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Arabidopsis genome project

Objective



Arabidopsis has been adopted as a model organism for the molecular analysis of complex plant processes, and consequently there has been a very large increase in the number of genes isolated by map-based cloning methods. Accompanying this work, physical maps of the 5 chromosomes are being established which will increase the ease and effectiveness of gene isolation. In addition, techniques for insertional mutagenesis, using transposons and T-DNA, have been developed and are being applied on a scale commensurate with obtaining multiple insertions in every gene. The next step in developing the full utility of Arabidopsis is the systematic sequencing of the genome, which is a foundation for significant advances for increasing the scope of many aspects of plant research, for making it more cost-effective, and for making the quality and likelihood of success of research programmes more assessable. The goal of sequencing the entire genome of selected model organisms is the first step in defining the structure of all transcripts, the expression patterns of all genes and the phenotypes of mutations in all genes. The conceptual framework and tools for this are now available in Arabidopsis. Therefore a strategy of genome sequencing which accumulates sequence at known positions in the genome, thus permitting an orderly strategy for completion and providing an immediate resource for systematic function search, has a high priority in plant science research.
This proposal aims to extend the pilot-scale genome sequencing project launched by the EC in 1993 to complete the sequence of chromosome 4. This is the first plant chromosome to be physically mapped, and several discoveries relevant to sequencing strategies were made in this work. The first is the assembly of 4 YAC contigs covering approximately 17 Mb of the chromosome, the second is the definition of the boundaries of the centromere, and the third is the extreme clustering of repeats at the centromere, subtelomeric and NOR regions. Thus the 17 Mb YAC contigs contain a very low level of repetitive DNA, indicating that a straightforward approach to sequencing, without having to consider low-accuracy sequencing of repetitive regions, will yield nearly all of the sequence of protein-coding DNA of this chromosome. The parameters of chromosome 4 can be used to estimate the relative size of Arabidopsis low-copy sequence as about 105 Mb. The aims of this proposal are to sequence the low-copy regions of chromosome 4 of Arabídopsis thaliana (Arabidopsis) and to contribute to an international strategy to complete the sequence of the 105 Mb low copy regions of the genome in an efficient, cost effective and timely manner. The Work Programme calls for 1O Mb of sequence; the remaining regions on the bottom arm of chr 4 cover 11.4 Mb, which will be sequenced using the potential funding available. An existing collaboration with US colleagues presently sequencing on the top arm of chromosome 4 will be extended such that they will complete the 3.5 Mb top arm as part of the contemporaneous US Arabidopsis genome sequencing project. The final deliverable of this collaboration will be the first sequence of a plant chromosome, from which important information about genome organization, repeat structures, recombination frequency as well as the sequence of about 3200 new genes can be obtained.

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Funding Scheme

CSC - Cost-sharing contracts

Coordinator

AMICA SCIENCE EEIG
EU contribution
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Address
Norwich Research Park John Innes Centre, Colney
NR4 7UH NORWICH
United Kingdom

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Last update: 5 March 2002

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Permalink: https://cordis.europa.eu/project/id/BIO4960338

European Union, 2024