Arabidopsis genome project

• Research unit: EU RFP
• Project number: 95.0795

Key words (English)

Sequencing arabidopsis thaliana; essa; genome project

Alternative project number (English)

EU project number: BIO4CT960338

Research programs (English)

EU-programme: 4. Frame Research Programme - 4.1 Biotechnology

Short description (English)

See abstract

Abstract (English)

Arabidopsis has been adopted as a model organsim for the moecular 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. 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 programms more assessable. The goal of sequencing the entire genome of selected model organsims 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 aims of the EU proposal are to sequence the low-copy regions of chromosome 4 of A. thaliana and to contribute to an international strategy to complete the sequence of the 105mb low copy regions of the genome in an efficient, cost effective and timely manner.
One main source was a TAMU Bac library. BAC clones with an average size of 100kb were distributed among 17 laboratories in the EU. A shotgun library from our clone F18A5 was prepared by GATC GmbH. The DNA was sheared by nebulisation to 1-3kb in size, the damaged ends of the DNA molecules are repaired and a 1kb or 3kb fraction was ligated into a phagemid vector.
We have isolated and sequenced the plasmids of 1800 E. coli clones using the cycle sequencing chemistry and dye terminators. All reactions were assembled on a power Mac Intosh using DNA Star as the computer programm. The final 10 contigs have been assembled by sequencing PCR products obtained directly from the Bac. Most difficulties during the assembling were due to the fact that our Bac contained several repetitions. A primer walking strategy of some 3kb inserts resolved these questions. The final size of Bac F18A5 was 123232 bp or 114725bp excluding the vector fragment. We could use 1571 sequences to assemble our Bac, the average reading lenght was 477 bases and the coverage 6.1.

References in databases (English)

Swiss Database: Euro-DB of the
State Secretariat for Education and Research
Hallwylstrasse 4
CH-3003 Berne, Switzerland
Tel. [phone]
Swiss Project-Number: 95.0795