11th ICRS Abstract book - Nova Southeastern University

Oral Mini-Symposium 6: Ecological and Evolutionary Genomics of Coral Reef Organisms
6-2
The Coral Transcriptome – A Beginner’s Guide
David MILLER* 1,2 , Eldon BALL 2
1 ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville,
Australia, 2 ARC Centre for the Molecular Genetics of Development, Australian National
University, Canberra, Australia
Although corals are amongst the simplest true animals at the morphological level, in
terms of the total number and types of genes they are comparable with the most complex
of animals – the vertebrates. The coral genome contains a large number of genes once
thought of as vertebrate-specific, including clear homologs of many key components of
the vertebrate innate immune repertoire; considerable effort is presently being directed
into exploring the roles of these in combating coral disease. The genomes of anthozoan
cnidarians such as corals also contain a significant number of “non-metazoan” genes –
genes only previously known from members of the other kingdoms of life. These are not
the products of recent lateral gene transfers, but long-term residents of cnidarian genomes
that potentially increase the biochemical complexity of the organism. The unexpected
complexity and heterogeneity of the coral transcriptome represents a major challenge in
understanding the functional biology of corals; essentially, one cannot predict how corals
will respond based on what is known about other animals.
Whole genome sequences are now available for two cnidarians – the sea anemone
Nematostella vectensis and the freshwater Hydra magnipapillata – and comparisons
between the coral Acropora and these organisms have the potential to provide insights
into nominally coral-specific processes such as calcification and symbiosis. Moreover,
comparisons between the Indo-Pacific coral Acropora millepora and the Caribbean
species Acropora palmata permit the identification of genes under positive selection that
are candidates for roles in allorecognition, gamete interactions and other coral-specific
traits. Future progress in coral functional biology will increasingly rely on microarray and
genomic approaches based on high-throughput DNA sequencing, coupled with use of
biological ‘models’ for coral traits.
6-3
Gene Expression in Symbiodinium Under Stress
Bill LEGGAT 1,2 , David YELLOWLEES 2 , Sophie DOVE 3,4 , Ove HOEGH-
GULDBERG* 3,4
1 Biochemistry and Molecular Science, James Cook University, Townsville, Australia,
2 ARC CoE for Coral Reef Studies, James Cook University, Townsville, Australia,
3 Centre for Marine Studies, University of Queensland, Brisbane, Australia, 4 ARC CoE
for Coral Reef Studies, Brisbane, Australia
It is now well documented that the dinoflagellate Symbiodinium (zooxanthellae) are a
weak link in the coral symbiosis. An obvious example of this is the fact that small
increases in temperature lead to damage to the Symbiodinium photosynthetic apparatus
and their eventual expulsion from their coral host (coral bleaching). However we know
very little about how Symbiodinium copes with stress. Characterisation of a
Symbiodinium stress transcriptome, which is made up of over 5000 contigs, has found
that a large number of genes that are expressed when under temperature, nutrient or CO2
stress are novel and do not match any sequences in the available databases
(approximately 55%). In fact the function of the most highly expressed gene, which
makes up to 3% of the transcriptome, is also unknown. In addition to these unknown
genes Symbiodinium contains a variety of typical “stress” response genes (e.g. heat shock
proteins, catalase, super-oxide dismutase etc). However even these are sometimes often
not what would be expected a typical alga; for example the Symbiodinium catalase is
most closely related to that found in bacteria and fungi rather than a traditional eukaryote
catalase. This unique genetic make up means that how the genes that are up- or downregulated
in response to stress in Symbiodinium may differ from what is seen in other
photoautrophs. The use of a newly developed Symbiodinium microaray is now allowing
us to examine how these ecologically key dinoflagellates respond to stress at the gene
expression level. We are examining how changes in temperature, CO2 and nutrients
affect the Symbiodinium transcriptome and the phenotype of the alga.
6-4
Integrating Genomics With Coral Reef Biology And Management
Cheryl WOODLEY* 1 , Craig DOWNS 2
1 NOAA National Ocean Service, Charleston, SC, 2 Haereticus Environmental Laboratory,
Clifford, VA
Genomics is a methodology for studying genomes (the chromosomes and their genes). The
original purpose was to sequence the genomes of organisms, identify and map genes to the
genome, categorizing (annotate) new genes based on similarities with previously identified
genes of known function, and document which genes are activated under various conditions.
The initial focus for these efforts was aimed at improving human health. One of the most
successful outcomes of genomic efforts has been identifying genes responsible for heritable
diseases involving only a few genes. Diagnostic tests were quickly developed and drug
development began targeting specific steps in disease pathways. Genomics uncovered disease
variations that allow more discriminating diagnosis such as subtyping tumors (e.g., breast
cancers) and individualized treatments. Sequencing genomes quickly spread to model
organisms, domestic animals and crops, and more recently to commercially valuable marine
organisms (e.g., salmon, shrimp, oysters). The rationale varied for each genome but included
understanding development, comparative studies for altered physiological or environmental
conditions, pathology, population genetics, breeding, crop improvement or drug development.
Coral reef biologists have recently turned to genomics in hopes of answering questions in
toxicology, symbiosis, pathology, development, evolutionary and ecological processes and
environmental monitoring. Genomics alone, however, will fail in trying to address these
questions. It is a tool that can provide unprecedented amounts of data, but more data does not
mean more knowledge. Not until we view genomics as a tool to be used in the context of a
scientific research plan or resource management strategy with other methods and disciplines
(e.g., genetics, physiology, biochemistry and cell biology) for conducting hypothesis driven
experiments, will our understanding coral reef biology and health move forward.
6-5
Differential Gene Expression During The Initial Onset Of Coral/algal Symbiosis Using A
Cdna Microarray
Christine SCHNITZLER* 1 , Virginia WEIS 1
1 Department of Zoology, Oregon State University, Corvallis, OR
Very little is known about the molecular and cellular mechanisms controlling the successful
establishment of a stable relationship in the early stages of coral/algal symbiosis. The planula
larva of the solitary Hawaiian scleractinian coral Fungia scutaria and its dinoflagellate
symbiont Symbiodinium sp. type C1f represents an ideal model for studying the onset of
coral/algal symbiosis due to the predictable availability of gametes, and the ability to raise nonsymbiotic
larvae and establish the symbiosis experimentally. The goal of this study was to
identify genes differentially expressed in F. scutaria larvae during the initiation of symbiosis
with its algal symbiont using a high-throughput technique. We predicted that our discoverybased
approach would identify expression differences in host genes involved in cellular
processes critical to the establishment of coral/algal symbiosis, such as cell signaling,
proliferation, metabolism and immunity. Symbiotic larvae were compared to non-symbiotic
larvae using a custom cDNA microarray. The 5,184-feature array was constructed with cDNA
libraries from newly symbiotic and non-symbiotic larvae, including 3,072 features (60%) that
were enriched for either state by subtracted hybridization. The array was hybridized with cDNA
from newly symbiotic and non-symbiotic F. scutaria larvae using a multiple dye swap design
and six biological replicates. Following normalization to control features, transcripts
differentially expressed (up- or down-regulated) as a function of the symbiotic state were
sequenced and used to identify homologs, and differential expression was quantified using real
time PCR. Specific primers were constructed for use in PCR with host-only and algae-only
genomic DNA to confirm the source of genes expressed from the symbiotic larval cDNA
library. Future studies will focus on functional and biochemical assays in an attempt to further
characterize individual target genes.
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