cgi-bin/solanaceae-project/summary.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('summary.html','html2pl converter');
   4 $page->header('Meeting Summary');
   5 print<<END_HEREDOC;
   6
   7
   8 <h3>Meeting Summary</h3>
   9
  10 <p><strong>Topic:</strong> <em>An International Workshop to Discuss Sequencing of the Tomato Genome: Feasibility, Benefits and Strategy</em></p>
  11 <p><strong>Location:</strong> Washington, D.C. (Holiday Inn Dulles International)</p>
  12 <p><strong>Date:</strong> November 3, 2003</p>
  13
  14 <h4>Objectives</h4>
  15
  16 <p>The purpose of this
  17 gathering was to determine the feasibility, utility, strategy and
  18 level of international interest/commitment for sequencing the
  19 tomato genome as a reference for the family Solanaceae and other
  20 closely related plant families. The workshop brought
  21 together and international group of scientists to
  22 discuss:</p>
  23 <ol>
  24 <li>the current status of Solanaceae research, including aspects of plant biology for
  25 which Solanaceous species are a preferred model</li>
  26 <li>the impact of sequencing the tomato genome on research in the Solanaceae and plant biology in general</li>
  27 <li>sequencing strategy</li>
  28 <li>mechanisms by which such a sequencing project can be conducted as part of a multinational consortium</li>
  29 <li>strategies for sequence information management, curation and public dissemination</li>
  30 </ol>
  31
  32 <h4>Summary of Events</h4>
  33
  34 <ul>
  35
  36 <li>Broad international interest in tomato genome sequencing as a central
  37 component to a larger Solanaceae Genome Initiative
  38
  39 <p>Sixty-nine researchers representing academic and government research labs, industry and
  40 extension/outreach specialists with interest in the Solanaceae met
  41 for a full day to discuss how the tomato genome could be sequenced
  42 as a reference for the broader Solanaceae. Representatives of eleven
  43 countries summarized national interest and prospects for
  44 state-sponsored sequencing support within their respective
  45 countries. The
  46 Netherlands has already funded sequencing of 20 Mb of the R-gene
  47 rich region of tomato chromosome 6 (apx. 8\% of the estimated 250 Mb
  48 tomato gene space) and the US is nearing completion of an anchored
  49 tomato physical map to facilitate targeted sequencing of the gene
  50 space. Representatives
  51 of France and the UK reported on discussions with administrators of
  52 their respective national funding agencies and indicated proposals
  53 to sequence one or two tomato chromosomes were
  54 encouraged. Similar,
  55 though less specific positions were relayed by representatives of
  56 Spain, Italy, Canada and S. Korea and all agreed that funding would
  57 depend on the initiation of efforts in other countries to insure
  58 that the outcome of their investments would be ultimately
  59 realized. There was
  60 general agreement among those working on other members of the
  61 Solanaceae (pepper, potato, eggplant, tobacco) that tomato
  62 presented the appropriate reference genome for the
  63 Solanaceae. Ongoing
  64 and proposed activities in these species including development of
  65 comparative maps, EST and low density shotgun sequencing which
  66 would facilitate connection of the various Solanaceae genomes to
  67 the tomato reference.</p></li>
  68
  69 <li>Developing the Solanaceae as a model for systems biology in plant research
  70
  71 <p>Systems biology takes advantage of diverse and integrated knowledge
  72 to yield novel biological insights which could not be established
  73 via more traditional narrow analyses. Systems biology is an outcome of
  74 the "omics" era and the Solanaceae are positioned to be a model for
  75 Systems biology.
  76 Following the morning breakout discussion session, summaries of the
  77 state of comparative Solanaceae genomics, host-pathogen
  78 interactions, fruit and tuber development, ecological genetics,
  79 quantitative traits, systematics, germplasm resources, metabolism,
  80 and proteomics were presented. A major outcome of these
  81 discussions was that there are clear and optimal opportunities for
  82 system analysis in the Solanaceae. Comparative maps link the major
  83 members of this family to tomato and each other and extensive
  84 marker resources are publicly available. Diverse germplasm including large
  85 collections of mutations, wild species, and multiple fixed and
  86 ordered introgression populations provide unsurpassed allelic
  87 variation for simple and quantitative trait analysis. In particular, the use of fixed
  88 homozygous introgression collections developed in tomato has
  89 facilitated extensive analysis of diverse metabolites and QTLs
  90 which can now be linked to mapped gene loci, allelic variation,
  91 gene expression and protein accumulation. The repertoire of molecular and
  92 germplasm resources available in the Solanaceae make this family
  93 and ideal model for systems biology. In addition and as pointed out by
  94 several of the discussion presenters, the ease of tomato
  95 transformation and its relatively short life cycle (apx. 12 weeks
  96 seed to seed) has made tomato an increasingly popular model crop
  97 for testing hypotheses developed in model systems such as
  98 Arabidopsis, further extending the biological insights that can be
  99 gained through the Solanaceae.</p></li>
 100
 101 <li>Strategy for tomato genome sequencing
 102
 103 <p>There was general
 104 agreement to sequence the euchromatic gene space of tomato via a
 105 targeted minimal tiling approach in which BACs would be anchored to
 106 the genetic map and those from the gene space would serve as
 107 initiation points for genome sequencing. BAC fingerprinting and
 108 end-sequencing would provide the information needed to make
 109 additional steps down the tiling path. This approach would also
