Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea

Pokhrel, A.; Haridas, S.; Calhoun, S.; Kuo, A.; Lipzen, A.; Riley, R.; LaButti, K.; Pangilinan, J.; Andreopoulos, B.; He, G.; Yan, M.; Barry, K.; Ma, L.-J.; Geiser, D. M.; Freitag, M.; Grigoriev, I. V.; Coleman, J.

doi:10.64898/2026.06.29.735274

bioRxiv · 10.64898/2026.06.29.735274

Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea

Pokhrel, A.·Haridas, S.·Calhoun, S.·Kuo, A.·Lipzen, A.·Riley, R.·LaButti, K.·Pangilinan, J.·Andreopoulos, B.·He, G.·Yan, M.·Barry, K.·Ma, L.-J.·Geiser, D. M.·Freitag, M.·Grigoriev, I. V.·Coleman, J.

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Abstract

The contribution of accessory or conditionally dispensable chromosomes to host-specific virulence was first demonstrated in members of the Fusarium solani species complex (FSSC) that are pathogens of garden pea, Pisum sativum L. The phenomenon has since been shown to exist in many fungal plant pathogens, including the closely related F. oxysporum species complex (FOSC). Genome analysis of members of the FSSC and FOSC pathogenic on pea revealed a diverse size range of the accessory genome of these fungi. Despite the [~]65 million years of diverging time, regions on a chromosome known to carry host-specific virulence factors for pea, including the cytochrome P450 pisatin demethylase (PDA) and other pea pathogenicity (PEP) genes, were present in all genomes of these pea pathogens. Genes directly involved in virulence on pea - PEP2, PDA, and PEP5- were the most frequently clustered together. Transcriptome analysis of fungal mycelia treated with the pea phytoalexin pisatin, identified 1,155 differentially expressed genes where many were involved in cellular stress responses. As wilt pathogens that invade host xylem, members of the FOSC encode more putative effectors, when compared to those in the FSSC, and several FOSC effectors were identified to confer race specificity. The conservation of part of the accessory genomes across two evolutionarily diverged species complexes suggests a common origin. Horizontal transfer of accessory chromosomes containing genetic loci involved in pathogenesis for garden pea offers a parsimonious explanation of the polyphyletic origin of host specificity.

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Pokhrel, A., Haridas, S., Calhoun, S., Kuo, A., Lipzen, A., Riley, R., LaButti, K., Pangilinan, J., Andreopoulos, B., He, G., Yan, M., Barry, K., Ma, L.-J., Geiser, D. M., Freitag, M., Grigoriev, I. V., Coleman, J.. 2026-07-03. Comparative genomics reveals shared accessory regions between members of two Fusarium species complexes virulent on garden pea. https://doi.org/10.64898/2026.06.29.735274

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