11th ICRS Abstract book - Nova Southeastern University

Oral Mini-Symposium 6: Ecological and Evolutionary Genomics of Coral Reef Organisms
6-14
Preliminary Characterization Of The Genomic "Defensome"in A Model Cnidarian,
Nematostella Vectensis, And Predicted Stress Response Genes in Reef-Associated
Corals
Nikki TRAYLOR-KNOWLES* 1 , Adam REITZEL 2 , James SULLIVAN 1 , Les
KAUFMAN 1 , John FINNERTY 1
1 Department of Biology, Boston University, Boston, MA, 2 Wood Hole Oceanographic
Institution, Woods Hole, MA
There is a pressing need for quantitative stress and resilience indicators in globally
embattled coral reefs to be used to track the efficacy of conservation efforts. One way to
start addressing this issue is to use genomics and bioinformatics. Nematostella vectensis
is a burrowing anemone common to estuarine habitats along the east coast of North
America, from Nova Scotia to Louisiana. It’s a superb model for studying the evolution
and ecology of cnidarian stress response because (1) it is easy to cultivate in the
laboratory and collect in the field, (2) it inhabits hyper-variable habitats across a wide
geographic range, (3) it is known to exhibit pronounced genetic structure at small spatial
scales, and (4) its genome has been sequenced. Comparing the genomic complement of
stress-genes in Nematostella and Triploblastica will help illuminate the stress-response
system of early animals, perhaps revealing the importance of transcriptional control.
Furthermore, the stress-response genes in Nematostella are likely to exhibit a
homologous function in other cnidarians, including tropical reef-associated corals. A
bioinformatics screen of the Nematostella genome identified 110 predicted chemical
response proteins, 384 predicted wound healing proteins, and 128 predicted innate
immunity proteins. Key elements of the innate immune system were identified, including
members of the Toll and interleukin signaling cascades: IRAK, TRAF, ECSIT, IKK,
MKK, JNK, IKB, p38, NF-κB and AP-1. Complements of genes active during wound
healing in vertebrates were also identified. The highly conserved transcription factor,
Grainy head has been shown to be a critical component in the formation of an epithelial
barrier and can be recognized by the possession of a highly conserved CP2 domain. A
search for this domain identified a single significant match. Identification and structural
characterization of these genes will allow for functional assays to be performed. This
work is a contribution of the MMAS Program.
6-15
Coral Reef Metagenomics
Forest ROHWER* 1 , Elizabeth DINSDALE 1 , Robert EDWARDS 2 , Linda WEGLEY 1 ,
Rebecca THURBER 1 , Kristen MARHAVER 3 , Stuart SANDIN 3 , Dana HALL 1 , Florent
ANGLY 4 , Beltran BRITO RODRIGUEZ 4 , Nancy KNOWLTON 3
1 Biology Department, San Diego State University, San Diego, CA, 2 Computer Science,
San Diego State University, San Diego, CA, 3 Marine Biology, Scripps Intitution of
Oceanography, San Diego, CA, 4 Computational Sciences, San Diego State University,
San Diego, CA
An increasing body of evidence suggests that microbes are key players in both healthy
and degraded coral reefs. We have been using metagenomics (i.e., shotgun sequencing of
community DNA) to characterize the microbial communities within the coral holobiont,
as well as in the surrounding water column. In the Northern Line Islands, the water
column metagenomes showed that the microbial and viral communities changed from an
even mix of autotrophs and heterotrophs to predominantly heterotrophs along a gradient
of human disturbance and oceanographic conditions. In metagenomic studies of coralassociated
microbial communities, we have found that the endolithic fungi are important
to nitrogen recycling within the holobiont. Finally, metagenomic analyses of viral
communities from corals showed that herpes-like viruses are induced by natural and
anthropogenic stressors. Together, these studies demonstrate the power of metagenomics
to deconvolute the complex interactions of corals and microbes.
6-16
Settling On The Right Genes: Functional Genomics Of Variation in Marine Invertebrate
Larval Settlement
Sandie DEGNAN* 1
1 School of Integrative Biology, University of Queensland, Brisbane, Australia
The capacity of marine animals to cope with the rapid environmental challenges they now are
facing is likely to be encoded in their genomes. Responses on the generational time scale will
rely on natural genetic variation already existing within species and populations, especially
where this is manifested as variable gene expression during crucial developmental stages. In the
pelagobenthic life cycle shared by most marine invertebrates, a particularly crucial stage is
when the dispersing larva settles out of the plankton onto the benthos, and metamorphoses into
a reproductive adult. Settlement and metamorphosis cannot proceed without the larva first
reaching developmental competency, and then encountering an appropriate inductive cue. The
timing and success of these steps directly determine the structure, stability and evolution of
natural populations. Variation around this transition is thus likely to be an important source of
response to environmental change. We have used microarray gene profiling in two coral reef
invertebrates - a haliotid mollusc and a pyurid ascidian - to identify candidate genes
underpinning this critical developmental and ecological transition. We have found large
numbers of genes that show differential expression associated with the onset of competency and
settlement. Of particular interest are genes putatively involved in the innate immune pathway,
which appear to be involved in responding to benthic cues, and coping with new challenges
presented by the plankton – benthos transition. Importantly, we have documented extensive
variation in the expression of these and other settlement genes both within and between
populations, much of it correlated with specific environmental conditions. This inherent
variation in gene expression is cause for hope that natural populations carry within
themselves the capacity to cope with the inevitable changes in coral reef
environments.
6-17
Coral Population Genomics: Genome Evolution In Action
Mikhail MATZ* 1
1 Integrative Biology, University of Texas at Austin, Austin, TX
Population genomics is a novel integrative approach to study the evolutionary process in natural
populations on a whole-genome level. Population genomics integrates information about genes
involved in the biological process of interest, variation of their expression in natural
populations, genomic determinants of this variation and evolution of the corresponding loci as
revealed through population genetic analysis. One of the technical foundations of this workflow
is the microarray-based whole-genome genotyping methodology called iDART, developed in
my lab. Currently our main focus is evolution of stress resilience and dispersal potential in
Acropora millepora in response to climate change. The project takes advantage of the
possibility to perform controlled crosses and assess physiological parameters, genotype and
profile gene expression in individual A. millepora larvae.
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