ADVERTIMENT. Lʼaccés als continguts dʼaquesta tesi queda condicionat a lʼacceptació de les condicions dʼús establertes per la següent llicència Creative Commons: http://cat.creativecommons.org/?page_id=184 ADVERTENCIA. El acceso a los contenidos de esta tesis queda condicionado a la aceptación de las condiciones de uso establecidas por la siguiente licencia Creative Commons: http://es.creativecommons.org/blog/licencias/ WARNING. The access to the contents of this doctoral thesis it is limited to the acceptance of the use conditions set by the following Creative Commons license: https://creativecommons.org/licenses/?lang=en Transposable element misregulation in Drosophila buzzatii–Drosophila koepferae interspecific hybrids Valèria Romero Soriano Departament de Genètica i Microbiologia Universitat Autònoma de Barcelona A thesis submitted for the degree of Doctor in Genetics (PhD) Director: Dr. Maria Pilar García Guerreiro June 2016 i ii Memòria presentada per la Llicenciada en Biotecnologia Valèria Romero Soriano per a optar al títol de Doctora en Genètica de la Universitat Autònoma de Barcelona. Valèria Romero Soriano Bellaterra, a 15 de juny de 2016 iii iv La Doctora María del Pilar García Guerreiro, Professora agregada del Departament de Genètica i Microbiologia de la Facultat de Biociències de la Universitat Autònoma de Barcelona, Certifica que Valèria Romero Soriano ha dut a terme sota la seva direcció el treball de recerca realitzat al Departament de Genètica i Microbiologia de la Facultat de Biociències de la Universitat Autònoma de Barcelona, que ha portat a l'elaboració d'aquesta Tesi Doctoral, titulada «Transposable element misregulation in Drosophila buzzatii–Drosophila koepferae interspecific hybrids». Per a que consti als efectes oportuns, signa el present certificat a Bellaterra, a 15 de juny del 2016. Maria del Pilar García Guerreiro v vi A tots aquells que no hi han pogut ser. Al somriures ja llunyans d’un Manel, i de l’altre (que de la foto era el més alt). A l’inoblidable Mercè, i a la meravellosa Pepita. vii viii Ens quedarem aquí baix. A tot estirar, cregui’m, ens espera l’improbable paradís del registre fòssil. Jesús Moncada (Calaveres atònites, 1999) ix x Contents Abstract ............................................................................................................................................xv Resum .............................................................................................................................................xvii 1 Introduction .............................................................................................................1 1.1 Interspecific hybridization ..........................................................................................................3 1.1.1 Natural hybridization and evolution ...........................................................................................3 1.1.2 Reproductive isolation ................................................................................................................5 1.1.2.1 Prezygotic barriers ...................................................................................................................5 1.1.2.2 Postzygotic barriers .................................................................................................................7 1.2 D. buzzatii and D. koepferae ......................................................................................................10 1.3 Transposable elements ...............................................................................................................13 1.3.1 History and classification .........................................................................................................13 1.3.1.1 Historical perspective ............................................................................................................13 1.3.1.2 Classification of TEs .............................................................................................................14 1.3.2 Interaction with host genome ...................................................................................................17 1.3.2.1 TE life cycle ...........................................................................................................................18 1.3.2.2 Harmful vs. evolutionary potential ........................................................................................21 1.3.2.3 Regulation of TEs ..................................................................................................................23 2 Objectives ...............................................................................................................31 3 Results .....................................................................................................................35 3.1 Genome size evaluation in D. buzzatii, D. koepferae and their hybrids.................................37 3.1.1 Drosophila females undergo genome expansion after interspecific hybridization ..................37 3.2 Expression of Helena in D. buzzatii, D. koepferae and their hybrids ....................................44 3.2.1 Expression of the retrotransposon Helena reveals a complex pattern of TE deregulation in Drosophila hybrids ............................................................................................................................44 3.3 Transcriptomic analysis of TE deregulation in D. buzzatii-D. koepferae hybrids ................67 3.3.1 Divergence in piRNA pathway effector proteins partially explains Drosophila buzzatii-D. xi koepferae hybrid instability ...............................................................................................................67 3.3.1.1 Abstract ..................................................................................................................................68 3.3.1.2 Introduction ...........................................................................................................................68 3.3.1.3 Results ...................................................................................................................................71 3.3.1.4 Discussion ..............................................................................................................................90 3.3.1.5 Conclusion and perspectives .................................................................................................95 3.3.1.6 Methods .................................................................................................................................96 3.3.1.7 Acknowledgements ..............................................................................................................100 4 Discussion .............................................................................................................103 4.1 On hybrid genome size increase..............................................................................................104 4.1.1 An evolutionary role for TEs in shaping hybrid genome size and structure ..........................104 4.1.2 Transposition events account for a sex-biased genome expansion..........................................105 4.1.3 TE mobilization occurs in F1 female gametes .......................................................................106 4.2 On Helena retrotransposon expression .................................................................................107 4.2.1 Hybridization effects on somatic expression are specific to each individual and depend on the studied TE ........................................................................................................................................107 4.2.2 Hybridization effects on gonads are sex-biased and TE-dependent .......................................107 4.3 On global TE deregulation ......................................................................................................110 4.3.1 TE deregulation is sex-biased and diminish across generations..............................................110 4.3.2 Several mechanisms are at the origin of TE deregulation ......................................................111 5 Conclusions ...........................................................................................................113 6 Bibliography .........................................................................................................117 7 Acknowledgements ..............................................................................................145 8 Annexes .................................................................................................................149 8.1 Supplementary data of “Drosophila females undergo genome expansion after interspecific hybridization” ..................................................................................................................................151 xii 8.2 Supplementary data of “Expression of the retrotransposon Helena reveals a complex pattern of TE deregulation in Drosophila hybrids” .........................................................................................158 8.3 Supplementary data of “Divergence in piRNA pathway effector proteins partially explains Drosophila buzzatii–D. koepferae hybrid instability” .....................................................................165 xiii Index of Figures Figure 1: Schematic representation of the described TE classification system..................................16 Figure