Genoscope is sequencing a pericentromeric region in the genome of the fungal phytopathogen Leptosphaeria maculans. This genomic region is of peculiar interest since it contains three genetically clustered avirulence genes, AvrLm1-AvrLm2-AvrLm6. A preliminary collaboration between Genoscope and INRA-PMDV, in 2000, aimed at sequencing a contig of 3 BAC clones located 5’ of the Avr cluster. The clones originated from a 24 X BAC library (HindIII or NdeII partial restriction fragments cloned in pBeloBAC11) of isolate JN3 harbouring the avirulent alleles at loci AvrLm1 and AvrLm6. Following sequence assembly, the 184-kb sequence was shown to mainly comprise degenerated and truncated retrotransposons, except for a 32-kb island containing 11 functional ORFs.

Genoscope is currently expanding the sequencing to cover the whole pericentromeric region, and to identify the avirulence and pathogenicity genes within this region. For this purpose additional steps of chromosome walk were performed in the 3’ region of the 184-kb contig. This allowed the generation of an expanded contig comprising 13 new BAC clones and covering ca. 720 kb. This contig however still contains a ca. 80-kb gap which is in the process of being filled. Genoscope began the sequencing of the expanded contig in 2003 at 19 X coverage, and should provide the whole ungapped sequence by the end of 2004. In parallel, Genoscope is undertaking a partial sequencing of two additional contigs in two other L. maculans isolates, NZ-T and v29, differing from JN3 by the presence of the virulent allele at the avrLm1 locus. The contigs, selected to contain mostly the GC-rich parts of the region, cover 345 kb in isolate NZ-T (6 BACs) and 410 kb in isolate v29 (8 BACs).