Transcriptomics of coral-algal interactions

296 Pages·2017·4.88 MB·English

by  Amin Roushdy Mohamed

ResearchOnline@JCU

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Mohamed, Amin Roushdy (2016) Transcriptomics of
coral-algal interactions: novel insights into the
establishment of symbiosis. PhD thesis, James Cook
University.

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Transcriptomics of coral-algal interactions: novel insights into
the establishment of symbiosis

A Doctoral Thesis
Submitted by

Amin Roushdy Mohamed
BSc, Zoology and MSc, Marine Biology
July 2016

For the degree of Doctor of Philosophy (PhD)
Biochemistry and Marine Biology

ARC Centre of Excellence for Coral Reef Studies,
Department of Molecular and Cell Biology,
James Cook University
and
Australian Institute of Marine Science
Townsville, Queensland, Australia

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I dedicate this work to the soul of my mother, Nahed O. El-Sawwaf,
You were and will always be in my heart !

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ACKNOWLEDGEMENTS

Well, it has been a very long journey to get to this point. It gave me the
opportunity to meet many amazing people and work/visit many amazing places around
the globe. Despite being very heart broken to lose the most beloved person (my mother)
during my studies, there were many ups; I really enjoyed the Aussie life style and the
huge experience I gained is priceless.
First and for the most, I feel deeply indebted to Allah, the Lord of the world, the
most merciful and the most gracious for assisting and providing me with power and
patience to complete this work. A huge thank you goes to my beloved wife Marwa and
my little angels Hanin and Habiba. Marwa, thank you so much for being with me. You
really sacrificed for me, thank you for love, support and every thing. I also really want to
express my gratitude to my dear father (Roushdy Esmail) for being very supportive in all
aspects of my life especially financially, every time I had any difficulty you were there
and very generous.
I would like to give a big thank you to my supervisory team; Professor David
Miller, Professor Bette Willis, Dr David Bourne and Dr Vivian Cumbo. Actually, I was
very lucky to work with experts in the fileds of coral reef genomics and/or ecology during
my studies at James Cook University. David M, I would like to express my deep gratitude
to you for accepting me in your lab in the first place. It would take many pages to
acknowledge you enough, as you always do when you write recommendation letters for
me. I really appreciate that you took the risk of having a PhD student with no prior
experience in molecular genetics. It was my dream to do my PhD research in ecological
genomics in Australia and your work really inspired me to become a molecular ecologist.
Thank you so much for being supportive in many aspects of my life, not only in research.
Finally a big thank you for your advice regarding the future and supporting me during my
applications for postdoc fellowships/positions. Bette, it was a pleasure to be one of your
students. I really enjoyed and learnt a lot during our discussions. Thank you so much for
your encouragement, support and help. Thank you so much for inviting my family to your
house, we were very delighted to visit you and meet with your husband. David B, I really
enjoyed working with you. Thank you so much for being my supervisor. I would never
forget the opportunities that I had through your involvement in my work, access to
research facilities at AIMS and scholarships/awards from AIMS@JCU. I really appreciate
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your help and support during conducting experiments at the CMMG lab in AIMS during
GBR spawning in 2014. Vivian, it was a pleasure to work with you during my PhD. I
obtained great benefit from your great experience about Symbiodinium, Chromera and
coral-algal symbioses. I really enjoyed our field trip to Okinawa and learnt a lot from you
about coral spawning and infection experiments. Thank you so much for being there when
I needed to discuss with you my results.
I was very lucky again to have training on next-gen sequencing analysis with
Professor Mark Ragan group and Dr Cheong Xin Chan (CX) at the Institute of Molecular
Bioscience (IMB), the University of Queensland. Mark, it was a pleasure to be with your
group for few weeks to learn basics of bioinformatics. Thank you so much for allowing
me to come and visit your group and for being very welcoming and generous. I really
appreciate your support in my postdoc applications, despite the short time I spent with
your group. A big thank you CX, I was very lucky to meet and work closely with you. My
bioinformatics skills were suddenly very good after few days working with you. Thank
you so much for your help and patience during my visit at IMB. You really showed me
how to think as a bioinformatician, not as a biologist. Those few weeks were a real
turning point in my PhD research.
During my PhD I was lucky enough to be funded from different bodies. I’d like to
deeply thank the mission department of the Egyptian Ministry of Higher Education,
James Cook University and AIMS@JCU for their financial support during my studies in
Townsville. Also it doesn't go without saying thank you to many people for their help
during filed work among them: Chuya Shinzato, Saki Harri and Joana Figueiredo during
field work in Sesokok station; David Abrego, Allison Paley, Margaux Hein during coral
sampling at Heron Island Research Station (HIRS); Mei fang Lin and Chao-yang Kuo
during coral sampling at Orpheus Island Research Station (ORIS); SeaSim staff at AIMS
during GBR spawning in 2014. Finally, I would like to thank all the members of the
David Miller’s lab during 2012/16, especially Bruno Lapeyre and Sussanne Sprungala for
their help during my first days in the DM lab and teaching me basic molecular biology
techniques.

