The Future of Echinoderm Genomics
Hodin, J.1, Bishop, C.2, Hamdoun, A.1, Heyland, A.4
1. Stanford University, Hopkins Marine Station; 2. Dalhousie University; 3. Integrative Biology University of Guelph
Motivation and Scope
Justifications for future genome sequencing efforts will not be the same as
those used in the past. The human genome project (HGP) and related
sequencing efforts were heralded as a major step toward accelerating the
progress of health sciences. Since then, genomes of numerous species
have been sequenced, candidates for which have been based upon criteria
such as their presumed importance to human health, advanced knowledge of
their biology and genetics, their economic and ecological importance, and the
cohesion of the respective research communities.
The echinoderm
community has benefited greatly from the efforts of the sea urchin genome
sequencing consortium and the reference sequence that has been generated
for S. purpuratus. As a community, how can we best leverage this into a
persuasive argument for further sequencing efforts, and what criteria should
we use for our choices? To address this specific question and the broader
implications, we conducted a survey in 2006 and 2007 of a wide spectrum of
echinoderm biologists to ask what they would look for in additional genomics
candidates. We asked respondents to rank the importance of a range of
research questions, to estimate how heavily they plan to use the S.
purpuratus and any additional echinoderm genomes for their work, and to
offer suggestions for future echinoderm genomics candidates. We received
responses from 101 echinoderm biologists, consisting of ecologists,
evolutionary biologists, developmental & cell biologists and many other
specialties. In this presentation, we show the results of the survey (complete
results at http://virtualurchin.stanford.edu/GenomicsSurvey/survey.html ), and
draw on comparisons with other genome projects, such as the recently
released sequences and publications from the Drosophila 12 Genomes
Consortium.
Times mentioned
Species or Genus
31
Lytechinus spp.
24
Asterina spp.
18
Paracentrotus lividus
17
Asterias spp.
9
Strongylocentrotus spp.
9
Heliocidaris spp.
7
Holothuria spp.
6
Pisaster ochraceous
5
Metachrinus rotundus
5
Eucidaris spp.
5
Dendraster excentricus
5
Parvulastra/ Patiriella/
Meridiastra
4
Amphiura filiformis
4
Amphipholis squamata
4
Arbacia spp.
Class
Community suggestions of species for subsequent echinoderm genomics
projects ordered by species or genus. For simplicity we only list genus/species
that received 4 or more votes. Note that respondents could suggest multiple species
and some respondents suggested none.
Community suggestions of species for subsequent echinoderm genomics
projects ordered by taxonomic class. Note that respondents could suggest multiple
species and some respondents suggested none. Bars represent total number of times
any species within each of the five classes was mentioned.
Discussion Q uestions )General(
1.How will the criteria by which taxa are chosen for sequencing differ
from those which have been employed in the past?
2.What considerations should factor into species choice besides facilitating annotation efficiency while maximizing evolutionary divergence?
3.Are there diminishing informational returns on investments for
increasing numbers of species with sequenced genomes? If so, what
are they?
4.What are the explicit scientific questions at stake and how would
future sequencing efforts best complement current knowledge?
5.What are the primary reasons for which comparative genomics data
are sought?
Genetic distances between sequenced Drosophila species and potential
echinoderm candidates. Distances were calculated for 18s and ND1 (retrieved from
Genbank) using clustalW (default parameters). Diptera phylogeny and time scale data
from Wiegmann et al 2003 (Syst Biol 52:745-756) & Powell JR 1997 (Progress and Prospects in
Evolutionary Biology: The Drosophila Model); echinoderm phylogeny and time scale data from
Smith et al 2006 (Mol Biol Evol 23:1832-1851) & Biermann et al 2003 (Evol Dev 5:360-71)
Score (of 9)
Discussion Q uestions )Echinoderm Community(
1.Now that the S. purpuratus genome is complete, what biological
questions does it facilitate addressing? ...what questions does the S.
purpuratus genome notfacilitate addressing?
2.What aspects of comparative genomics, development, evolution, etc.
–that echinoderms in general or echinoids in particular can contribute–
would warrant modifying the general goals of increasing annotation
efficiency while maximizing evolutionary divergence?
3.What can echinoids in particular or echinoderms in general tell us
about biology that we can' t learn from genomes that have or are
currently being sequenced?
4.Who will do the work–proposals, sequencing, assembly, annotation?
5.Should the echinoderm community follow the lead of the Drosophila
12 Genomes Consortium by organizing a multiple day workshop, open
to all interested stakeholders, to discuss and arrive at a community
consensus on echinoderm genomics priorities?
1. Gene regulation/ transcriptional regulation of particular organs/ tissues/ processes
2. Gene regulation/ transcriptional regulation in early development
“The goal was to bring the interests and expertise of a wide range
of members of the fly community in order to decide upon the
species and draft the white papers … It was truly a community
effort, with much discussion and a final consensus…”
Therese Ann Markow – University of Arizona Tuscon
Research priorities of survey participants organized by the following groups:
I: heavy users of the S. purpuratus genome: namely, those who answered 4 or 5 of 5 when asked how
important the S. purpuratus genome is/will be to their work;
II: intended heavy users of additional echinoderm genomes: namely, those who answered 4 or 5 of 5 when
asked how important a second echinoderm genome is/will be to their work;
III: under-served echinoderm biologists: namely, those who answered 4 or 5 of 5 when asked how important a
second echinoderm genome is/will be to their work, but who answered 1-3 of 5 when asked how important the S.
purpuratus genome is/will be to their work;
IV: sea urchin colloquium members: namely, those respondents who were also members of the S. purpuratus
annotation consortium in October 2006. (12%) of consortium members responded to the survey.