A pseudo-phased genome assembly for Hemileia vastatrix reveals an isolate-specific chromosomal haploid trisomy
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 BatistaAbstract
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, localized to 18 chromosomes. We determined that the genomes are highly repetitive at ∼94%, with a guanine-cytosine (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.