A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

Tobias, P.; Edwards, R. J.; Botting, J.; di Lorenzo, G.; Inacio, V.; Diniz, I.; do Ceu Silva, M.; Varzea, V.; Park, R.; Batista, D.

doi:10.64898/2026.04.04.716458

bioRxiv · 10.64898/2026.04.04.716458

A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy

Tobias, P.·Edwards, R. J.·Botting, J.·di Lorenzo, G.·Inacio, V.·Diniz, I.·do Ceu Silva, M.·Varzea, V.·Park, R.·Batista, D.

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Abstract

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix, have constrained production of Arabica coffee for over 150 years. Here, we present a pseudo-phased, chromosome-level genome resource for H. vastatrix, isolate Hv178a, to guide research into disease management. The Hv178a genome assembly is 665 and 638 Mbp for haplotype A and B respectively, localised to 18 chromosomes. We determined that the genomes are highly repetitive at [~]90%, with a GC content of [~]33%. We present the full annotation of 13,760 and 17,998 protein coding genes, and we predicted 452 and 496 effectors in haplotype A and B respectively. Depth-based comparisons with 11 additional H. vastatrix isolates revealed increased chromosome 17 (chr17) copy number in Hv178a. Validation with qPCR supports a chr17 trisomy in Hv178a absent from the ancestral lineage and potentially explaining the observed change in virulence.

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Tobias, P., Edwards, R. J., Botting, J., di Lorenzo, G., Inacio, V., Diniz, I., do Ceu Silva, M., Varzea, V., Park, R., Batista, D.. 2026-04-07. A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy. https://doi.org/10.64898/2026.04.04.716458

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