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Acari Genomics: from Phylogenetics to Agricultural Applications Cover_Wannes_def.pdf 1 7/05/13 09:03 Acari genomics: from phylogenetics to agricultural applications agricultural to phylogenetics genomics: from Acari Acari genomics: from phylogenetics to agricultural applications C M Y CM MY CY Ir. Wannes Dermauw CMY K W annes Dermauw ISBN 978-9-0598960-8-6 2013 9 789059 896086 FACULTEIT BIO-INGENIEURSWETENSCHAPPEN Man is certainly crazy. He could not make a mite, and he makes gods by the dozen. (Michel de Montaigne 1533-1592) It only takes five minutes… (Thomas Van Leeuwen) Promoters: Prof. dr. ir. Luc Tirry Department of Crop Protection Faculty of Bioscience Engineering Ghent University Dr. ir. Thomas Van Leeuwen Department of Crop Protection Faculty of Bioscience Engineering Ghent University Dean: Prof. dr. ir. Guido Van Huylenbroeck Rector: Prof. dr. Paul Van Cauwenberge ACARI GENOMICS: FROM PHYLOGENETICS TO AGRICULTURAL APPLICATIONS ir. Wannes Dermauw Thesis submitted in fulfillment of the requirements for the degree of Doctor (PhD) in Applied Biological Sciences Dutch translation of the title of this PhD: Acari genomica: van fylogenetische analyses tot toepassingen in de landbouw To refer to this thesis: Dermauw W (2013). Acari genomics: from phylogenetics to agricultural applications. PhD thesis. Ghent University, Ghent, Belgium. ISBN-number: 978-90-5989-608-6 Front cover: top: ESEM photograph of the front part of the two-spotted spider mite, Tetranychus urticae (© Wannes Dermauw); bottom: ESEM photograph of the European house dust mite Dermatophagoides pteronyssinus (© David McCarthy); middle: DNA-helix structure. Back cover: top left corner: SEM photograph of the predatory mite Phytoseiulus persimilis (© David Evans Walter) The author and the promoters give the authorization to consult and to copy parts of this work for personal use only. Every other use is subject to copyright laws. Permission to reproduce any material contained in this work should be obtained from the author. The promoters, The author Prof. Dr. ir. Luc Tirry Dr. ir. Thomas Van Leeuwen ir. Wannes Dermauw Members of the examination committee Prof. dr. ir. Luc Tirry Laboratory of Agrozoology Department of Crop Protection Ghent University Dr. ir. Thomas Van Leeuwen Laboratory of Agrozoology Department of Crop Protection Ghent University Prof. dr. ir. Kris Verheyen Forest & Nature Lab Department of Forest and Water Management Ghent University Prof. dr. Lieve Gheysen Laboratory of Applied Molecular Genetics Department of Molecular Biotechnology Ghent University Prof. dr. ir. Tim De Meyer Department of Mathematical Modelling, Statistics and Bioinformatics Ghent University Prof. dr. John Vontas Laboratory of Molecular Entomology Department of Biology University of Crete, Greece Dr. René Feyereisen INRA - CNRS- Université Nice Sophia Antipolis Centre de Recherches de Sophia Antipolis, France VOOR/DANKWOORD “Je kan toch niet de rest van je leven parkeerlijnen blijven schilderen” zei mijn moeder in de zomer van 2006. Ze had ergens wel een punt. Na wat opzoekwerk viel mijn oog op een vacature bij het labo Agrozoölogie van professor Luc Tirry. De leuke herinneringen van mijn thesis in dit labo in gedachten, solliciteerde ik er voor de functie van assistent dierkunde. Ik kreeg de job en begon aan een nieuw avontuur. Ondertussen naderen we de