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STATEMENT OF THE CONTRIBUTION OF OTHERS

A supervisory committee consisted of Professor David Miller and Professor Bette Willis
James Cook University and Dr David Bourne from the Australian Institute of Marine
Science provided intellectual and editorial support.

The research work in the thesis was conducted with collaboration with other research
scientists in different institutions. I was responsible for designing and conducting
experiments, data generation/analyses and writing the thesis. Dr Vivian Cumbo provided
guidance in designing and conducting experiments in Chapters 2 and 3. She also allowed
access to Chromera cultures used to construct the Chromera de novo transcriptome in
Chapter 4. Prof Dee Carter provided culture of Chromera used in Chapter 3. Dr Saki
Harri provided the Symbiodinium culture used for infection experiment in Chapter 2 and
provided laboratory facilities at the Sesoko Island marine station during Acropora
digitifera spawning event in June/July 2013. Prof Nori Satoh and Dr Chuya Shinzato at
the Okinawa Institute of Marine Science (OIST) in Okinawa, Japan provided reagents for
RNA isolation and illumina RNA-Seq libraries preparations and illumina HiSeq
sequencing in Chapters 2 and 3. Prof Mark Ragan and Dr Chenog X Chan at the Institute
of Molecular Bioscience (IMB) of the University of Queensland (UQ) provided guidance
for the bioinformatics analysis required in the thesis specially Chapter 4.

Primary research funding was provided through an Australian Research Council Grant to
Prof David Miller. I was supported with a 4-year PhD scholarship from the Egyptian
Ministry of Higher Education and Research. I was also supported by a James Cook
University Postgraduate Research Scholarship (JCUPRS) and under the joint venture
between the Australian Institute of Marine Science and James Cook University
AIMS@JCU.

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Table of contents

TABLE OF CONTENTS i
LIST OF FIGURES vi
LIST OF TABLES xiii
THESIS ABSTRACT 1

CHAPTER 1 BACKGROUNG AND GENERAL INTRODUCTION 3
1.1 Background on coral biology and the coral holobiont 4
1.2 The coral-Symbiodinium symbiosis and its significance 5
1.3 Coral-associated apicomplexan-related lineages 7
1.4 Coral-Chromerida associations 9
1.5 Coral-Chromera symbiosis 10
1.6 Chromera as a proxy for Plasmodium 14
1.7 Coral reef ecological genomics 14
1.8 RNA-Seq approach to study coral reef biology 18
1.9 Aims, objectives and thesis structure 19
1.10 References 21

