Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales

Abstract

Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333 Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.

Flow cytometry reveals that the rust fungus, Uromyces bidentis (Pucciniales), possesses the largest fungal genome reported—2489 Mbp

“…As most of the genome sequences available for rusts represent relatively small genomes, it is expected that larger rust genomes could comprise even higher proportions of such repetitive elements, which is corroborated by preliminary data obtained from Hemileia vastatrix Berk. & Broome (Cristancho et al ., ) and Uromyces fabae de Bary ex Cooke (Link et al ., ). Polyploidy could also account for these large genomes, but no evidence supporting its occurrence has been gathered.…”

The Hemileia vastatrix effector HvEC‐016 suppresses bacterial blight symptoms in coffee genotypes with the SH1 rust resistance gene

“…We used BLASTN to compare the open reading frame (ORF) sequences of the 34 full-length ESTs with those reported previously Cristancho et al, 2014;Talhinhas et al, 2014) in order to identity novel candidate H. vastatrix effectors. Our analysis revealed that HvEC-032 and HvEC-120 (highlighted yellow in Table S2) were not reported by these authors.…”

Advances in understanding obligate biotrophy in rust fungi

“…pachyrhizi , Uromyces appendiculatus (Table S1; Loehrer et al ., ; Link T.I. et al ., ; Cristancho et al ., ; Tao et al ., ). Transcriptomic analyses of host infection and isolated haustoria have helped to prioritize candidate effectors in different rust species (Duplessis et al ., ; Aime et al ., ).…”

“…RNAsequencing (RNAseq) has been instrumental in providing valuable insights about rust fungi without reference genomes, for example H. vastatrix, Gymnosporangium spp., P. pachyrhizi, Uromyces appendiculatus (Table S1; Loehrer et al, 2014b;Link T.I. et al, 2014;Cristancho et al, 2014;Tao et al, 2017). Transcriptomic analyses of host infection and isolated haustoria have helped to prioritize candidate effectors in different rust species Aime et al, 2017).…”

“…Hundreds of candidate effectors have been identified in H. vastatrix by genomic and transcriptomic approaches (Fernandez et al, 2012;Cristancho et al, 2014;Talhinhas et al, 2014). Similar to effectoromic screens conducted in P. graminis f. sp.…”