Coffee rust genome measured using flow cytometry: does size matter?

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.

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“…These reads totaled >100X coverage for the expected genome size of H . vastatrix (~733.5 Mb according to [24]).…”

Section: Resultsmentioning

confidence: 99%

“…vastatrix among the largest genomes of rust fungi. The large size of the fungal nuclear genome was measured by flow cytometry, as ranging from 733.5 Mb [24] to 796.8 Mb [25]. However, the lack of a well-assembled genome and the unknown full repertoire of effector proteins has significantly impeded the investigation of H .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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“…Nevertheless, the c . 800‐Mbp genome of H. vastatrix (Carvalho et al ., ; Tavares et al ., ) stands out as one of the largest among rusts (Ramos et al ., ; Tavares et al ., ) and the largest genome of fungal pathogens of economic relevance. The genome of H. vastatrix appears to also vary in size: in a preliminary study including 11 isolates representing distinct races, the genome size ranged from 765 to 839 Mbp, with a general average (± standard deviation) of 797 ± 27 Mbp (CIFC team, unpublished data).…”

Section: Cytogenomics and Molecular Pathogenicitymentioning

confidence: 98%

The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics

Talhinhas

Batista

Diniz

et al. 2017

Molecular Plant Pathology

199

191

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Although exhibiting limited genetic polymorphism, the very large genome of H. vastatrix (c. 797 Mbp) conceals great pathological diversity, with more than 50 physiological races. Gene expression studies have revealed a very precocious activation of signalling pathways and production of putative effectors, suggesting that the plant-fungus dialogue starts as early as at the germ tube stage, and have provided clues for the identification of avr genes.

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“…Genomes range from the 53-and 56-Mbp genomes of Puccinia striiformis f. sp. tritici PST87/7 and PST-08/21, respectively, to the 733.5-Mbp and 1-Gbp genomes of Hemileia vastatrix and Phakopsora pachyrhizi, respectively (Cantu et al, 2013;Carvalho et al, 2013;Loehrer et al, 2014;Tavares et al, 2014).…”

Section: Obligate Biotrophy Does Not Constrain Genome Sizementioning

confidence: 99%

Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism

2015

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1207I.1208II.1209III.1211IV.1217V.1218VI.1219VII.1221VIII.12241224References1224 Summary Research on obligate biotrophic plant parasites, which reproduce only on living hosts, has revealed a broad diversity of filamentous microbes that have independently acquired complex morphological structures, such as haustoria. Genome studies have also demonstrated a concerted loss of genes for metabolism and lytic enzymes, and gain of diversity of genes coding for effectors involved in host defense suppression. So far, these traits converge in all known obligate biotrophic parasites, but unexpected genome plasticity remains. This plasticity is manifested as transposable element (TE)‐driven increases in genome size, observed to be associated with the diversification of virulence genes under selection pressure. Genome expansion could result from the governing of the pathogen response to ecological selection pressures, such as host or nutrient availability, or to microbial interactions, such as competition, hyperparasitism and beneficial cooperations. Expansion is balanced by alternating sexual and asexual cycles, as well as selfing and outcrossing, which operate to control transposon activity in populations. In turn, the prevalence of these balancing mechanisms seems to be correlated with external biotic factors, suggesting a complex, interconnected evolutionary network in host–pathogen–microbe interactions. Therefore, the next phase of obligate biotrophic pathogen research will need to uncover how this network, including multitrophic interactions, shapes the evolution and diversity of pathogens.

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Coffee rust genome measured using flow cytometry: does size matter?

Cited by 11 publications

References 43 publications

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

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

The coffee leaf rust pathogen Hemileia vastatrix: one and a half centuries around the tropics

Host–microbe and microbe–microbe interactions in the evolution of obligate plant parasitism

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