Genomic information on representative organisms distributed over the ToL
The First 100 - Jump Starting the Field
The importance of the robust phylogenies being pursued by ToL efforts was emphasized. In concert with this information, the most pressing need for the Evo-Devo community is to have access to genomic information on a wide range of organisms. A major initiative in Evo-Devo must be jump-started with the creation of BAC and cDNA libraries for 100 key taxa. This cast of 100 should represent the major trunks of the tree with broad synoptic coverage related to the major Evo-Devo questions. Some key taxa have already been fully sequenced and the First 100 will not duplicate this effort. It is essential that this initial group of organisms show some promise of being tractable in the lab. That is, specimen access and propagation need to be considered. A funding competition for groups to create these libraries will necessarily bring together the Evo-Devo and ToL communities in a synergistic way. The actual selection of the First 100 will be community driven. Peer review will ensure broad taxonomic coverage.
The First 100 and all subsequent organismal libraries need to be shared readily with the community and centralized repository and distribution centers are essential. The competition for the First 100 grants should result in genomic museums with the capability to catalog and distribute arrayed BAC and pooled cDNA libraries.
These centers should also be prepared to become repositories and distribution centers for fully- sequenced genomes, ESTs, cDNAs and additional BACs that will be completed in later phases of the Evo-Devo Initiative. There is definitely economy in subcontracting the construction of libraries and genomic museums should be encouraged to pursue this. Genomic museums will have tremendous value for both Evo-Devo and ToL community members, as well as any biologist interested in comparative molecular studies. Quality control is absolutely essential and the First 100 will not only provide an immediate and much needed resource, but will also establish an infrastructure for library deposition and distribution that is incredibly reliable and reproducible.
The informatics component of this effort is equally important. A dispersed model appears most efficacious and would be a joint effort between the Evo-Devo and ToL communities. ToL has solidly begun building a phyloinformatics infrastructure. Coalesced with data coming from Evo-Devo efforts this should provide a rich resource for a large component of the biological community. Informatics data must have user access that is transparent. All informatics (both from the genomics and phylogenetics perspective) must be vouchered. Phylogenetic data coupled with genomic and developmental data coming from the Evo-Devo community should be preserved in digital form for long lasting research and educational impact. The databases must be relational or object oriented. The initial investment in the infrastructure of this accessible resource is critical to both communities and will facilitate synergistic interactions. The NSF-supported Drosophila stock and information center is an example that should be considered in developing the informatics infrastructure.
Sequencing Major Developmental Gene Families in the First 100
ToL is beginning to integrate nuclear genome sequences into phylogenies and the participants explored the need and rationale for using developmentally significant genes in these trees. There are just a few dozen gene families in the developmental modules/cassettes in organisms investigated to date (e.g., Table 1). Sequencing homologous families in the First 100 organisms will be invaluable in addressing many Evo-Devo questions. It would be particularly interesting to find if some organisms lack certain modules and if they have evolved alternative strategies. This resource should be particularly helpful for the ToL community as they move towards using nuclear genes in phylogenetic analysis since these genes have central roles in development. Some of this sequencing may be very important in resolving uncertainties at important nodes in the Tree of Life. A discussion among phylogeneticists and developmental geneticists revealed how much they can learn from each other. For example, many of the highly conserved motifs in these major gene families are coupled with rapidly evolving neighboring sequences. This is a conceptual challenge in phylogenetic tree construction and is of fundamental mechanistic interest to Evo-Devo researchers. There are resolution challenges in dealing with families of genes in phylogenetic construction. This sequencing project would be valuable one for the ToL community to undertake and would facilitate community building between Evo-Devo and ToL researchers.
Table1. Examples of major gene families/protiens in
the evolution of development
|Zinc finger proteins||FGFs||Wnts||Apoptosis genes|
|Leucine zipper transcription factors||Smads||Frizzleds|
|polycomb genes||2 component kinases||SH2,SH3 Proteins|
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