AT-rich isochores as ecological niches for effectors in the genome of Leptosphaeria maculans The genome of the ascomycete Leptosphaeria maculans shows the unusual characteristics to be organized in isochores. GC-equilibrated isochores (average 52% GC) are gene-rich whereas AT-rich isochores (40–43% GC) are mostly devoid of active sequences and are made up of mosaics of intermingled and degenerated repeated elements. The three avirulence (AvrLm) genes identified so far in this species are isolated in the middle of large AT-rich isochores. Our postulate thus was that AT-rich isochores were specific “ecological niches” for avirulence genes and effectors in L. maculans. This was firstly validated by analysis of three genes lying in the same genome environment (LmCys genes) and showing the same characteristics as AvrLm genes (low GC content, strong overexpression at the onset of plant infection, encoding for small secreted proteins -SSP- often rich in cysteines). Of these, one, LmCys2, was shown to act as an effector, probably contributing to suppression of plant defense. A systematic search for SPP as effector candidates was performed using bioinformatics. 455 AT-rich isochores were extracted from the genome data and their repeat content masked using the L. maculans repeat database. Non-repeated regions were then investigated with a pipe-line dedicated to the identification of SSP. This provided us with three datasets: 529 SSP-encoding genes in GC-equilibrated isochores, 498 non- SSP- and 122 SSP-encoding genes in AT-rich isochores. Part of this latter set of genes was analyzed for their occurrence in natural populations and expression data in culture and in planta. Finally, the 122 AT-SSP putative proteins showed structural features reminiscent of the AvrLm and LmCys genes. Possible diversification mechanisms as a function of genome location will be discussed.