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UNIVERSITY of CALIFORNIA SAN DIEGO Comparative Genomics and Genome Mining Insights Into Natural Product Rich Marine Cyanobacter

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UNIVERSITY of CALIFORNIA SAN DIEGO Comparative Genomics and Genome Mining Insights Into Natural Product Rich Marine Cyanobacter UNIVERSITY OF CALIFORNIA SAN DIEGO Comparative Genomics and Genome Mining Insights into Natural Product Rich Marine Cyanobacteria A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Marine Biology by Tiago Ferreira Leao Committee in charge: William H. Gerwick, Chair Eric Allen, Co-chair Lena Gerwick, Co-chair Pieter Dorrestein Paul Jensen 2019 Copyright Tiago Ferreira Leao, 2019 All rights reserved SIGNATURE PAGE The dissertation of Tiago Ferreira Leao is approved, and it is acceptable in quality and form for publication on microfilm and electronically: Co-chair Co-chair Chair University of California San Diego 2019 iii DEDICATION This dissertation is dedicated to my incredible parents, Jorge Leao and Maria de Nazaré Ferreira, my beloved sister Camila and my inspiring brother Gabriel. iv EPIGRAPH “Education never ends It is a series of lessons with the greatest for the last.” – Sir Arthur Conan Doyle, His Last Bow “We are all smart. Distinguish yourself by being kind.” – Charles Gordon v TABLE OF CONTENTS SIGNATURE PAGE .......................................................................................................................... iii DEDICATION .................................................................................................................................. iv EPIGRAPH ....................................................................................................................................... v TABLE OF CONTENTS ..................................................................................................................... vi LIST OF ABBREVIATIONS .............................................................................................................. viii LIST OF FIGURES ............................................................................................................................. x LIST OF TABLES ............................................................................................................................. xii ACKNOWLEDGMENTS ................................................................................................................. xiii VITA .............................................................................................................................................. xv ABSTRACT OF THE DISSERATION ................................................................................................. xvii CHAPTER 1: IntroduCtion ................................................................................................................ 1 1.1. The importanCe of marine Cyanobacteria for ECoLogy and drug disCovery ....................................... 1 1.2. Overview of the genetiC diversity from Cyanobacteria ..................................................................... 4 1.3. Biosynthesis of CyanobaCtEriaL naturaL products .............................................................................. 6 1.4. TooL and strategies for analyzing biosynthesis of natural produCts ................................................ 11 1.5. Dissertation Contents ...................................................................................................................... 13 CHAPTER 2: A NovEL UnCuLturEd HeterotrophiC Bacterial AssoCiate of thE Cyanobacterium Moorea producens JHB ................................................................................................................ 16 2.1. Abstract ........................................................................................................................................... 16 2.2. IntroduCtion ..................................................................................................................................... 16 2.3. Methods .......................................................................................................................................... 19 2.3.1. Cyanobacterial CuLtures ............................................................................................................ 19 2.3.2. DNA extraction and sequenCing ............................................................................................... 20 2.3.3. AssembLy and other bioinformatiCs ......................................................................................... 20 2.3.4. 16S rRNA gene LoCation and analysis ....................................................................................... 22 2.3.5. CuLturing attempts of the assoCiatEd baCtEriaL Community from Moorea producEns JHB ...... 23 2.3.6. ElECtron miCrosCopy ................................................................................................................. 25 2.3.7. Semi-quantitativE PCR of DNA from washed and unwashed fiLamEnts ................................... 25 2.3.8. Examination for the presenCe of Mor1 in other CuLtures ......................................................... 26 2.3.9. Co-cuLturing of thE JHB strain with other CyanobaCtEria ......................................................... 26 2.3.10. ACCession number .................................................................................................................. 27 2.4. ResuLts and disCussion ..................................................................................................................... 27 2.4.1. Genome assembLy and annotation .......................................................................................... 27 2.4.2. RELative abundanCe and estimated Consortium Composition .................................................. 30 2.4.3. Efforts to CuLture Mor1 frEe of M. producens JHB ................................................................... 31 2.4.4. IndiCatives that Mor1 exists mainLy on the exterior of the M. producens JHB shEath ............. 32 2.4.5. Examination of the spECifiCity of Mor1 on Moorea spp. .......................................................... 33 2.4.6. Genome Comparison between M. producens JHB and Mor1 .................................................. 35 2.5. ACknowLedgement ........................................................................................................................... 41 vi CHAPTER 3: ComparativE gEnomiCs unCovErs thE proLifiC and distinCtivE mEtaboLiC potential of thE Cyanobacterial gEnus Moorea ................................................................................................ 42 3.1. Abstract ........................................................................................................................................... 42 3.2. IntroduCtion ..................................................................................................................................... 43 3.3. Methods .......................................................................................................................................... 44 3.3.1. SampLing, CuLturing, miCrosCopy and previous sequenCing efforts .......................................... 44 3.3.2. DNA extraction, PacBio sequenCing of M. producens PAL and de novo assembLy ................... 45 3.3.4. Comparative genomiCs ............................................................................................................. 47 3.3.5. PhyLogenomiCs ......................................................................................................................... 47 3.3.6. BiosynthetiC gene CLusters ........................................................................................................ 48 3.4. ResuLts and disCussion ..................................................................................................................... 49 3.4.1. GeographiCal, morphoLogiCal and ChemiCal features of four fiLamentous marine Cyanobacteria ............................................................................................................................................................ 49 3.4.2. The Use of Hybrid AssembLy and Long Reads ScaffoLding to Obtain the First CompLete GenomE of TropiCaL FiLamEntous CyanobaCtErium ............................................................................ 51 3.4.3. Genome Comparison Among Moorea Strains Reveals SignifiCant Synteny ............................. 53 3.4.4. The EvoLved Loss of Nitrogen Fixation in the Genus Moorea? ................................................. 55 3.4.5. UnCovering the MetaboLiC Potential of the Genus Moorea ..................................................... 57 3.5. ACknowLedgements ......................................................................................................................... 61 3.6. Appendix ......................................................................................................................................... 62 CHAPTER 4: GEnomiC insights into an ExpandEd divErsity of fiLamEntous marinE Cyanobacteria rEvEals thE Extraordinary biosynthEtiC potential of Moorea and Okeania .................................. 65 4.1. Abstract ........................................................................................................................................... 65 4.2. IntroduCtion ..................................................................................................................................... 66 4.3 Methods ........................................................................................................................................... 67 4.3.1 CoLLECtion, DNA extraction
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