CHAPTER 2 UNRAVELLING THE MOLECULAR MECHANISMS 27
UDERLYING ESTABLISHMENT OF CORAL-
SYMBIODINIUM SYMBIOSIS USING RNA-SEQ
2.1 ABSTRACT 28
2.2 INTRODUCTION 28
2.3 MATERIAL AND METHODS 32
2.3.1 Coral larvae 32
2.3.2 Symbiodinium culture 33
2.3.3 Symbiodinium acquisition experimental design 33
2.3.4 Larval sampling and RNA isolation 34
2.3.5 High-throughput sequencing Illumina RNA-Seq 34
2.3.6 RNA-Seq data analysis 34
2.3.6.1 Reads quality check and reference mapping 34
2.3.6.2 Differential gene expression analysis 35
2.3.6.3 Hierarchical clustering analysis 35
2.3.6.4 Functional annotations and gene ontology (GO) enrichment analyses 36
2.4 RESULTS 37
2.4.1 General results and overall transcriptome changes 37
2.4.2 Differential gene expression analysis 42
2.4.3 Gene Ontology (GO) enrichment analysis 45
2.4.4 GO enrichment analysis reveals suppression of ribosome, Endoplasmic 45
Reticulum and mitochondria functions
2.4.5 Focus on symbiosis-related coral genes 51
2.4.5.1 The coral host might recognize symbionts via MAMP-PRR 51
interactions
2.4.5.2 Role of cell adhesion proteins during recognition 52
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2.4.5.3 Genes involved in vesicular trafficking likely used in symbiosome 54
formation
2.4.5.4 Transcription factors and epigenetic tags for silencing were affected 56
2.4.5.5 Genes involved in regulating the host cell cycle during symbiosis
establishment 57
2.4.5.6 Immune-related genes are suppressed during onset of coral-
Symbiodinium symbiosis 59
2.4.5.7 Establishment of symbiosis alters expression of genes involved in
host apoptosis 60
2.4.5.8 Genes involved in host response to reactive oxygen species
(ROS), inflammation and stress 61
2.5 DISCUSSION 65
2.5.1 The coral host transcriptome showed rapid and transient changes upon 65
symbiosis onset
2.5.2 Metabolic suppression during coral and Symbiodinium initial 66
interactions
2.5.3 PRR-MAMP signaling is used to recognize competent 67
Symbiodinium during infection
2.5.4 Role of cell adhesion genes during symbiosis establishment 68
2.5.5 The symbiosome is formed as a result of arresting phagosomal 69
maturation
2.5.6 Regulation of the host cell cycle during symbiont tolerance 71
2.5.7 Regulation of the host apoptotic repertoire during symbiont tolerance 72
2.5.8 Suppression of host immunity during onset of symbiosis 73
2.5.9 Responses to stress and ROS during symbiont tolerance 74
2.5.10 Conclusion 75
2.6 REFERENCES 75

CHAPTER 3 DECIPHERING THE NATURE OF THE CORAL- 81
CHROMERA ASSOCIATION VIA NEXT GENERATION
SEQUENCING
3.1 ABSTRACT 82
3.2 INTRODUCTION 82
3.3 MATERIALS AND METHODS 84
3.3.1 Chromera velia culture 84
3.3.2 Coral larvae and Chromera infection experiment 85
3.3.3 Larval sampling and RNA isolation 85
3.3.4 High-throughput next generation sequencing 85
3.3.5 RNA-Seq data analysis 85
3.3.5.1 Reads quality check and reference mapping 85
3.3.5.2 Differential gene expression analysis 86
3.3.5.3 Hierarchical clustering analysis 86
3.3.3.5.4 Functional annotations, gene ontology (GO) and KEGG pathway 86
enrichment analyses 86
3.4 RESULTS 87
3.4.1 General results and overall transcriptome changes 87
3.4.2 Differential gene expression analysis 92
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3.4.3 Functional profiles 96
3.4.4 GO enrichment in the late response to Chromera 99
3.4.5 Focus on genes involved in host-microbe interactions 105
3.4.5.1 Coral immune response against Chromera 107
3.4.5.2 Genes involved in phagocytosis and the host endocytic pathway, an in 112
particular phagosome maturation, were affected
3.4.5.3 Genes involved in host apoptosis were affected 117
3.5 DISCUSSION 121
3.5.1 Coral responses common to Chromera and Symbiodinium infection 122
3.5.2 The late response of coral to Chromera infection 122
3.5.3 Suppression of the host immune response during Chromera infection 123
3.5.4 Modulation of the endocytic pathway and phagosome maturation in the 124
coral host response to Chromera infection
3.5.5 Apoptosis as a double-edged sword for both coral host and Chromera 126
survival
3.5.6 Conclusion 127
3.6 REFERENCES 128

