Dispensable genome and segmental duplications drive the genome plasticity inFusarium solani

Abstract

AbstractFusarium solaniis a species complex encompassing a large phylogenetic clade with diverse members occupying varied habitats. We recently reported a unique opportunisticF. solaniassociated with unusual dark galls in sugarbeet. We assembled the chromosome-level genome of theF. solanisugarbeet isolate strain SB1 using Oxford Nanopore and Hi-C sequencing. SB1 has a large genome (59.38 Mb) organized into 15 chromosomes. The genome expansion is due to the high repeats and massive segmental duplications within its three potentially accessory chromosomes. These chromosomes are absent in the closest reference genome with chromosome-level assembly,F. vanettenii77-13-4. The extensive segmental duplications between the two SB1 chromosomes suggest that this isolate may have doubled its accessory genes. Further comparison of theF. solanistrain SB1 genome demonstrates inversions and syntenic regions to an accessory chromosome ofF. vanettenii77-13-4. The pan-genome of 12 publicly availableF. solaniisolates nearly reached gene saturation, with few new genes discovered after the addition of the last genome. Based on orthogroups and average nucleotide identity,F. solaniis not grouped by lifestyle or origin. The pan-genome analysis further revealed the enrichment of several enzymes-coding genes within the dispensable (accessory + unique genes) genome, such as hydrolases, transferases, oxidoreductases, lyases, ligases, isomerase, and dehydrogenase. The evidence presented here suggests that genome plasticity, genetic diversity, and adaptive traits inFusarium solaniare driven by the dispensable genome with significant contributions from segmental duplications.