Genome sequencing and transcript analysis of Hemileia vastatrix reveal expression dynamics of candidate effectors dependent on host compatibility

Abstract

Coffee leaf rust caused by the fungus Hemileia vastatrix is one of the most important leaf diseases of coffee plantations worldwide. Current knowledge of the H . vastatrix genome is limited and only a small fraction of the total fungal secretome has been identified. In order to obtain a more comprehensive understanding of its secretome, we aimed to sequence and assemble the entire H . vastatrix genome using two next-generation sequencing platforms and a hybrid assembly strategy. This resulted in a 547 Mb genome of H . vastatrix race XXXIII (Hv33), with 13,364 predicted genes that encode 13,034 putative proteins with transcriptomic support. Based on this proteome, 615 proteins contain putative secretion peptides, and lack transmembrane domains. From this putative secretome, 111 proteins were identified as candidate effectors (EHv33) unique to H . vastatrix , and a subset consisting of 17 EHv33 genes was selected for a temporal gene expression analysis during infection. Five genes were significantly induced early during an incompatible interaction, indicating their potential role as pre-haustorial effectors possibly recognized by the resistant coffee genotype. Another nine genes were significantly induced after haustorium formation in the compatible interaction. Overall, we suggest that this fungus is able to selectively mount its survival strategy with effectors that depend on the host genotype involved in the infection process.

Spatial and Temporal Genetic Diversity and Population Structure of Hemileia vastatrix from Peruvian Coffee Plantations

“…Notwithstanding, some molecular studies did not detect recombination and support the asexual status of H. vastatrix ( Rozo et al, 2012 ), whereas others found evidence of recombination among fungus isolates under certain specific conditions ( Cabral et al, 2016 ; Maia et al, 2013 ). Likewise, in the absence of sexual reproduction, which is still a debatable topic, hybridization between divergent isolates ( Silva et al, 2018 ), parasexuality ( Carvalho et al, 2011 ; Wang and McCallum, 2009 ) and transposons activity ( Cristancho et al, 2014 ; Porto et al, 2019 ) could also be playing an important role in generating genetic variability in H. vastatrix .…”

“…Previous studies in population genetics showed that H. vastatrix has characteristics of a large population, with a high probability for new fungus variants to arise by rapid multiplication and mutation events ( McDonald and Linde, 2002 ). Additionally, they showed that the pathogen has high mutation rate and adaptive capacity ( Cabral et al, 2009, 2016 ; Cristancho et al, 2007 ; Maia et al, 2013 ; Porto et al, 2019 ). These features allow it to quickly break the resistance of coffee cultivars derived from the Timor Hybrid (HDT) ( Diniz et al, 2012 ), which is a resistant natural hybrid between C. arabica and C. canephora ( Lashermes et al, 1993 ) widely used in coffee breeding programs in the world ( Gichuru et al, 2012 ; Zambolim, 2016 ).…”

The Conifer Root and Stem Rot Pathogen (Heterobasidion parviporum): Effectome Analysis and Roles in Interspecific Fungal Interactions

“…No NECT-specific gene was observed in the transcriptome analysis. Effector proteins are believed to be temporally expressed, with a set of effectors highly expressed during the early infection and some highly expressed at the later stages [30,31]. In our previous study [21], necrotic tissue was collected after three and a half months of infection, and some effectors were probably already expressed before the sampling.…”

Recent Advances in Molecular Diagnostics of Fungal Plant Pathogens: A Mini Review

“…A hybrid and hierarchical de novo association strategy was used to sequence the genome of M. fructicola Mfrc123 strain through an amalgamation of Illumina short read NGS and Pacific Biosciences (PacBio) long read third-generation sequencing platforms ( Angelini et al., 2019 ). In another hybrid approach, the genome of the coffee rust fungus Hemileia vastarix was sequenced using PacBio RS II and Illumina HiSeq platforms and a total genome of 547 Mb of H. vastatrix race XXXIII was generated ( Porto et al., 2019 ). The sequenced reference genomes can be used to study the genome biology and evolution with other species.…”