Plant & Animal Genome V Conference
Town & Country Hotel, San Diego, CA, January 12-16, 1997.
PAG-V: W15 - THE ARABIDOPSIS EST PROGRAMME : PROGRESS, APPLICATIONS AND PERSPECTIVES
W15
THE ARABIDOPSIS EST PROGRAMME : PROGRESS, APPLICATIONS AND PERSPECTIVES
DELSENY, MICHEL
LPBMV, Universite de Perpignan, 52, avenue de Villeneuve, 66860 PERPIGNAN-CEDEX, FRANCE
The ESSA programme has contributed about half the non redundant Arabidopsis thaliana ESTs in dbEST. With approximately 30000 ESTs, increasing redundancy makes this strategy no longer cost effective to tag new genes. Our effort was redirected in four directions : Using TIGR assembler, it was possible to reconstruct about 12000 unique contigs. This is likely an overestimate of effectively tagged genes due to sequencing errors and non-overlapping ESTs which appear to tag different genes. A detailed investigation of ESTs tagging ribosomal protein genes identified 104 full length cDNAs corresponding to 50 types of non ambiguously identified ribosomal proteins. They are coded by up to four members of small multigene families. We mapped about 600 ESTs corresponding to genes of interest to our labs (genes expressed in etiolated seedlings, genes for LEA proteins or protein kinases), combining classical RFLP or CAPS genetic mapping and physical mapping by PCR on the CIC YAC library 3-D pools. In collaboration with the Gent Group, we considered the possibility of completing the physical map of chromosome 3, for which there are so far 12 contigs and at most 5 gaps corresponding to regions which are apparently not represented in the CIC library. It is now clear that many genes in Arabidopsis are organised as mosaic structures with short exons and multiple introns. In the region we have sequenced around the Em locus on chromosome 3, this type of analysis has been determinant in identifying genes and isolating cognate cDNAs. We could use not only Arabidopsis ESTs but also those from rice and C. elegans. We have used the 1-2 % of ESTs showing conservation at the nucleotide level between Arabidopsis and Rice to carry out comparative mapping, with common identified markers which are likely to exist in all plant species.