CHAPTER 4 CHROMERA TRANSCRIPTOMICS: A FUNCTIONAL 132
GENOMIC RESOURCE FOR A CHROMERID ALGA
ISOLATED FROM THE GREAT BARRIER REEF AND
COMPARATIVE TRANSCRIPTOMIC ANALYSES WITH
PARASITIC AND PHOTOSYNTHETIC RELATIVES
4.1 ABSTRACT 133
4.2 INTRODUCTION 134
4.3 MATERIAL AND METHODS 135
4.3.1 Chromera velia culture 135
4.3.2 Chromera culturing conditions for transcriptome construction 135
4.3.3 RNA isolation and high-throughput next generation sequencing 136
4.3.4 RNA-Seq data quality control, processing and quality filtering 137
4.3.5 Transcriptome de novo assembly using the TRINITY software 137
4.3.6 Assessing the quality of the de novo assembly 138
4.3.7 Transcriptome functional annotations 138
4.3.7.1 Gene Ontology (GO) terms 138
4.3.7.2 KEGG pathways 139
4.3.8 Chromera strains comparative transcriptome analysis 140
4.3.8.1 Identification of the orthologous genes between two Chromera strains 140
4.3.8.2 Chromera orthologs functional profile 141
4.3.8.3 Estimation of substitution rates between Chromera strains 141
4.3.9 Chromera, Symbiodinium and Plasmodium comparative transcriptome 142
analyses
4.3.9.1 Symbiodinium and Plasmodium sequences and functional 142
annotation
4.3.9.2 GO enrichment and KEGG pathways analyses based on shared 142
genes
4.4 RESULTS 143
4.4.1 Illumina sequencing and de novo assembly of Chromera transcriptome 143
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4.4.2 Transcriptome annotations 145
4.4.2.1 GO terms distribution 146
4.4.2.2 KEGG pathway analysis 146
4.4.3 Assessing the quality of the de novo transcriptome assembly 151
4.4.4 Comparative transcriptomics of Chromera stains 151
4.4.4.1 Identification of orthologous genes between Sydney and GBR 151
Chromera strains
4.4.4.2 Chromera orthologs functional profile 152
4.4.4.3 Analysis of Ka/Ks, a test for selection 153
4.4.5 Comparative analyses of Chromera, Symbiodinium and Plasmodium 155
transcriptome data
4.4.5.1 Functional profile for the set of genes shared between Sydney and 156
GBR Chromera
4.4.5.2 Functional profile for the set of genes shared between Chromera and 162
Symbiodinium
4.4.5.3 Functional profile for the set of genes shared between Chromera and 165
Plasmodium
4.4.6 KEGG pathways comparative analysis 168
4.4.6.1 Glycan biosynthesis in Chromera, Symbiodinium and Plasmodium 171
4.4.6.2 Transcription machinery in Chromera, Symbiodinium and 174
Plasmodium
4.5 DISCUSSION 180
4.5.1 Transcriptome assembly and completeness 180
4.5.2 Identification of Chromera orthologs and genes under selection 181
4.5.3 Functional profile of shared genes among Chromera strains 182
4.5.4 Functional profiles of genes shared between Chromera and Symbiodinium or 183
Chromera and Plasmodium
(cid:5)(cid:4)5.5 KEGG pathways comparison reveals similarity between Chromera and 184
Symbiodinium suggesting the potential of Chromera being a coral symbiont
4.5.6 Variation in N-Glycan biosynthesis enzymes might explain the coral host 184
recognition specificity
4.5.7 Reduction of the transcription machinery in Symbiodinium; a unique feature 185
of dinoflagellates
4.5.8 Conclusion 186
4.6 REFERENCES 186

CHAPTER 5 GENERAL DISCUSSION, MAJOR THESIS FINDINGS AND 189
FUTURE RESEARCH
5.1 General discussion 189
5.2 Major thesis findings 194
5.3 Future research 195
5.4 Conclusion and impact 197
5.5 REFERENCES 198

APPENDICES 200
Appendix I 200
The transcriptomic response of the coral Acropora digitifera to a competent
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