ASM Conference on Candida and Candidiasis:
Genome Workshop

A C. albicans Genome Annotation Workshop was held during the evenings of January 14 and 15, 2001, as part of the Sixth ASM Conference on Candida and Candidiasis. The goal of the workshop was to update the community on efforts, developments, and available resources, and to ensure that the Candida research community has uniform genomic information from the many resources that are and will be available.

Several people summarized their groups' accomplishments and objectives, including Christophe d'Enfert (Institut Pasteur and European Consortium Galar Fungail, CandidaDB), Jan Dungan (Agabian Lab, UCSF), Andre Nantel (Whiteway Lab, National Research Council Canada), Mike Lorenz (Fink Lab, MIT), Diane Inglis (Johnson Lab, UCSF), Maria Costanzo (Proteome/Incyte), Nicole Hauser (Rupp Lab, Fraunhoffer IGB Stuttgart), Eric Bensen (Berman Lab, U. Minnesota), and Kara Dolinski (Candida Genome Database). It was clear that the Candida research community will benefit enormously from access to these annotations, all based mainly on sequence Assembly 6 from the Stanford Genome Technology Center. Equally clear was the potential for confusion if each resource utilizes slightly different gene lists and deduced genetic relationships (e. g., linkage or allelism). Clear definition of genetic relationships will require ongoing experimental and informatics efforts.

At the conclusion of the workshop, we mapped out a strategy to create a uniform gene list and agreed-upon repository for new information. The strategy is this:

  1. The current annotations will be shared among the annotators. They are or will soon be publicly available, but should be used with the understanding that there is not complete agreement among the gene lists.

  2. Each of the annotators will attempt to resolve differences among the annotations for a fraction of the genes. Six groups will proceed with these efforts, so each group will focus on 1500 genes (9000 genes/6 groups). All groups will include GO Ontology descriptions with their assigned gene annotations. As necessary, the individuals will call upon experts from the community to help to resolve questions about genetic relationships.

  3. Seven annotators comprise the Annotation Working Group, and they are Christophe d'Enfert, Jan Dungan, Andre Nantel, Mike Lorenz, Diane Inglis, M. Andrew Uhl, and Steffen Rupp.

  4. These efforts will begin by exchange of electronic information. However, we will arrange for a face-to-face meeting in May, 2002 to iron out details of rectifying gene lists. This meeting will be supported by the Burroughs Wellcome Fund, the Wellcome Trust, and by Pharmacia Corporation, to whom we are very grateful.

  5. We have in place an Advisory Panel, who will help to resolve any difficult issues that the Working Group faces. The panel includes Neil Gow (U. Aberdeen), Dominique Sanglard (University Hospital Lausanne), Judith Berman (U. Minnesota), and Aaron Mitchell (Columbia U.).

  6. The Candida Genomic Database will house the master gene list once the annotations are merged. They will be responsible for updating gene information, based on publicly available sequence information and input from the Candida research community. They will also be responsible for disseminating the information, and for alerting other genomics resources to updates in a timely manner.

  7. All members of the Candida research community will ensure that the Candida Genomic Database receives their comments and updated genetic and functional information.

  8. Discordance concerning such issues as gene names will be resolved by the CGD in two steps. First, the interested parties will be urged to contact one another and resolve differences among themselves. Second, if this avenue is not productive, the Advisory Panel will reach a resolution after consultation with the interested parties and with members of the Candida research community.

The Candida research community owes a debt of gratitude to the Annotation Working Group for taking on a difficult and time-consuming task as a service. Our community also expresses the deepest gratitude to Stewart Scherer, whose advocacy for and analysis of the C. albicans genomic sequence has provided a pioneering contribution to our understanding of biology. We are also grateful to those at the Stanford Genome Technology Center who have been directly responsible for the sequencing of the Candida genome, Dr. Ron Davis, Director of SGTC, Dr. Nancy Federspiel who supervised the sequencing project and Dr. Ted Jones for his analysis of the genomic sequence and construction of Assembly 6, which provide the basis for our current annotation. The community also thanks the NIDR and the Burroughs Wellcome Fund for supporting this work.

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