zomer van 2013 en een heuse doctoraatsthesis ligt voor jullie neus. Geen thesis echter zonder resultaten. Elke doctoraatsstudent weet dat het behalen van dat laatste niet altijd evident is, maar een goede begeleiding kan wonderen doen. Luc, en Thomas, zonder jullie was dit doctoraat er nooit gekomen. Luc, bedankt dat je me de kans gaf om een doctoraat te beginnen en steeds bereid was om mij met raad en daad, op eender welk vlak, bij te staan. Was het niet wat betreft de determinatie van een kever van het genus Cetonia (of was het Netocia ?) in een pak diepvries broccoli dan wel met hoe je een goede presentatie moet opbouwen. Thomas, waar zal ik beginnen? Je niet aflatende enthousiasme voor wetenschap werkte heel stimulerend. Weinig wetenschappelijke (en levensbeschouwelijke) vragen bleven bij jou onbeantwoord, maar dan wel liefst na een goede nachtrust, een Gauloise en, niet te vergeten, een blik cola ;-). Via jouw contacten kon ik ook 3 maanden ervaring opdoen in een labo in Kreta, een unieke belevenis die ik mij nog lang zal herinneren. Voor dit alles en nog veel meer, oprecht bedankt. Je zal het ongetwijfeld (rookvrij?) uitstekend doen in Amsterdam! In Kreta heb ik drie onvergetelijke maanden beleefd, zowel in het labo als daarbuiten. John, Evangelia en Aris, bedankt voor jullie fantastische gasthvrijheid. Ας ελπίσουμε ότι, θα συναντηθούν σύντομα στην Κρήτη. Maar ook in het labo aan de Coupure was het fijn vertoeven. In het bureau van de assistenten, eerst samen met Bjorn en Steven, daarna met Jochem en Astrid. Mijn oprechte excuses als mijn koffie soms iets te lang stond te beschimmelen of als ik de deur weeral vergeten te sluiten was! Jochem en Astrid, het verschuiven van bureaus kan nu eindelijk beginnen ;-). Onder het motto “afzien in groep is leuker dan alleen”, ben ik ook veel dank verschuldigd aan mijn collega’s van de mijtenclub. Pieter, Jahangir, Peter, Nicky, Astrid, Wim, Arash en Sabina, zonder jullie was het اب :mijtenonderzoek maar een eenzame aangelegenheid geweest! Speciaal voor Jahangir رد دوخ ﻩداعلا قوف ﯼزاون نامﻩم ﯼارب امش زا رﮎشت اب.نانوﯼ رد نم ﻩوﻩق تخاس ﯼارب امش زا رﮎشت .نات ﻩداوناخ و امش ﯼارب اﻩوزرﺁ نﯼرتﻩب اب.تسا نارﯼا Ook personen buiten de “Acarology crew” hebben mij goed geholpen. Bedankt Bartel Vanholme om mij in mijn eerste doctoraatsjaren wegwijs te maken in de wereld van de moleculaire biotechnologie en de bioinformatica (en om je bench met ons labo te delen ;-)). Joachim Jacob, je Southern blot (en Corel Draw) skills zijn mij heel goed van pas gekomen tijdens mijn doctoraat! Thijs, merci om tot vervelens toe competente cellen te gaan halen en voor je goede vinyl- en metseltips. Nick en Maarten, zonder jullie geen leuke labo-uistapjes! Rik, Leen en Didier, zonder jullie technische en administratieve hulp zou mijn doctoraat niet zo vlot verlopen zijn, bedankt! Aan de leden van mijn PhD-commissie: John, thank you very much for the excellent feedback and cooperation. René, from now on the Fifth of Beethoven will always sound different to me. Your help was indispensable for the success of my PhD. Bedankt ook aan Prof. Verheyen, Prof. Gheysen en Prof. De Meyer voor de positieve commentaar en het nauwkeurig nalezen van mijn doctoraat. In die zeven jaar was er natuurlijk ook een leven buiten de wetenschap. Wat zou een mens doen zonder zijn vrienden? Jullie zorgden voor de ideale afleiding tijdens mijn doctoraat! Ondertussen zijn de