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Background  Wheat leaf rust ( Puccinia triticina  Eriks;  Pt ) and stem rust fungi ( P. graminis f.sp. tritici; Pgt ) are significant economic pathogens having similar host ranges and life cycles, but different alternate hosts. The  Pt  genome, currently estimated at 135 Mb, is significantly larger than  Pgt , at 88 Mb, but the reason for the expansion is unknown. Three genomic loci of  Pt  conserved proteins were characterized to gain insight into gene content, genome complexity and expansion.    Results  A bacterial artificial chromosome (BAC) library was made from  P. triticina  race 1, BBBD and probed with  Pt  homologs of genes encoding two predicted  Pgt  secreted effectors and a DNA marker mapping to a region of avirulence. Three BACs, 103 Kb, 112 Kb, and 166 Kb, were sequenced, assembled, and open reading frames were identified. Orthologous genes were identified in  Pgt  and local conservation of gene order (microsynteny) was observed. Pairwise protein identities ranged from 26 to 99%. One  Pt  BAC, containing a RAD18 ortholog, shares syntenic regions with two  Pgt  scaffolds, which could represent both haplotypes of  Pgt . Gene sequence is diverged between the species as well as within the two haplotypes. In all three BAC clones, gene order is locally conserved, however, gene shuffling has occurred relative to  Pgt . These regions are further diverged by differing insertion loci of LTR-retrotransposon,  Gypsy ,  Copia ,  Mutator , and  Harbinger  mobile elements. Uncharacterized  Pt  open reading frames were also found; these proteins are high in lysine and similar to multiple proteins in  Pgt .    Conclusions  The three  Pt  loci are conserved in gene order, with a range of gene sequence divergence. Conservation of predicted haustoria expressed secreted protein genes between  Pt  and  Pgt  is extended to the more distant poplar rust,  Melampsora larici-populina . The loci also reveal that genome expansion in  Pt  is in part due to higher occurrence of repeat-elements in this species.

Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements