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

• DOI: 10.1371/journal.pone.0114682
• Publication Date: 2014-12-08T19:22:45Z
• Authors: Lieschen De Vos; Emma T. Steenkamp; Simon H. Martin; Quentin C. Santana; Gerda Fourie; Nicolaas A. van d...; Michael J. Wingfield; Brenda D. Wingfield
• Keywords: Unmapped supercontigs; 0301 basic medicine; Genomic synteny; Science; Q; Molecular Sequence Data; R; Computational Biology; Sequence Analysis, DNA; 15. Life on land; Fusarium verticillioides; Synteny; 03 medical and health sciences; Gibberella fujikuroi; Fusarium; Medicine; Amplified Fragment Length Polymorphism Analysis; Genome, Fungal; DNA, Fungal; Phylogeny; Research Article

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.