Rodrigues AS¹, Silva DN¹, Várzea V², Paulo OS¹, Batista D²

1- cE3c – Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal, 2- CIFC/LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal

Coffee Leaf Rust, caused by Hemileia vastatrix (Hv), has been the major constraint to global coffee production. Only recently the evolutionary history of this pathogen began to be dissected. Silva et al. (2018) found for the first time the species to be structured into three divergent genetic lineages with marked host tropism (C1 and C2 infecting diploid coffee species; and C3 infecting tetraploid coffee species). Nevertheless, no significant structuring was found within the C3 lineage, which represent the most widespread and epidemiological relevant Hv group. Here, we extended the investigation to a worldwide scale sampling for obtaining a deeper insight on the dynamics and adaptive patterns of Hv populations

Oral communication

Laureano A¹, Rodrigues ASB², Macedo C¹, Diniz I¹, Pereira AP¹, Várzea V¹, Talhinhas P³, Batista D¹

1- CIFC/LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal, 2- cE3c – Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal, 3- LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal

Coffee leaf rust is a devastating disease caused by Hemileia vastatrix (Hv), leading to huge field losses and economic consequences. Understanding the genetic variation and mechanisms underlying pathogen virulence is thus crucial to address disease control. Retrotransposons have been reported to play a role in genome shaping and expansion events, in association with the ability of plant pathogens to rapidly evolve virulence. In this study, the genome size, copy number and sequence polymorphism of three retrotransposons were investigated in a set of a Hv isolates comprising different pathotypes to assess diversity and differentiation patterns as well as putative associations with virulence profiles

Digital Poster, selected for 3 min. flash talk

Chaves Inês^{1, 2}, Barros Danielle Ribeiro^{3, 4}, Batista Dora^{3, 5}, Miguel Célia⁵ ,Ricardo Cândido Pinto¹, Várzea Vitor³, Guerra-Guimarães Leonor*³

1-ITQB NOVA, Universidade NOVA de Lisboa, Oeiras, Portugal ; 2-Instituto de Biologia Experimental e Tecnológica, Oeiras, Portugal ; 3-CIFC, LEAF, Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal ; 4-Departamento de Fitossanidade, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil ; 5-cE3c, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal

The obligate biotrophic rust fungus Hemileia vastatrix (causal agent of Coffee Leaf Rust), which is the most widespread pathogen of Arabica coffee, causes severe yield losses. More than 50 rust physiological races have been detected resorting to 27 coffee differentials, since their molecular identification has not yet been possible. In the present study we have identified small-RNAs from urediniospores of three rust races with different spectra for virulence: race VI (v?-unknown) non-pathogenic to all known C. arabica genotypes and races II (v5) and XXIV (v2,4,5) pathogenic to the majority of C. arabica genotypes.

Poster presentation

Birg João¹, Macedo C¹, Silva MC², Guerra-Guimarães L², Pereira AP², Várzea V², Paulo O¹, Batista D²

1- cE3c – Centre for Ecology, Evolution and Environmental Changes, Lisboa, Portugal, 2- CIFC/LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal

Hemileia vastatrix (Hv), the pathogen responsible for Coffee Leaf Rust, has been spreading across the globe and causing devastating socio-economic consequences within coffee production. Nowadays, more than 50 races of Hv have been identified, but its virulence mechanisms are still poorly understood. To achieve a sustainable disease control, it is crucial to unveil the evolutionary adaptation behind this host-pathogen interaction. In this study, we applied a transcriptomic approach to identify candidate virulence genes harboring differential expression patterns, related to rust pathotypes during its compatible interaction.

Digital Poster, selected for 3 min. flash talk

Batista D¹, Macedo C¹, Diniz I¹, Loureiro A¹, Várzea V¹, Guerra-Guimarães L¹, Silva MC¹.

1- CIFC/LEAF, ISA, Universidade de Lisboa, Lisboa, Portugal

Hemileia vastatrix (Hv) causing coffee leaf rust, remains the major threat to Arabica coffee production worldwide. Under the constant risk of new Hv pathotypes emerging under a strong selective pressure, a better understanding of the adaptive genetic variation of Hv populations is needed. Since genes involved in coffee-rust interaction are expected to evolve under strong selection, this study aimed at the analysis of expression differences in putative candidate genes under positive selection that could provide insights on the pathogen virulence evolution.

