Plant Genome IV Conference Plant Genome IV Conference
In the past two years an EU consortium of 9 labs have been sequencing, on a pilot scale , the FCA region on the lower arm of chromsome 4. To date approximately 850kb of near-contiguous sequence has been obtained, and a further 250kb is in shotgun phase. Sequence substrates have been Lorist cosmids obtained from the Goodman contigs (50%), pLAFR3 cosmids (20%) and cosmids derived from subcloning YACs (30%). Future sequence work will use more stable clones with larger inserts, such as the BAC and P1 libraries which are now available. Most labs use a standard shotgun sequencing approach which gives over 5-fold coverage on each strand, leading to an accuracy of about 1 in 5,000. There is an independent verification of each lab's accuracy, ensuring the amalgamated sequence is of similar standard. Sequence has been analysed using a variety of gene prediction programmes, and the XGRAIL suite trained on Arabidopsis sequence has proved to be the most useful in predicting splice junctions. Nevertheless, cognate cDNAs for a significant proportion of the putative genes are also being sequenced to provide a more comprehensive dataset for refining genefinder procedures. Preliminary analysis of the sequence reveals a striking periodicity of putative gene density, varying from one gene every 4-5 kb near FCA to one gene every 7 kb several 100 kb distant from FCA. About 150 putative genes have been identified, of which 3 have been sequenced previously and of which 25 match an EST from either rice or Arabidopsis. About 30% of the genes have no close database match (BLAST score less than 100), and these may represent plant specific genes. several interesting putative genes involved in metabolism and transport have been identified, but no very striking finds have occurred yet. Future plans include completing 1.85 Mb of the lower arm by the end of next year, and the complete sequencing of chromosome 4 by the end of 1998.