Dear members of the Xenopus community,

We are a large and diverse community, with rather few shared resources, compared to those who work on other animal models. In February 1999 a workshop was held at NIH to set priorities for facilitating the structural and functional analysis of non-mammalian model organisms. The following members of the Xenopus community were invited (by an unknown selection mechanism): Igor Dawid, Eddy de Robertis, Rob Grainger, Janet Heasman, Marc Kirschner, Sally Moody, Randy Moon, John Newport, and Masanori Taira. Co-Chairs for this group were Rob Grainger and Janet Heasman. Other non-mammalian organisms were represented by similar-sized groups. The Xenopus group was asked to evaluate the current status of genomic resource development in Xenopus, and to identify future needs, in the form of a two-page report presented to the larger committee. One purpose of this message is to send the report, which is included below, to all members of the Xenopus community for whom we have e-mail addresses. If this message gets to you indirectly, please don't feel excluded. We simply did not have your address. The report incorporated the results of an e-mail survey of members of the Xenopus community made by Janet and Rob before the meeting, and the discussion by the Xenopus group at the meeting.

One major perception of the Xenopus group at the meeting was that the Xenopus community would benefit better from funds likely to come available if they were more unified, so that applications for genomics resources can be made in an organized way, and resulting reagents and data shared between all Xenopus researchers. As you will see in the report, the large sums of money involved will probably not be achieved by simply incorporating genomics needs into individual RO1-type grant applications, nor will NIH simply offer these resources. The approach that has been successful in human, mouse, zebrafish, and other systems, so far, has been for organized groups to work with NIH officials to establish the best mechanisms (which might include RFA's, contracts, and supplements to existing grants) for supporting such projects.

The Xenopus group felt that the best way to proceed was to establish an informal committee, to represent the wider Xenopus community, and to get on with achieving the goals outlined in the report. The intention is that this committee would carry out the following:

-interact with NIH to fulfill the goals of the report

-involve all those in the Xenopus community in this process

-generate an information service on the work being done and resources generated

-generate resource centers to make available reagents arising from the work.

The committee unanimously agreed to invite Chris Wylie to Chair this committee, and to increase representation, initially by inviting Jim Smith (UK), Enrique Amaya (UK), John Gurdon (UK), Christof Niehrs (Germany), and Naoto Ueno (Japan) to join the group. This will help significantly in making available information and resources from other countries in addition to USA.

Please respond if you wish to be put on the e-mailing list for more information. Your comments on the report would be very welcome. You should relay your messages and comments to Chris Wylie (e-mail: wylie@lenti.med.umn.edu; phone: 612-625-4477).

Best Wishes,

The Xenopus Committee

Xenopus laevis is a unique resource for two critical vertebrate biological areas: early embryonic development and cell biology. In the former, X. laevis has led the way in establishing the mechanisms of early fate decisions, patterning of the basic body plan, and organogenesis. Contributions in cell biology and biochemistry include seminal work on chromosome replication, chromatin and nuclear assembly, cell cycle components, cytoskeletal elements, and signaling pathways. Information amassed from these studies provides a strong underpinning for future work, and, although X. laevis is superb for characterizing the activities of particular genes, only a tiny fraction have as yet been assayed. A major goal now is to examine the expressed genome in the context of the biological phenomena mentioned above using genomic technology, specifically ESTs and full-length cDNA libraries.

In recent years, Xenopus tropicalis has emerged as a complementary system in which to combine genetic approaches with the established strengths of the X. laevis system. New strategies will be feasible when genetic variants are examined in an embryological context, e.g. by making genetic chimeras, and generation of stable transgenic reporter lines in the short-generation X. tropicalis will increase the feasibility of many embryological assays. Since the degree of sequence similarity and functional interchangeability is high, X. tropicalis studies will also benefit from the X. laevis EST and cDNA cloning experiments.

In preparation for this workshop, the opinions of the Xenopus community were canvassed and the proposals below are based on this information together with discussions at this workshop.

• EST Database. The highest priority, one which is ready to be undertaken immediately, is the generation of an X. laevis EST database that should consist of 500,000 clones (estimated to be at least half of the expressed sequence complexity). Initially this should capitalize on existing cDNA libraries and should be complemented with normalized libraries from selected stages. A small EST database in X. tropicalis (50,000 clones) will provide a beginning for genomic research in this organism. Estimated cost: $5,500,000 over two years.
• Full length cDNA Sequences. Full length sequenced, unique cDNAs from X. laevis eggs and embryos are needed for functional studies (e.g. expression cloning strategies). Estimated cost for preparation, sequencing and arraying 50,000 full length cDNAs is $15,000,000 over three years.
• Microarrays. This rapidly evolving technology promises major advances. The utility of Xenopus for developmental studies, e.g. explantation, induction, and overexpression assays, make array technology especially valuable in this system. Array technology will become applicable as EST/cDNA sequences come on line. Therefore, funding to produce and make available Xenopus chips to the community should begin one year after EST/cDNA sequencing is initiated. Estimated cost: $1,000,000 over three years.
• Model Organism Database. There is an immediate need for expansion of the present Xenopus database, the Xenopus Molecular Marker Resource (XMMR). The expanded database should encompass the existing data, more comprehensive information concerning gene expression patterns, additional fate maps and anatomical atlases of embryonic stages, and information generated from the EST database and cDNA libraries. Sequences should be organized along the lines of databases for other organisms so that data is easily retrievable. Initial requirements include computational facilities and a skilled data manager; as the sequence database matures, a bioinformatics professional will become essential. Estimated cost: $400,000 per year.
• PAC and BAC Libraries. The high efficiency transgenesis procedure recently developed for Xenopus creates the need for large insert libraries for cloning and analysis of genomic sequences, specifically for promoter analysis of the X. tropicalis, diploid genome. Similar libraries in X. laevis will enable comparison of putative control elements. Estimated cost: $1,000,000.
• X. tropicalis genomic resources. Creation and preliminary characterization of radiation hybrid panels are required in anticipation of genetic screens and transgenic insertions. Additional support is needed for pilot genetic studies, including chemical and insertional mutagenesis. Estimated cost: $150,000 for the RHP project and $300,000 a year for pilot genetic studies.
• Training and Stock Centers. Resource centers are urgently needed for broader dissemination of new technology and for animal stocks. In the case of new technologies this should take the form of training centers in host labs experienced in transgenesis or antisense ablation. For animal stocks, including transgenic and genetically altered lines, one stock center is initially required with the expectation that this will expand as more permanent lines are established. Estimated cost: for training centers, $100,000 per year per host lab by supplementation of existing grants; for a stock center, $500,000-$1,000,000 for construction and $100,000 per year for operating costs.