Verfügbarkeit: Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics

Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics: = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik

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Bibliographische Detailangaben
1. Verfasser:	Slaby, Beate (VerfasserIn)
Format:	Abschlussarbeit Buch
Sprache:	English
Veröffentlicht:	Würzburg March 2017
Schlagworte:	Metagenom Aplysina aerophoba Mikroorganismus metagenomics single-cell genomics sponge microbiome differential coverage binning PacBio sequencing Illumina HiSeq hybrid assembly Hochschulschrift
Online-Zugang:	Volltext Volltext Inhaltsverzeichnis
Beschreibung:	xiii, 131 Blätter Illustrationen CD-ROM (12 cm): Appendix
Format:	Langzeitarchivierung gewährleistet, LZA

Internformat

MARC


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Datensatz im Suchindex

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adam_text	TABLE OF CONTENTS AFFIDAVIT......................................................................................................................... ILL ACKNOWLEDGEMENTS................................................................................................ IV TABLE OF CONTENTS......................................................................................................V LIST OF FIGURES............................................................................................................VII LIST OF TABLES............................................................................................................... IX SUMMARY............................................................................................................................X ZUSAMMENFASSUNG................................................................................................... XII 1 INTRODUCTION.........................................................................................................14 1.1 SPONGES (PHYLUM PORIFERA)...................................................................................14 1.2 SPONGE-MICROBE SYMBIOSIS...................................................................................17 1.2.1 MICROBIAL DIVERSITY..........................................................................................17 1.2.2 MICROBIAL FUNCTION...........................................................................................18 1.3 APLYSINA AEROPHOBA................................................................................................19 1.3.1 GEOGRAPHIC DISTRIBUTION AND PHYSICAL PROPERTIES.............................................19 1.3.2 THE A. AEROPHOBA MICROBIOME ...................................................................... 20 1.4 SEQUENCE-BASED ANALYSES OF MICROBIOMES .......................................................... 21 1.4.1 RECENT DEVELOPMENTS IN SEQUENCING TECHNOLOGIES..........................................22 1.4.2 WHY SHORT-READS FALL SHORT...............................................................................24 1.4.3 LONG-READ SEQUENCING IN METAGENOMICS ........................................................ 24 2 MATERIAL AND METHODS................................................................................... 26 2.1 RESEARCH QUESTIONS AND AIM S.............................................................................. 26 2.2 SPONGE COLLECTION AND ENRICHMENT OF PROKARYOTIC CELLS .................................... 27 2.3 SEQUENCING AND ANALYSIS OF CYANOBACTERIAL SPONGE SYMBIONTS ......................... 28 2.3.1 LABORATORY METHODS: FROM SAMPLE TO SEQUENCE ............................ 28 2.3.2 BIOINFORMATIC METHODS: FROM SEQUENCING READS TO GENOME COMPARISON ..... 30 2.4 DEVELOPMENT OF A HYBRID ASSEMBLY PIPELINE FOR PACBIO LONG-READS AND ILLUMINA SHORT-READS........................................................................................................ 32 2.4.1 SIMULATING SEQUENCING READS FOR A TEST DATASET ........ . ................... 32 2.4.2 TESTING ASSEMBLERS AND SETTINGS . ....... 33 2.4.3 COMPARING AND EVALUATING OF ASSEMBLIES AND BINS............... 34 2.5 APYLSINA AEROPHOBA METAGENOMICS..................................................................... 36 2.5.1 LABORATORY METHODS: DNAE EXTRACTION AND SEQUENCING.......................... 36 2.5.2 BIOINFORMATIC METHODS: FROM ASSEMBLY TO ANNOTATION ............ . ............. 36 2.5.3 STATISTICAL ANALYSIS: COMPARISON TO REFERENCES AND WITHIN SYMBIONTS ............ 37 3 RESULTS......................................................................................................................40 3.1 ASSESSING THE GENOME OF THE CA. SYNECHOCOCCUS SPONGIARUM GROUP ........... 40 3.1.1 ASSESSMENT OF CLADE F GENOMES FROM A. AEROPHOBA ..................................... 40 3.1.2 COMPARISON WITHIN THE CA. SYNECHOCOCCUS SPONGIARUM GROUP AND TO FREE- LIVING REFERENCES............................................................................................................. 44 3.2 PACBIO-ILLUMINA HYBRID ASSEMBLY PIPELINE DEVELOPMENT ................................. 63 3.2.1 STATISTICS OF THE TESTED ASSEMBLY STRATEGIES ..................................................... 