Bioinformatic as a tool to highlight and characterize extragenomic sequences within Fusarium verticillioides strains isolated from Italian Zea mays kernels

Fusarium Link is a genus including ubiquitous plant-pathogenic fungi that may cause severe crop losses. The Fusarium genus is divided in species complexes; the species are grouped by physiological, biological, ecological and genetic similarity. The Fusarium fujikuroi species complex (FFSC) is one of the largest complexes. Although species within the FFSC complex are closely related, they may have distinct phenotypic traits like mycotoxin production and pathogenicity. In addition to a set of species-specific core chromosomes, some FFSC species may have extra, or supernumerary chromosomes (SCs) that may even differ between isolates in presence/absence or length. SCs in other Fusarium have been shown to have important roles in the biology and virulence of these fungi. In a previous study, bioinformatics analysis pinpointed the presence of two additional mega base (Mb) of sequence data in the genome of an “Italian” strain 10027 of Fusarium verticillioides (Sacc.) Nirenberg (Fv) as compared to the reference strain (Fv 7600) sequenced by the Broad Institute. This additional Fv sequence data shares significant similarity to sequence present in the genome of F. fujikuroi (Sawada) Wollenw as well as other species within the FFSC. We used sequences within the two Mb of sequence as markers for classifying about 200 Fv strains isolated from Zea mays L. kernels collected between 2013 to 2016 from northern Italy. A representative subset of 24 of these strains were sequenced using Next Generation Sequencing technology. The sequence data was used to develop a pipeline for highlighting the inter-intra specific differences present in the additional two Mb, potential SCs. Moreover, this pipeline identified interesting set of genes belonging to Ascomycota genus with a different Gene Onthology enrichment among the various Fv strains isolated across northern Italy.