 110 facilitate the division of labor among participating
 111 groups/countries based on whole or partial chromosomes thus
 112 providing clear references for group and national
 113 contributions. There
 114 was strong and broad agreement to development of a single virtual
 115 entry point for Solanaceae genome sequence and related genomics and
 116 systems information to facilitate utility by the user
 117 community. A plan for
 118 implementation of a mirrored informatics interface that could be
 119 developed in multiple participating countries but with a single
 120 external face was also viewed positively by the group as the
 121 objective of such a plan would be to maximize input and
 122 participation while delivering a user friendly and comprehensive
 123 product.</p></li>
 124
 125 </ul>
 126
 127 <h4>Followup and Next Steps</h4>
 128
 129 <p>Given the strong
 130 international interest in sequencing the tomato genome and
 131 developing the Solanaceae as a model for systems
 132 biology, several
 133 specific items were agreed upon as next steps.</p>
 134
 135 <ol>
 136
 137 <li>Formation of Steering Committee for the International Solanaceae Genome Project (ISGP)
 138
 139 <p>It was decided that the
 140 committee will be
 141 comprised of representative scientists from each of the countries
 142 actively
 143 participating in the ISGP. Marc Zabeau (Belgium) and
 144 Dani Zamir (Israel) have agreed to serve as initial co-chairs of
 145 this committee and will work with the international community to
 146 establish membership of this committee no later than Dec 31,
 147 2003. This committee
 148 will be charged with facilitating and helping coordinate research
 149 and funding for the various components of the ISGP. They will also be charged with
 150 drafting a white paper for the ISGP (see
 151 below). The
 152 committee will meet annually at the Solanaceae Genomics meeting
 153 which will be held annually in one of the participating countries
 154 (also see below).</p></li>
 155
 156 <li>Drafting of a white paper for the Solanaceae Genome Initiative
 157
 158 <p>A white paper describing the
 159 goals, components and (where possible) time tables for the ISGP
 160 will be drafted and distributed to the participants of the meeting
 161 for comments and suggestions no later than December 1,
 162 2003. The goal
 163 is to have a final draft of this white paper no later than December
 164 31, 2003 so that various participating countries can use the
 165 document to help with planning and funding of the components in
 166 which they will be involved.</p></li>
 167
 168 <li>Drafting of a technical document for sequencing of the tomato genome
 169
 170 <p>A central component of
 171 the ISGP is sequencing of the tomato genome. Based on the November 3,
 172 2003 meeting in Washington DC, a general strategy was decided (see
 173 earlier section) which would accomplish a fully contiged sequence
 174 of the euchromatic portion of the genome. The sequencing project would be
 175 conducted in a manner that would allow multi-country
 176 participation.
 177 To facilitate this central component of the ISGP, a
 178 technical document describing the specifics of the
 179 sequencing project will be drafted and distributed to the
 180 participants of the meeting no later than December 1,
 181 2003. The goal is to
 182 have a final technical document for the sequencing
 183 portion of the ISGP completed no later than December 31,
 184 2003.</p></li>
 185
 186 <li>Formation of an International Bioinformatics Steering
 187 Committee to oversee bioinformatics for the ISGP and especially
 188 sequencing of the tomato genome
 189
 190 <p>Lukas Mueller (curator for Solanaceae Genome Network (SGN) database/website) has agreed to organize and serve
 191 as the chair of this
 192 committee. This committee will be charged
 193 with drafting and overseeing both the bioinformatics components of
 194 the ISGP as well as the technical document for
 195 sequencing the tomato genome. This committee will work
 196 hand-in-hand with the ISGP Steering Committee. These bioinformatics
 197 components will be contained in the drafts of both the
 198 white paper for the ISGP and the technical
 199 document for the tomato sequencing project.</p></li>
 200
 201 <li>Establishment of an annual International Solanacaeae
 202 Genomics Conference
 203
 204 <p>It was agreed
 205 that an annual
 206 conference will be held devoted to the topic of genomics research
 207 in the Solanaceae. The
 208 first meeting will be held in July 2004 and hosted by
 209 Holland. The meeting times and
 210 locations for the 2005 and 2006 meetings will be decided within the
 211 next 6 months.
 212 It was suggested that the 2006 meetings might be held at the
 213 University of Wisconsin as part of the Solanaceae systematics
 214 meetings. Both the
 215 ISGP Steering
 216 Committee and the Bioinformatics Steering Committee will hold
 217 discussion sections at these gatherings.</p></li>
 218
 219 <li>Assimilation and distribution of both the powerpoint
 220 presentations and digitally filmed copies of the November 3, 2003
 221 Washington DC meeting
 222
 223 <p>Currently, Lindsay Welsh (cugenomics\@cornell.edu) at Cornell
 224 University is collecting the powerpoint files which will be ready
 225 for distribution to participants by December 1, 2003. Likewise, digital copies of the
 226 meeting proceedings will be ready shortly for
 227 distribution. Several
 228 of the participants thought these items would be useful in
 229 discussing participation and funding in their own countries.</p></li>
 230
 231 <li>Compilation of a comprehensive list of Solanaceae
 232 researchers worldwide, including institutional affiliations,
 233 contact information (e.g. e.mail addresses) and major research
 234 focus areas
 235
 236 <p>The first draft of this list should be completed
 237 and ready for distribution by December 31, 2003.</p></li>
 238 </ol>
 239
 240 END_HEREDOC
 241 $page->footer();