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Supernumerary chromosome segments are known to harbor different transposons from their essential counterparts. The aim of this study was to investigate the role of transposons in the origin and evolution of supernumerary segments in the asexual fungal pathogen  Fusarium virguliforme . We compared the genomes of 11 isolates comprising six  Fusarium  species that cause soybean sudden death syndrome (SDS) or bean root rot (BRR), and identified significant levels of genetic variation in A+T-rich repeat blocks of the essential chromosomes and in A+T-neutral regions of the supernumerary segments. The A+T-rich repeat blocks in the essential chromosomes were highly variable between  F. virguliforme  and non- F. virguliforme  isolates, but were scarcely variable between  F. virguliforme  isolates. The A+T-neutral regions in the supernumerary segments, however, were highly variable between  F. virguliforme  isolates, with a statistically significant number (21 standard deviations above the mean) of single nucleotide polymorphisms (SNPs). And supernumerary sequence types and rearrangement patterns of some  F. virguliforme  isolates were present in an isolate of  F. cuneirostrum  but not in the other  F. virguliforme  isolates. The most variable and highly expressed region in the supernumerary segments contained an active DNA transposon that was a most conserved match between  F. virguliforme  and the unrelated fungus  Tolypocladium inflatum . This transposon was absent from two of the  F. virguliforme  isolates. Furthermore, transposons in the supernumerary segments of some  F. virguliforme  isolates were present in non- F. virguliforme  isolates, but were absent from the other  F. virguliforme  isolates. Two supernumerary P450 enzymes were 43% and 57% identical to their essential counterparts. This study has raised the possibility that transposons generate genetic variation in supernumerary chromosome segments by frequent horizontal transfer within and between closely related species.

Identification of Highly Variable Supernumerary Chromosome Segments in an Asexual Pathogen