Arabidopsis Workshop at PGIII

Report by Mary Anderson

17 January 1995, San Diego, USA

Chair: Caroline Dean

This workshop focussed on the more global aspects of Arabidopsis research looking at progress in the mapping and sequencing of the genome.

Renate Schmidt (John Innes, UK) presented progress on the physical mapping of chromosome 4 and 5 by the Dean Group. Using 140 markers in hybridisation experiments on the four available YAC libraries, in combination with chromosome walking, they have managed to generate eight contigs which span chromosome 4. Current estimates on the size of this chromosome are around 20.5 Mb. The position of the centromere and the rDNA have been identified. Renate reported that repeated DNA around the centromere proves problematical in the chromosome walking experiments, as some tandemly repeated sequences localized in the centromeric region are likely to be lost from the YAC inserts following replication. Good progress was also reported for chromosome 5, which now is covered by 40 contigs.

Bertrand Lemieux (York University, Canada) presented an overview of his EST mapping project. He described the use of a PCR-based approach to identify YACs that contain a limited set of ESTs from the NCBI repository. This work is being done in collaboration with Ron Davis at Stanford, the French Arabidopsis genome mapping group and Joe Ecker at Penn State. The YAC libraries being used are the CIC and the yUP banks with a few EG clones included. So far 600 primers and 140 ESTs have been used to anchor 192 YAC clones.

Tom Newman (Michigan State) reported on the progress of the MSU Arabidopsis cDNA project. Their goal is to generate Expressed Sequence Tags (ESTs) for about 85% of the expressed genes in this model system. This effort is complementary to the French cDNA sequencing initiative, which was reported on at one of the main sessions. The MSU group are now sequencing approximately 1000 ESTs per month and have already deposited 10,000 ESTs in dbEST at NCBI. Sequence analysis before submission to dbEST is conducted through a collaboration with Ernie Retzel's Biocomputing Group at Minnesota (see his article). Clones and libraries are available from the Arabidopsis Biological Resource Center at Ohio State. The generation of a subtracted library is a major priority. Tom reported that all the clones from which ESTs have been generated will be removed from the cDNA library so that low abundance cDNAs can be identified.

Howard Goodman (Massachussets General Hospital, Boston) reported on progress of mapping chromosome 2. Using anchored markers, the new CIC YAC library, and walking with end-probes they have established approximately 8 YAC contigs covering approximately 75% of chromosome 2. Current efforts are directed toward closing the remaining gaps. In addition, they have initiated a sequencing effort on chromosome 2 using the multiplex method. Data is in the process of being collected on 4 cosmids as part of an initial feasibility study.

George Murphy (John Innes, UK) reported on the EC-funded European Scientists Sequencing Arabidopsis (ESSA) program, which involves seven laboratories across the EC that aim to sequence a contiguous region of two million bases of chromosome 4 of arabidopsis over a period of three years. The program is coordinated from Norwich by Mike Bevan and about 40% of the sequencing will be performed there. Analysis of the first two cosmids sequenced in Norwich shows that the gene density is about one gene every 5 kb. Interestingly, although a number of computing techniques were applied to identify coding regions, none were able to detect two genes eventually located by hybridization of a cDNA library to the cosmids.

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