Meeting Summary
Topic: An International Workshop to Discuss Sequencing of the Tomato Genome: Feasibility, Benefits and Strategy
Location: Washington, D.C. (Holiday Inn Dulles International)
Date: November 3, 2003
Objectives
The purpose of this
gathering was to determine the feasibility, utility, strategy and
level of international interest/commitment for sequencing the
tomato genome as a reference for the family Solanaceae and other
closely related plant families. The workshop brought
together and international group of scientists to
discuss:
- the current status of Solanaceae research, including aspects of plant biology for
which Solanaceous species are a preferred model
- the impact of sequencing the tomato genome on research in the Solanaceae and plant biology in general
- sequencing strategy
- mechanisms by which such a sequencing project can be conducted as part of a multinational consortium
- strategies for sequence information management, curation and public dissemination
Summary of Events
- Broad international interest in tomato genome sequencing as a central
component to a larger Solanaceae Genome Initiative
Sixty-nine researchers representing academic and government research labs, industry and
extension/outreach specialists with interest in the Solanaceae met
for a full day to discuss how the tomato genome could be sequenced
as a reference for the broader Solanaceae. Representatives of eleven
countries summarized national interest and prospects for
state-sponsored sequencing support within their respective
countries. The
Netherlands has already funded sequencing of 20 Mb of the R-gene
rich region of tomato chromosome 6 (apx. 8% of the estimated 250 Mb
tomato gene space) and the US is nearing completion of an anchored
tomato physical map to facilitate targeted sequencing of the gene
space. Representatives
of France and the UK reported on discussions with administrators of
their respective national funding agencies and indicated proposals
to sequence one or two tomato chromosomes were
encouraged. Similar,
though less specific positions were relayed by representatives of
Spain, Italy, Canada and S. Korea and all agreed that funding would
depend on the initiation of efforts in other countries to insure
that the outcome of their investments would be ultimately
realized. There was
general agreement among those working on other members of the
Solanaceae (pepper, potato, eggplant, tobacco) that tomato
presented the appropriate reference genome for the
Solanaceae. Ongoing
and proposed activities in these species including development of
comparative maps, EST and low density shotgun sequencing which
would facilitate connection of the various Solanaceae genomes to
the tomato reference.
- Developing the Solanaceae as a model for systems biology in plant research
Systems biology takes advantage of diverse and integrated knowledge
to yield novel biological insights which could not be established
via more traditional narrow analyses. Systems biology is an outcome of
the "omics" era and the Solanaceae are positioned to be a model for
Systems biology.
Following the morning breakout discussion session, summaries of the
state of comparative Solanaceae genomics, host-pathogen
interactions, fruit and tuber development, ecological genetics,
quantitative traits, systematics, germplasm resources, metabolism,
and proteomics were presented. A major outcome of these
discussions was that there are clear and optimal opportunities for
system analysis in the Solanaceae. Comparative maps link the major
members of this family to tomato and each other and extensive
marker resources are publicly available. Diverse germplasm including large
collections of mutations, wild species, and multiple fixed and
ordered introgression populations provide unsurpassed allelic
variation for simple and quantitative trait analysis. In particular, the use of fixed
homozygous introgression collections developed in tomato has
facilitated extensive analysis of diverse metabolites and QTLs
which can now be linked to mapped gene loci, allelic variation,
gene expression and protein accumulation. The repertoire of molecular and
germplasm resources available in the Solanaceae make this family
and ideal model for systems biology. In addition and as pointed out by
several of the discussion presenters, the ease of tomato
transformation and its relatively short life cycle (apx. 12 weeks
seed to seed) has made tomato an increasingly popular model crop
for testing hypotheses developed in model systems such as
Arabidopsis, further extending the biological insights that can be
gained through the Solanaceae.
