SUPPLEMENTARY MATERIALS : FIGURE S1. Phylogenetic relationship of paralogs with regards to the respective host-range-associated gene. FCIR = Fusarium circinatum; FFRAC = Fusarium fracticaudum; FPIN = Fusarium pininemorale; FSUB = Fusarium subglutinans; FIGURE S2. Host-range-associated genes with ancestral origins that emerged within the FFSC. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S3. Host-range-associated genes with ancestral origins that emerged within the FFSC and FOSC. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S4. Host-range-associated genes with ancestral origins that emerged within the broader Fusarium outside the FFSC and FOSC. The investigated host-range associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S5. Host-range-associated genes with less than 10 ancestral origin hits and mostly Fusarium. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S6. Host-range-associated genes with ancestral origins hits and mostly not Fusarium. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S7. Host-range-associated genes with ancestral origins outside Fusarium but in the Ascomycetes. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S8. Host-range-associated genes with ancestral origins outside Fungi. The investigated host-range-associated genes are highlighted in yellow; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum; FIGURE S9. The distribution of host-range-associated genes from pine-host-associated Fusarium species and conservation of synteny across and between chromosomes and genomes. Pine-host-associated genes distribution across each of the chromosomes as indicated by the blue lines. The conservation of synteny and inversion between the relevant genomes are indicated in the brown blocks and red lines. FCIR = F. circinatum; chromosome size is given in kbp; FIGURE S10. The distribution of hostrange- associated genes from Poaceae-host-associated Fusarium species and conservation of synteny across and between chromosomes and genomes. Poaceae-host-associated gene distribution across each of the chromosomes as indicated by the blue lines. The conservation of synteny and inversion between the relevant genomes are indicated in the brown blocks and red lines. FTEMP = F. temperatum; chromosome size is given in kbp; FIGURE S11. The syntenous relationship between genes from F. circinatum versus F. temperatum; FIGURE S12. The syntenous relationship between genes from F. temperatum and F. circinatum; TABLE S1. BUSCO results for the relevant Fusarium genomes; TABLE S2. The size difference between the chromosomes of four of the six Fusarium species; TABLE S3. Presence of telomeres at chromosomal ends for the two representative Fusarium species examined; TABLE S4. The Blast2GO data for the 72 unique pine-host-associated genes specifically for (A) Fusarium circinatum, (B) F. fracticaudum and (C) F. pininemorale; TABLE S5. The Blast2GO data for the 47 unique Poaceae-host-associated genes, specifically for (A) Fusarium konzum, (B) F. subglutinans and (C) F. temperatum; TABLE S6. The Fischer exact test data for (A) the 72 unique pine-host-associated genes and (B) the 47 unique Poaceae-host-associated genes; TABLE S7. The EST and RNA-seq data for F. circinatum, obtained from Wingfield et al. [52] and Phasha et al. [53], respectively; TABLE S8. The placement of host-range-associated genes in groups that infer their evolutionary origins; TABLE S9. The gene information for the unique F. circinatum genes, in terms of chromosome location, subtelomeric placement, ancestral origin and BLAST description; TABLE S10. The gene information for the unique F. temperatum genes, in terms of chromosome location, subtelomeric placement, ancestral origin and BLAST description; TABLE S11. The host-range-associated gene density for both F. circinatum and F. temperatum; TABLE S12. The SynChro data for genes downstream and upstream of the host-rangeassociated genes of both the pine- and Poaceae-host-associated Fusarium species; FCIR = Fusarium circinatum and FTEMP = Fusarium temperatum.The Fusarium fujikuroi species complex (FFSC) includes socioeconomically important
pathogens that cause disease for numerous crops and synthesize a variety of secondary metabolites
that can contaminate feedstocks and food. Here, we used comparative genomics to elucidate processes
underlying the ability of pine-associated and grass-associated FFSC species to colonize tissues of
their respective plant hosts. We characterized the identity, possible functions, evolutionary origins,
and chromosomal positions of the host-range-associated genes encoded by the two groups of fungi.
The 72 and 47 genes identified as unique to the respective genome groups were potentially involved
in diverse processes, ranging from transcription, regulation, and substrate transport through to
virulence/pathogenicity. Most genes arose early during the evolution of Fusarium/FFSC and were
only subsequently retained in some lineages, while some had origins outside Fusarium. Although
differences in the densities of these genes were especially noticeable on the conditionally dispensable
chromosome of F. temperatum (representing the grass-associates) and F. circinatum (representing the
pine-associates), the host-range-associated genes tended to be located towards the subtelomeric
regions of chromosomes. Taken together, these results demonstrate that multiple mechanisms drive
the emergence of genes in the grass- and pine-associated FFSC taxa examined. It also highlighted
the diversity of the molecular processes potentially underlying niche-specificity in these and other
Fusarium species.The South African Department of Science and Innovation’s South African Research Chair Initiative, the DSI-NRF Centre of Excellence in Plant Health Biotechnology at the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, the Food Safety National Program at the United States Department of Agriculture, Agricultural Research Service.https://www.mdpi.com/journal/pathogensam2023BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog
