UNIVERSITA’ DEGLI STUDI DI TRIESTE XXV CICLO DEL DOTTORATO DI RICERCA IN BIOLOGIA AMBIENTALE ANALISI E GESTIONE INFORMATICA DI SEQUENZE TRASCRITTE IN ORGANISMI NON-MODELLO Settore scientifico-disciplinare BIO/18 DOTTORANDO GIANLUCA DE MORO RELATORE PROF. ALBERTO PALLAVICINI ANNO ACCADEMICO 2011/2012 INDICE INDICE ............................................................................................................................................... 2 INTRODUZIONE .............................................................................................................................. 5 Le tecnologie di sequenziamento di nuova generazione e la loro applicazione in ambito trascrittomico di organismi non-modello .................................................................................................. 5 Problematiche legate all'elaborazione di dati RNA-seq ........................................................................... 9 Software di assemblaggio e analisi ........................................................................................................... 10 PRODUZIONE SCIENTIFICA DEL CANDIDATO .................................................................. 17 Mytilus galloprovincialis ................................................................................................................... 20 RNA sequencing and de novo assembly of the digestive gland transcriptome in Mytilus galloprovincialis fed with toxinogenic and non-toxic strains of Alexandrium minutum ............ 24 Abstract ...................................................................................................................................................... 24 Introduction ............................................................................................................................................... 25 Results and Discussion .............................................................................................................................. 27 Conclusion .................................................................................................................................................. 33 Methods ...................................................................................................................................................... 34 Tables .......................................................................................................................................................... 39 Figures ........................................................................................................................................................ 44 References .................................................................................................................................................. 53 The C1q domain containing proteins of the Mediterranean mussel Mytilus galloprovincialis: A widespread and diverse family of immune-related molecules ..................................................... 61 Abstract ...................................................................................................................................................... 61 Introduction ............................................................................................................................................... 62 Materials and methods .............................................................................................................................. 63 Results ......................................................................................................................................................... 65 Discussion ................................................................................................................................................... 67 Conclusions ................................................................................................................................................ 70 Tables .......................................................................................................................................................... 71 Figures ........................................................................................................................................................ 75 References .................................................................................................................................................. 78 Big defensins and mytimacins, new AMP families of the Mediterranean mussel Mytilus galloprovincialis ................................................................................................................................ 81 Introduction ............................................................................................................................................... 82 Materials and methods .............................................................................................................................. 83 Results and discussion ............................................................................................................................... 85 Mytimacins ................................................................................................................................................. 87 2 Conclusions ................................................................................................................................................ 90 Tables .......................................................................................................................................................... 91 Figures ........................................................................................................................................................ 93 References ................................................................................................................................................ 100 How gene expression profiles disclose vital processes and immune responses in Mytiluss spp. .......................................................................................................................................................... 103 Abstract .................................................................................................................................................... 103 Introduction ............................................................................................................................................. 104 Concluding remarks ................................................................................................................................ 113 Acknowledgments .................................................................................................................................... 113 Figures ...................................................................................................................................................... 114 References ................................................................................................................................................ 120 Physiological and molecular responses of bivalves to toxic dinoflagellates .............................. 125 Abstract .................................................................................................................................................... 125 Introduction ............................................................................................................................................. 126 Conclusion ................................................................................................................................................ 140 Tables ........................................................................................................................................................ 141 Figures ...................................................................................................................................................... 144 References ................................................................................................................................................ 146 Latimeria menadoensis: .................................................................................................................. 156 Analysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis. ............. 159 Abstract .................................................................................................................................................... 159 Introduction ............................................................................................................................................. 160 Results ....................................................................................................................................................... 162 Discussion ................................................................................................................................................. 167 Conclusion ................................................................................................................................................ 173 Methods .................................................................................................................................................... 175 Figures 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