meeste van jullie vanuit Gent uitgezwermd naar Brussel, Kortrijk, Oostakker of zelfs London. Na mijn doctoraat moeten we er dringend werk van maken om elkaar eens meer te zien! Beloofd! Ook mijn ouders waren essentieel in het slagen van mijn doctoraat. Ze boden mij de kans om te studeren en steunden mij in alles wat ik deed. Vake, geef toe, mijtendokter klinkt ook niet slecht ;-). Daarnaast mag ik natuurlijk mijn twee zusjes, Liselotte en Annelore, niet vergeten. Jullie zijn er in geslaagd om allebei een goede man te pakken te krijgen, en zorgden dat ik twee neefjes en twee nichtjes erbij kreeg. Bruna en Oskar, ik ben trots om jullie peter te zijn. Ondertussen is er tijdens mijn doctoraat ook een hele schoonfamilie bijgekomen en ook op dat vlak heb ik het getroffen. Patrik en Ann, jullie gastvrijheid zowel in Kortrijk als in Lissoir zijn ongeëvenaard! Lieve Nathalie, natuurlijk wordt de laatste paragraaf van dit dankwoord aan jou opgedragen. Eindelijk trekken we er samen weer op uit voor een groot reisavontuur. Reeds zes jaar samen, reeds zes jaar een feest met jou. Jouw optimisme en niet aflatende energie hielpen mij door die laatste moeilijke doctoraatsmaanden. Bedankt voor alles! Wannes, mei 2013 Table of contents List of abbreviations v Scope vii Chapter I – Introduction to Acari Genomics 1 1 Acari 3 1.1 Classification 3 1.2 Acari of agricultural and medical importance: a brief survey 7 2 Acari genomics 9 2.1 Introduction 9 2.2 Arthropod genomics 10 2.2.1 Arthropod mitochondrial genomes 10 2.2.2 Arthropod nuclear genomes 13 2.2.3 Arthropod transcriptomes 16 2.3 Acari genomics 17 2.3.1 Acari mitochondrial genomes 17 2.3.1 Acari nuclear genomes 20 2.3.1 Acari transcriptomes 22 3 From Acari genomes to Acari biology 24 3.1 Phylogenetics 24 3.1.1 Mitochondrial genomes 24 3.1.2 Nuclear genomes 25 3.2 Comparative genomics 26 3.3 Post-genomics 27 3.3.1 Transcriptomics 27 3.3.2 Proteomics 29 3.3.3 RNA interference 30 3.3.4 DNA methylation 31 4 Applied Acari genomics 33 4.1 Acari and pest management 33 4.1.1 Resistance research 33 4.1.2 Exploiting mite-plant and tick-host-pathogen interactions 35 4.1.3 RNAi to control Acari pests? 36 4.2 Industrial and medical applications of Acari molecules? 37 Chapter II - The complete mitochondrial genome of the house dust mite Dermatophagoides pteronyssinus (Trouessart): a novel gene arrangement among arthropods 39 1 Introduction 41 2 Materials and methods 43 2.1 Mite identification 43 i 2.2 Mite strain, mass rearing and isolation 43 2.3 DNA extraction 43 2.4 PCR 44 2.5 Amplification of the mt genome 44 2.6 Annotation and bioinformatics analysis 45 2.7 Construction of secondary structures of RNAs and non-coding regions 46 2.8 Multiply-primed rolling circle amplification (RCA) and restriction enzyme digestion 46 2.9 Phylogenetic analysis 47 3 Results and discussion 49 3.1 Genome organisation 49 3.2 Base composition and codon usage 54 3.3 Protein coding genes 57 3.4 Transfer RNAs 58 3.5 Non-coding regions 62 3.6 Ribosomal RNAs 63 3.7 Phylogenetic analysis 67 4 Conclusions 71 Chapter III - Mitochondrial genome analysis of the predatory mite Phytoseiulus persimilis and a revisit of the Metaseiulus occidentalis mitochondrial genome 73 1 Introduction 75 2 Materials and methods 77 2.1 Specimen sampling, DNA extraction and PCR 77 2.2 Amplification strategy of the mt genome of P.
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