Thesis Committee for Jennifer L. Hackett certifies that this is the approved version of the following thesis: Genetic Contributions of desatF and eloF to Courtship Mating Behavior and Cuticular Hydrocarbon Production in Drosophila simulans and D. sechellia ________________________________ Chairperson Jennifer M. Gleason Date approved: 02 September 2011 ii Abstract Sexual isolation occurs between Drosophila simulans and D. sechellia due to differences in cuticular hydrocarbon (CHC) productions. A wide variety of hydrocarbons are produced, but D. simulans males and females predominantly produce 7-tricosene (7-T), a 23 carbon monoene, while D. sechellia males produce 7-T and D. sechellia females produce 7,11-heptacosadiene (7,11-HD), a 27 carbon diene (Coyne et al. 1994). An asymmetric mating pattern occurs due to hydrocarbon differences: D. simulans males only court D. simulans females and D. sechellia males court both D. simulans and D. sechellia females (Cobb and Jallon 1990). Previous quantitative trait locus (QTL) studies (Gleason et al. 2005; Gleason et al. 2009) identified desatF and eloF as candidate genes contributing to production of D. sechellia pheromone 7,11-HD. In this thesis, the effect of D.
    [Show full text]
  • 1 a Locus in Drosophila Sechellia Affecting Tolerance of a Host Plant
    Genetics: Early Online, published on September 13, 2013 as 10.1534/genetics.113.154773 A Locus in Drosophila sechellia Affecting Tolerance of a Host Plant Toxin Eric A. Hungate1, Eric J. Earley2, Ian A. Boussy3, David A. Turissini1, Chau-Ti Ting4, Jennifer R. Moran1, Mao-Lien Wu1, Chung-I Wu1, Corbin D. Jones2,* 1 Department of Ecology and Evolution, University of Chicago, 1101 E. 57th Street, Chicago, IL 60637, USA. 2 Department of Biology, University of North Carolina, 120 South Road, Chapel Hill, NC 27599, USA. 3 Department of Biology, Loyola University Chicago, 1032 W. Sheridan Road, Chicago, IL 60660, USA. 4 Institute of Ecology and Evolutionary Biology, National Taiwan University, Taipei, 10617 Taiwan. *Corresponding author Data deposited in the Dryad Repository: http://doi.org/10.5061/dryad.rp6gt Running title: Genetics of octanoic acid tolerance in D. sechellia Key words: Drosophila, octanoic acid, adaptation, speciation, host specialization 1 Copyright 2013. Abstract – Many insects feed on only one or a few types of host. These host specialists often evolve a preference for chemical cues emanting from their host and develop mechanisms for circumventing their host’s defenses. Adaptations like these are central to evolutionary biology, yet our understanding of their genetics remains incomplete. Drosophila sechellia, an emerging model for the genetics of host specialization, is an island endemic that has adapted to chemical toxins present in the fruit of its host plant, Morinda citrifolia. Its sibling species, D. simulans, and many other Drosophila species do not tolerate these toxins and avoid the fruit. Earlier work found a region with a strong effect on tolerance to the major toxin, octanoic acid, on chromosome arm 3R.
