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

Authors

Peri A Tobias, Richard J Edwards, Jamie Botting, Giullia di Lorenzo, Vera Inácio, Inês Diniz, Maria do Céu Silva, Leonor Guerra-Guimarães, Vitor Várzea, Robert F Park, Dora Batista

Published in

G3 (Bethesda, Md.). Aug 01, 2026. Epub Aug 01, 2026.

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 ∼94%, with a GC content of 33.5%. 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. qPCR validation supports a chr17 trisomy in Hv178a absent from the ancestral lineage and potentially explaining the observed change in virulence.

PMID:
42538812
Bibliographic data and abstract were imported from PubMed on 01 Aug 2026.

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