Digital Poster

Ana Sofia Rodrigues¹, Andreia Loureiro^2,3, Diogo Nuno Silva^1,2,3, Vitor Várzea^2,3, Octávio S. Paulo¹, Dora Batista^1,2,3

1- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 2- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal, 3- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Oeiras, Portugal

Coffee Leaf Rust, caused by Hemileia vastatrix (Hv), has been the major constraint to global coffee production for more than a century. Only recently the population evolutionary history of this pathogen began to be unveiled. Silva et al. (2018) found for the first time the species to be structured into three divergent genetic lineages with marked host tropism (C1 and C2 infecting diploid coffee species; and C3 infecting tetraploid coffee species), and signals of introgression. Nevertheless, no significant structuring was found within the C3 lineage, which represent the most widespread and epidemiological relevant Hv group. Here, we extended the investigation to a worldwide scale sampling for obtaining a deeper insight on the dynamics and adaptive evolution of Hv populations. We used restriction site-associated DNA sequencing (RADseq) to generate around 21,520 SNPs across 108 Hv isolates. Phylogenetic analyses corroborated the existence of the three well-diverged Hv groups, but furthermore showed a well-supported structuring within C3, with three main sub-groups: African, Asian and Timor. This pattern seems to reflect Hv geographical origin associated to the historical distribution and exchange of coffee materials. The Asian origin clade comprises the higher number of isolates and exhibits a ladder-like diversification pattern, with relatively low genetic diversity, suggesting rapid evolution and population expansion. On the contrary, the African and Timor populations appear to more restricted, revealing some degree of differentiation. In addition, our results reinforce the potential role of introgression in Hv lineage and virulence evolution. From the 7909 loci (comprising 9628 “diagnostic” SNPs) differentiating C2 and C3 groups, 2,63% mapped against NCBI nt database, with the majority of the hits corresponding to retrotransposons (82,76%) and putative secreted protein genes (9.58%).

Oral presentation

Cintia Macedo¹, Andreia Loureiro^2,3, Inês Diniz^1,2,3, Diogo Nuno Silva^1,2,3, Vitor Várzea^2,3, Leonor Guerra-Guimarães^2,3, Maria Do Céu Silva^2,3, Dora Batista^1,2,3

1- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal, 2- Linking Landscape, Environment, Agriculture and Food (LEAF), Instituto Superior de Agronomia, Universidade de Lisboa, Lisboa, Portugal, 3- Centro de Investigação das Ferrugens do Cafeeiro (CIFC), Instituto Superior de Agronomia (ISA), Universidade de Lisboa, Oeiras, Portugal

Hemileia vastatrix (Hv) is a complex biotrophic fungal pathogen that causes coffee leaf rust (CLR), a disease that has been a permanent threat to Arabica coffee production. Under the constant threat of new pathotypes emerging under a strong selective pressure and becoming epidemically spread on a continental scale, a better understanding of the adaptive genetic variation of Hv populations is an immediate priority. Since genes involved in coffee-rust interaction are expected to evolve under strong selection, the analysis of genetic and expression differences in putative candidate genes could provide insights on the pathogen virulence evolution. In this study, we identified 34 Hv candidate genes with a signature of positive selection by applying a genome-wide scan integrated into a phylogenomics framework previously developed (Silva et al., 2015). Functional annotation assigned the higher proportion of these genes to the categories “Posttranslational modification, protein turnover, chaperones” (21%) and “Energy production and conversion” (15%). Given that the signal of positive selection was captured at the phylogenetic branch leading specifically to H. vastatrix, these genes may have a role in adaptive changes at the species level. To assess their potential association with Hv virulence profiles, the analysis of gene expression profiles of 4 selected candidate genes was initiated by qPCR for 5 isolates with contrasting pathotypes during compatible interactions, at 3 key stages of the infection process. First results show differences in expression among isolates, either regarding up or down-regulation at different infection stages, or the level of expression. Putative causal relations and possible adaptive significance is being assessed. This study provides a first insight on the molecular variation underlying virulence divergence in coffee rust.

Poster presentation

Batista D, Silva DN, Modesto I, Miguel C, Paulo OS, Várzea V, Silva MC

Recurrent epidemics of coffee leaf rust, caused by the fungal pathogen Hemileia vastatrix (Hv), have been constraining the sustainable production of Arabica coffee for more than one and a half centuries. Although the deployment of coffee-resistant varieties has successfully contributed to control the disease, the highly adaptability of the fungus shaped by the dynamic system of host-pathogen co-evolution has been leading to the gradual breakdown of resistance in the field [1]. This extreme situation has triggered a deep sense of urgency to improve pathogen surveillance and control measures, and Hv’s research has gained considerable momentum. However, no direct link between such high phenotypic diversity and molecular diversity has been found yet. In this sense, we are focused on understanding host adaptation and virulence evolution through pathogen population and evolutionary genomic studies.

[1] Talhinhas et al. (2017). Mol Plant Pathol., 18:1039–1051; [2] Silva et al. (2018). Mol Plant Pathol., 19: 1742–1753

Oral presentation

Received award attributed by the Association for Science and Information on Coffee (ASIC)