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

Talhinhas, Pedro; Batista, Dora; Diniz, Inês; Vieira, Ana; Silva, Diogo N.; Loureiro, Andreia; Tavares, Sílvia; Pereira, Ana Paula; Azinheira, H. G.; Guerra‐Guimarães, Leonor; Várzea, Vítor; Silva, Maria do Céu

doi:10.1111/mpp.12512

Cited by 187 publications

(248 citation statements)

References 105 publications

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“…Even with the application of thousands of SNPs, no significant genetic structuring was found according to geographical origin or pathotype within this group, apart from the incipient separation of isolates with basal pathotypes. To explain this apparent panmixia, in addition to the previously identified factors of worldwide expansion of coffee trade and high vagility of Hv spores (McCook and Vandermeer, ; Talhinhas et al ., ), this work suggests two additional factors that may be tightly linked to the evolutionary potential of the C3 group: a recent origin and reticulate evolution, i.e. evolution shaped by hybridization/recombination between diverging lineages.…”

Section: Discussionmentioning

confidence: 83%

“…Coffee leaf rust (CLR), caused by the obligate biotrophic fungus Hemileia vastatrix (Hv), is currently one of the biggest challenges to global coffee production and amongst the most serious crop diseases in history (Talhinhas et al, 2017). The disease causes premature defoliation on several species of the Coffea genus found at lower altitudes (<1000 m), but only C. canephora and C. arabica are considered to be economically relevant at a global scale (McCook and Vandermeer, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust

Silva

Várzea

Paulo

et al. 2018

Molecular Plant Pathology

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Coffee leaf rust, caused by Hemileia vastatrix (Hv), represents the biggest threat to coffee production worldwide and ranks amongst the most serious fungal diseases in history. Despite a recent series of outbreaks and emergence of hypervirulent strains, the population evolutionary history and potential of this pathogen remain poorly understood. To address this issue, we used restriction site-associated DNA sequencing (RADseq) to generate ∼19 000 single nucleotide polymorphisms (SNPs) across a worldwide collection of 37 Hv samples. Contrary to the long-standing idea that Hv represents a genetically unstructured and cosmopolitan species, our results reveal the existence of a cryptic species complex with marked host tropism. Using phylogenetic and pathological data, we show that one of these lineages (C3) infects almost exclusively the most economically valuable coffee species (tetraploids that include Coffea arabica and interspecific hybrids), whereas the other lineages (C1 and C2) are severely maladapted to these hosts, but successfully infect diploid coffee species. Population dynamic analyses suggest that the C3 group may be a recent 'domesticated' lineage that emerged via host shift from diploid coffee hosts. We also found evidence of recombination occurring within this group, which could explain the high pace of pathotype emergence despite the low genetic variation. Moreover, genomic footprints of introgression between the C3 and C2 groups were discovered and raise the possibility that virulence factors may be quickly exchanged between groups with different pathogenic abilities. This work advances our understanding of the evolutionary strategies used by plant pathogens in agro-ecosystems with direct and far-reaching implications for disease control.

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Section: Discussionmentioning

confidence: 83%

Section: Introductionmentioning

confidence: 99%

Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust

Silva

Várzea

Paulo

et al. 2018

Molecular Plant Pathology

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“…For example, myrtle rust ( Austropuccinia psidii ) is currently decimating a wide range of Myrtaceae around the world (Fernandez Winzer, Carnegie, Pegg, & Leishman, ; Glen, Alfenas, Zauza, Wingfield, & Mohammed, ), such as the endemic Eugenia koolauensis in Hawai‘i and the endemic Rhodamnia rubescens in native forests in Australia (Carnegie et al, ). Coffee leaf rust ( Hemileia vastatrix ) is substantially damaging Coffee plantations worldwide (Talhinhas et al, ). Similarly, wheat leaf rusts like Puccinia triticina , Puccinia recondite , and Puccinia striiformis are causing serious production losses for one of the world's biggest food crops (McCallum, Hiebert, Huerta‐Espino, & Cloutier, ).…”

Section: Introductionmentioning

confidence: 99%

“…Coffee leaf rust (Hemileia vastatrix) is substantially damaging Coffee plantations worldwide (Talhinhas et al, 2017). Similarly, wheat leaf rusts like Puccinia triticina, Puccinia recondite, and Puccinia striiformis are causing serious production losses for one of the world's biggest food crops (McCallum, Hiebert, Huerta-Espino, & Cloutier, 2012).…”

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confidence: 99%

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

et al. 2018

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Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost‐effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next‐generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large‐scale detection and quantification of rust fungi, but not for confirming the absence of species.

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“…cultivars (Silva, Várzea, Paulo, & Batista, 2018). Today, more than 50 races of H. vastatrix are known (Talhinhas et al, 2017). This is an inexplicable evolution for a pathogen that supposedly only utilizes clonal reproduction (Silva et al, 2018).…”

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confidence: 99%

On the hunt for the alternate host of Hemileia vastatrix

Koutouleas

Jørgensen

Jensen

et al. 2019

Ecology and Evolution

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Coffee leaf rust (CLR), caused by the fungal pathogen Hemileia vastatrix, has plagued coffee production worldwide for over 150 years. Hemileia vastatrix produces urediniospores, teliospores, and the sexual basidiospores. Infection of coffee by basidiospores of H. vastatrix has never been reported and thus far, no alternate host, capable of supporting an aecial stage in the disease cycle, has been found. Due to this, some argue that an alternate host of H. vastatrix does not exist. Yet, to date, the plant pathology community has been puzzled by the ability of H. vastatrix to overcome resistance in coffee cultivars despite the apparent lack of sexual reproduction and an aecidial stage. The purpose of this study was to introduce a new method to search for the alternate host(s) of H. vastatrix. To do this, we present the novel hypothetical alternate host ranking (HAHR) method and an automated text mining (ATM) procedure, utilizing comprehensive biogeographical botanical data from the designated sites of interests (Ethiopia, Kenya and Sri Lanka) and plant pathology insights. With the HAHR/ATM methods, we produced prioritized lists of potential alternate hosts plant of coffee leaf rust. This is a first attempt to seek out an alternate plant host of a pathogenic fungus in this manner. The HAHR method showed the highest‐ranking probable alternate host as Psychotria mahonii, Rubus apetalus, and Rhamnus prinoides. The cross‐referenced results by the two methods suggest that plant genera of interest are Croton, Euphorbia, and Rubus. The HAHR and ATM methods may also be applied to other plant–rust interactions that include an unknown alternate host or any other biological system, which rely on data mining of published data.

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

Cited by 187 publications

References 105 publications

Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust

Population genomic footprints of host adaptation, introgression and recombination in coffee leaf rust

Biases in the metabarcoding of plant pathogens using rust fungi as a model system

On the hunt for the alternate host of Hemileia vastatrix

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