    [Show full text]
  • Network Analysis and Comparative Phylogenomics of Micrornas and Their Respective Messenger RNA Targets Using Twelve Drosophila Species
    Virginia Commonwealth University VCU Scholars Compass Theses and Dissertations Graduate School 2010 Network Analysis and Comparative Phylogenomics of MicroRNAs and their Respective Messenger RNA Targets Using Twelve Drosophila species M Ryan Woodcock Virginia Commonwealth University Follow this and additional works at: https://scholarscompass.vcu.edu/etd Part of the Life Sciences Commons © The Author Downloaded from https://scholarscompass.vcu.edu/etd/155 This Dissertation is brought to you for free and open access by the Graduate School at VCU Scholars Compass. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of VCU Scholars Compass. For more information, please contact [email protected]. Network Analysis and Comparative Phylogenomics of MicroRNAs and their Respective Messenger RNA Targets Using Twelve Drosophila species By M. Ryan Woodcock, B.S. Fall 2010 Integrative Life Science Ph.D. Program, Virginia Commonwealth University (VCU) Chairperson and Mentor: Danail G. Bonchev, Ph.D., D.Sc., Committee Members: Gregory M. Plunkett, Ph.D., Lemont Kier, Ph.D., Maria Rivera, Ph.D., J. M.Turbeville, Ph.D., Tarynn Witten, Ph.D. TABLE of CONTENTS 2 ABSTRACT 5 THESIS OVERVIEW 7 ACKNOWLEDGEMENTS 9 CHAPTER I. MicroRNA Target Prediction and Network Properties in Drosophila Abstract 13 Introduction 14 Methods 16 Results 23 Discussion 36 CHAPTER II. Drosophilid Patterns of MicroRNA Network Conservation across Interactions, Targets, and Species Abstract 44 Introduction 45 Methods 46 Results 47 Discussion 68 CHAPTER III. Reconstruction of Drosophila Phylogeny using MicroRNA-Target Network Edges Abstract 76 Introduction 77 Methods 78 Results 79 Discussion 85 2 CHAPER IV. MicroRNA-Target Network Topology across Regions of Chromosomal Synteny (Muller Elements) and Genes linked to species Diagnostic Phenotype in Drosophila.
    [Show full text]
  • Species Bioproject Data Type #Individuals Publication Reference Genome Prado-Martinez Gorilla Gorilla PRJNA189439 Genome 20 Ensembl (Release 89) Et Al
    Species Bioproject data_type #individuals publication Reference genome Prado-Martinez Gorilla gorilla PRJNA189439 Genome 20 Ensembl (release 89) et al. 2013 Teixeira et al. Homo sapiens PRJEB8350 Exome 19 Ensembl (release 89) 2015 Teixeira et al. Pan troglodytes PRJEB8350 Exome 20 Ensembl (release 89) 2015 unpublished Papio anubis PRJNA54005 Genome 5 baboon genome Ensembl (release 89) project PRJNA189439 Prado-Martinez Pongo abelii Genome 10 Ensembl (release 89) and PRJEB1675 et al. 2013 Macaca mulatta PRJNA251548 Exome 20 Xue et al. 2016 Ensembl (release 89) Wright et al. Meleagris gallopavo PRJNA271731 RNA-seq 10 NA 2015 Wright et al. Phasianus colchicus PRJNA271731 RNA-seq 11 NA 2015 Wright et al. Pavo cristatus PRJNA271731 RNA-seq 10 NA 2015 Wright et al. Numida meleagris PRJNA271731 RNA-seq 7 NA 2015 Wright et al. Anas platyrhynchos PRJNA271731 RNA-seq 10 NA 2015 Wright et al. Anser cygnoides PRJNA271731 RNA-seq 10 NA 2015 Ellegren et al. Ficedula albicollis PRJEB2984 Genome 20 NCBI FicAlb1.5 2012 Lamichhaney et Geospiza difficilis PRJNA263122 Genome 8 NCBI Geofor1.0 al. 2015 //ftp.ncbi.nlm.nih.gov/g enomes/all/GCF/001/52 Corcoran et al. 2/545/GCF_001522545. Parus major PRJNA381923 Genome 10 2017 2_Parus_major1.1/GCF_ 001522545.2_Parus_ma jor1.1_genomic.gff.gz //ftp.ncbi.nlm.nih.gov/g enomes/all/GCF/000/73 8/735/GCF_000738735. Corvus sp. PRJEB9057 Genome 10 Vijay et al. 2017 2_ASM73873v2/GCF_00 0738735.2_ASM73873v 2_genomic.gff.gz //ftp.ncbi.nlm.nih.gov/g enomes/all/GCF/000/15 Singhal et al. 1/805/GCF_000151805. Taniopygia guttata
    [Show full text]