Times mentioned Species or Genus Class

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 PatiriellaMeridiastra

4 Amphiura filiformis

4 Amphipholis squamata

4 .Arbacia spp

The Future of Echinoderm GenomicsHodin, 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

Discussion Questions ) (General1. 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 facili

tating 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?

Discussion Questions ) (Echinoderm Community1. Now that the S. purpuratus genome is complete, what biological

... questions does it facilitate addressing? what questions does the S. purpuratus genome not facilitate 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?

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.

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.

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.

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. purpuratusannotation consortium in October 2006. (12%) of consortium members responded to the survey.

“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

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)

1. Gene regulation/ transcriptional regulation of particular organs/ tissues/ processes2. Gene regulation/ transcriptional regulation in early development

Score (of 9)