63 3.2.2 COMPARISON BACK TO ORIGINAL REFERENCE GENOMES ........................................... 64 3.2.3 REFERENCE-INDEPENDENT BINNING ..................................................................... 65 3.3 BINNING 37 SYMBIONT GENOMES FROM THE METAGENOME OF A. AEROPHOBA ........... 68 3.3.1 ASSESSMENT OF METAGENOMIC DNA EXTRACTION AND SEQUENCING ...................... 68 3.3.2 COMPARISON OF ILLUMINA-ONLY AND PACBIO-ILLUMINA HYBRID ASSEMBLIES ........ 69 3.3.3 BACTERIAL GENOMES BINNED FROM HYBRID ASSEMBLY .......................................... 72 3.3.4 SYMBIONT-REFERENCE COMPARISON .................................................................... 78 3.3.5 WITHIN-SYMBIONT COMPARISON ......................................................................... 84 4 DISCUSSION............................................................................................................... 88 4.1 CO. SYNECHOCOCCUS SPONGIARUM GROUP - CLOSELY RELATED BUT DIFFERENT IN GENE CONTENT............................................................................................................................... 88 4.1.1 AN OPTIMAL CANDIDATE FOR MINI-METAGENOMICS ............................................ 88 4.1.2 LIFESTYLE EVOLUTION IN CYANOBACTERIAL SYMBIONTS OF SPONGES .......................... 89 4.2 PACBIO-ILLUMINA HYBRID ASSEMBLY PIPELINE DEVELOPMENT ................................. 97 4.3 METAGENOMIC BINS FROM THE MICROBIOME OF A. AEROPHOBA REVEAL UNITY IN DEFENSE BUT METABOLIC SPECIALIZATION .............................................................................. 98 4.3.1 BREAKING NEW GROUND IN ASSEMBLY STRATEGY AND CHOICE OF REFERENCES ............ 98 4.3.2 UNITY IN DEFENSE............................................................................................. 99 4.3.3 METABOLIC SPECIALIZATION...............................................................................100 4.3.4 CONCLUSIONS...................................................................................................100 4.4 GENERAL CONCLUSIONS AND FUTURE DIRECTIONS.......................................................101 5 BIBLIOGRAPHY___________________________________________________ 107 6 APPENDIX ________________________________________________________ 128 7 PUBLICATIONS LIST ______________________________________________ 129 8 CURRICULUM VITAE ______________________________________________ 130
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author	Slaby, Beate
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spelling	Slaby, Beate Verfasser (DE-588)108842354X aut Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik Würzburg March 2017 xiii, 131 Blätter Illustrationen CD-ROM (12 cm): Appendix txt rdacontent n rdamedia nc rdacarrier Dissertation Julius-Maximilians-Universität Würzburg 2017 Langzeitarchivierung gewährleistet, LZA Zusammenfassung in deutscher und englischer Sprache Metagenom (DE-588)7635820-3 gnd rswk-swf Aplysina aerophoba (DE-588)4778447-7 gnd rswk-swf Mikroorganismus (DE-588)4039226-0 gnd rswk-swf metagenomics single-cell genomics sponge microbiome differential coverage binning PacBio sequencing Illumina HiSeq hybrid assembly (DE-588)4113937-9 Hochschulschrift gnd-content Aplysina aerophoba (DE-588)4778447-7 s Mikroorganismus (DE-588)4039226-0 s Metagenom (DE-588)7635820-3 s DE-604 Erscheint auch als Online-Ausgabe, PDF urn:nbn:de:bvb:20-opus-151869 https://nbn-resolving.org/urn:nbn:de:bvb:20-opus-151869 Resolving-System kostenfrei Volltext http://d-nb.info/1137836040/34 Langzeitarchivierung Nationalbibliothek kostenfrei Volltext DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=029857615&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis
spellingShingle	Slaby, Beate Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik Metagenom (DE-588)7635820-3 gnd Aplysina aerophoba (DE-588)4778447-7 gnd Mikroorganismus (DE-588)4039226-0 gnd
subject_GND	(DE-588)7635820-3 (DE-588)4778447-7 (DE-588)4039226-0 (DE-588)4113937-9
title	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik
title_alt	Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik
title_auth	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik
title_exact_search	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik
title_full	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München
title_fullStr	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München
title_full_unstemmed	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics = Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik submitted by Beate Magdalena Slaby from München
title_short	Exploring the microbiome of the Mediterranean sponge Aplysina aerophoba by single-cell and metagenomics
title_sort	exploring the microbiome of the mediterranean sponge aplysina aerophoba by single cell and metagenomics untersuchungen am mikrobiom des mittelmeerschwamms aplysina aerophoba mittels einzelzell und metagenomik
title_sub	= Untersuchungen am Mikrobiom des Mittelmeerschwamms Aplysina aerophoba mittels Einzelzell- und Metagenomik
topic	Metagenom (DE-588)7635820-3 gnd Aplysina aerophoba (DE-588)4778447-7 gnd Mikroorganismus (DE-588)4039226-0 gnd
topic_facet	Metagenom Aplysina aerophoba Mikroorganismus Hochschulschrift
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