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The  Gibberella fujikuroi  complex includes many  Fusarium  species that cause significant losses in yield and quality of agricultural and forestry crops. Due to their economic importance, whole-genome sequence information has rapidly become available for species including  Fusarium circinatum, Fusarium fujikuroi  and  Fusarium verticillioides , each of which represent one of the three main clades known in this complex. However, no previous studies have explored the genomic commonalities and differences among these fungi. In this study, a previously completed genetic linkage map for an interspecific cross between  Fusarium temperatum  and  F. circinatum , together with genomic sequence data, was utilized to consider the level of synteny between the three  Fusarium  genomes. Regions that are homologous amongst the  Fusarium  genomes examined were identified using  in silico  and pyrosequenced amplified fragment length polymorphism (AFLP) fragment analyses. Homology was determined using BLAST analysis of the sequences, with 777 homologous regions aligned to  F. fujikuroi  and  F. verticillioides . This also made it possible to assign the linkage groups from the interspecific cross to their corresponding chromosomes in  F. verticillioides  and  F. fujikuroi , as well as to assign two previously unmapped supercontigs of  F. verticillioides  to probable chromosomal locations. We further found evidence of a reciprocal translocation between the distal ends of chromosome 8 and 11, which apparently originated before the divergence of  F. circinatum  and  F. temperatum . Overall, a remarkable level of macrosynteny was observed among the three  Fusarium  genomes, when comparing AFLP fragments. This study not only demonstrates how  in silico  AFLPs can aid in the integration of a genetic linkage map to the physical genome, but it also highlights the benefits of using this tool to study genomic synteny and architecture.

Genome-Wide Macrosynteny among Fusarium Species in the Gibberella fujikuroi Complex Revealed by Amplified Fragment Length Polymorphisms