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Using phylogenomics to infer evolutionary history within Fusarium oxysporum

Species recognition and evolutionary inference in the Fusarium oxysporum species complex (FOSC) has been challenging, but addressing this question is critical for understanding the diversity and evolutionary dynamics of this species complex. Previous phylogenetic studies indicated a lack of concordance between molecular markers within the complex, reflecting either some form of genetic exchange or marker behavior that conceals evolutionary history. To determine whether a consistent evolutionary pattern could be inferred from markers within the F. oxysporum genome, we performed phylogenetic analysis using DNA sequences from 40 inferred open reading frames evenly distributed across F. oxysporum chromosomes in eleven F. oxysporum isolates with available complete genome sequences. Analysis of polymorphic sites at the 40 multi-locus regions combined showed 89.3% similarity between the FOSC and F. verticillioides, and 96.3% similarity among members of the FOSC. 22/40 markers showed the same topology as the combined 40 multi-locus phylogeny; however, phylogenies for 14 loci showed topologies that differed from the consensus tree. Also, four individually-constructed phylogenies show very low bootstrap support on most branches, creating un-resolved trees. Two distinct groups were identified among 10/11 FOSC isolates, with the eleventh strain II5 (F. oxysporum f.sp. cubense) shown as distinct from the other strains in most gene trees. These results strongly indicate that most unlinked genes within FOSC contain a record of the evolutionary history of the group, reflecting either clonal reproduction or a record of speciation. This work also identifies a number of candidate markers for further investigation of evolutionary patterns within FOSC, and demonstrates the utility of the Fusarium Comparative Genomics Platform for performing phylogenomic studies in this group.

Bongsoo Park, David M. Geiser, Kerry O'Donnell, Seogchan Kang.

>> A list of 40 multi loci and single gene phylogeny
>> The polymorphic site analysis

>> The first 40 loci
>> The finally selected informative loci