- Strategy for tomato genome sequencing
There was general
agreement to sequence the euchromatic gene space of tomato via a
targeted minimal tiling approach in which BACs would be anchored to
the genetic map and those from the gene space would serve as
initiation points for genome sequencing. BAC fingerprinting and
end-sequencing would provide the information needed to make
additional steps down the tiling path. This approach would also
facilitate the division of labor among participating
groups/countries based on whole or partial chromosomes thus
providing clear references for group and national
contributions. There
was strong and broad agreement to development of a single virtual
entry point for Solanaceae genome sequence and related genomics and
systems information to facilitate utility by the user
community. A plan for
implementation of a mirrored informatics interface that could be
developed in multiple participating countries but with a single
external face was also viewed positively by the group as the
objective of such a plan would be to maximize input and
participation while delivering a user friendly and comprehensive
product.
Followup and Next Steps
Given the strong
international interest in sequencing the tomato genome and
developing the Solanaceae as a model for systems
biology, several
specific items were agreed upon as next steps.
- Formation of Steering Committee for the International Solanaceae Genome Project (ISGP)
It was decided that the
committee will be
comprised of representative scientists from each of the countries
actively
participating in the ISGP. Marc Zabeau (Belgium) and
Dani Zamir (Israel) have agreed to serve as initial co-chairs of
this committee and will work with the international community to
establish membership of this committee no later than Dec 31,
2003. This committee
will be charged with facilitating and helping coordinate research
and funding for the various components of the ISGP. They will also be charged with
drafting a white paper for the ISGP (see
below). The
committee will meet annually at the Solanaceae Genomics meeting
which will be held annually in one of the participating countries
(also see below).
- Drafting of a white paper for the Solanaceae Genome Initiative
A white paper describing the
goals, components and (where possible) time tables for the ISGP
will be drafted and distributed to the participants of the meeting
for comments and suggestions no later than December 1,
2003. The goal
is to have a final draft of this white paper no later than December
31, 2003 so that various participating countries can use the
document to help with planning and funding of the components in
which they will be involved.
- Drafting of a technical document for sequencing of the tomato genome
A central component of
the ISGP is sequencing of the tomato genome. Based on the November 3,
2003 meeting in Washington DC, a general strategy was decided (see
earlier section) which would accomplish a fully contiged sequence
of the euchromatic portion of the genome. The sequencing project would be
conducted in a manner that would allow multi-country
participation.
To facilitate this central component of the ISGP, a
technical document describing the specifics of the
sequencing project will be drafted and distributed to the
participants of the meeting no later than December 1,
2003. The goal is to
have a final technical document for the sequencing
portion of the ISGP completed no later than December 31,
2003.
- Formation of an International Bioinformatics Steering
Committee to oversee bioinformatics for the ISGP and especially
sequencing of the tomato genome
Lukas Mueller (curator for Solanaceae Genome Network (SGN) database/website) has agreed to organize and serve
as the chair of this
committee. This committee will be charged
with drafting and overseeing both the bioinformatics components of
the ISGP as well as the technical document for
sequencing the tomato genome. This committee will work
hand-in-hand with the ISGP Steering Committee. These bioinformatics
components will be contained in the drafts of both the
white paper for the ISGP and the technical
document for the tomato sequencing project.
- Establishment of an annual International Solanacaeae
Genomics Conference
It was agreed
that an annual
conference will be held devoted to the topic of genomics research
in the Solanaceae. The
first meeting will be held in July 2004 and hosted by
Holland. The meeting times and
locations for the 2005 and 2006 meetings will be decided within the
next 6 months.
It was suggested that the 2006 meetings might be held at the
University of Wisconsin as part of the Solanaceae systematics
meetings. Both the
ISGP Steering
Committee and the Bioinformatics Steering Committee will hold
discussion sections at these gatherings.
- Assimilation and distribution of both the powerpoint
presentations and digitally filmed copies of the November 3, 2003
Washington DC meeting
Currently, Lindsay Welsh (cugenomics@cornell.edu) at Cornell
University is collecting the powerpoint files which will be ready
for distribution to participants by December 1, 2003. Likewise, digital copies of the
meeting proceedings will be ready shortly for
distribution. Several
of the participants thought these items would be useful in
discussing participation and funding in their own countries.
- Compilation of a comprehensive list of Solanaceae
researchers worldwide, including institutional affiliations,
contact information (e.g. e.mail addresses) and major research
focus areas
The first draft of this list should be completed
and ready for distribution by December 31, 2003.
|
