Rodrigues AS¹, Silva DN^1,2,3, Várzea V^2,3, Paulo OS¹, Batista D^1,2,3

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

The devastating disease Coffee Leaf Rust, caused by the fungal pathogen Hemileia vastatrix (Hv), has been the major constraint to global coffee production. Only recently the evolutionary history of this pathogen began to be dissected. For the first time the species was found 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) (Silva et al., 2018). However, no significant structuring was found within the C3 lineage, the most widespread and epidemiological relevant Hv group. In this study, we extended the investigation to a worldwide scale sampling for obtaining a deeper insight on the dynamics and adaptive patterns of Hv populations. By using a RAD-sequencing approach we obtained a set of 13804 SNPs across 99 isolates of H. vastatrix from 23 geographical regions, different pathotypes and different coffee hosts. Phylogenetic analyses corroborated the existence of the previous Hv groups (C1 – C3), but furthermore showed a well-supported structuring within C3, with three main lineages (I, II, III). This pattern seems to reflect Hv geographical origin associated to the historical distribution and exchange of coffee materials. Signals of selection were detected in 75 SNP loci, which seem to have a very strong contribution in shaping Hv genetic structure. Furthermore, Single and Multi-SNP association analyses detected 46 SNPs (BF0.99) and 67 SNPs (PIP0.99) associated with the different C3 genetic lineages, respectively. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix, revealing for the first time a clear structuring within rusts infecting tetraploid coffee hosts, which seems to follow an adaptive pattern, with coffee host as a major selective pressure.

Oral communication - online

JOÃO BIRG^1,2, CÍNTIA MACEDO¹, MARIA DO CÉU SILVA^1,3, LEONOR GUERRA-GUIMARÃES^1,3, ANA PAULA PEREIRA^1,3, VITOR VÁRZEA^1,3, OCTÁVIO S. PAULO ², DORA BATISTA ^1,2

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

The devastating disease Coffee Leaf Rust, caused by the fungal pathogen Hemileia vastatrix (Hv), has been the major constraint to global coffee production. Only recently the evolutionary history of this pathogen began to be dissected. For the first time the species was found 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) (Silva et al., 2018). However, no significant structuring was found within the C3 lineage, the most widespread and epidemiological relevant Hv group. In this study, we extended the investigation to a worldwide scale sampling for obtaining a deeper insight on the dynamics and adaptive patterns of Hv populations. By using a RAD-sequencing approach we obtained a set of 13804 SNPs across 99 isolates of H. vastatrix from 23 geographical regions, different pathotypes and different coffee hosts. Phylogenetic analyses corroborated the existence of the previous Hv groups (C1 – C3), but furthermore showed a well-supported structuring within C3, with three main lineages (I, II, III). This pattern seems to reflect Hv geographical origin associated to the historical distribution and exchange of coffee materials. Signals of selection were detected in 75 SNP loci, which seem to have a very strong contribution in shaping Hv genetic structure. Furthermore, Single and Multi-SNP association analyses detected 46 SNPs (BF0.99) and 67 SNPs (PIP0.99) associated with the different C3 genetic lineages, respectively. Our study provides a higher-resolution perspective on the evolutionary history of H. vastatrix, revealing for the first time a clear structuring within rusts infecting tetraploid coffee hosts, which seems to follow an adaptive pattern, with coffee host as a major selective pressure

Oral communication, Flash talk 3 min; Awarded as Best Flash Talk 2020, read the full interview

Laureano A¹, Rodrigues ASB², Modesto I³, Macedo C¹, Diniz I¹, Várzea V¹, Azinheira HG¹, Pereira AP¹, Loureiro J⁴, Miguel C³, Talhinhas P, Batista D²

1- CIFC-Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, 2- cE3c- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 3- BioISI- BioSystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, 4- CFE-Centro de Ecologia Funcional, Departamento de Ciências da Vida, Faculdade de Ciências, Universidade de Coimbra, 5 - LEAF-Linking Landscape, Environment, Agriculture and Food – Instituto Superior de Agronomia, Universidade de Lisboa

Coffee leaf rust is a devastating disease caused by Hemileia vastatrix (Hv), leading to huge losses in coffee production. There are over 50 races/pathotypes of Hv, so it is of great importance to comprehend how the genetic variation is promoted, as well as the regulator mechanisms of the differentiated pathogen virulence profiles. Retrotransposons are associated with genome structural variations and gene expression regulation in plant pathogens. These features may be associated to their capacity to rapidly evolve virulence. In this study, the genome size and the variability of a Ty1/Copia-like retrotransposon, concerning nucleotide sequence and copy number, were investigated among Hv contrasting pathotypes to assess their putative association with virulence profiles. Estimation of the holoploid genome size (1C) by flow cytometry for 46 Hv pathotypes revealed a huge genomic variation, ranging from 713 to 879 Mbp, with a global average of 789 Mbp. This is in sharp contrast with the global average for the kingdom Fungi (60 Mbp) and still over 10× larger than that of the phylum Basidiomycota (74 Mbp). To start assessing a putative causal relation of genome size variation with retrotransposon expansion, we analyzed a Ty1/Copia-like retrotransposon previously selected from an annotated EST database of three H. vastatrix differentiation/ infection stages (Talhinhas et al. 2014). Upon cloning and sequencing, 16 different copies were identified with a high level of genetic variation in 7 Hv isolates. Absolute quantification of retrotransposon copy number by qPCR ranged from 2 to 8 copies per diploid nucleus. Further analyses are being carried out and will allow us to better understand the genetic variation pattern and putative causal relations with virulence profiles. This study provides a novel approach to address coffee rust adaptive evolution and offers a first insight on H. vastatrix virulence divergence as related to genome size fluctuations and retrotransposon copy number.

Talhinhas et al. 2014 Frontiers in Plant Science doi: 10.3389/fpls.2014.00088

Digital poster

Batista D^1,2,3, Silva, DN^1,2,3, Vieira A^1,2,3, Loureiro A ², Pina-Martins F¹, Pereira AP³, Guerra-Guimarães L^2,3, Azinheira HG^2,3, Miguel C⁴, Silva, MC^2,3, Várzea V ^2,3, Paulo OS¹

1- cE3c - Centre for Ecology, Evolution and Environmental Changes, FCUL University of Lisbon, Lisbon, Portugal, 2- LEAF- Linking Landscape, Environment, Agriculture and Food, Instituto Superior de Agronomia (ISA), University of Lisbon, Lisbon, Portugal, 3- CIFC- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia (ISA), University of Lisbon, Oeiras, Portugal, 4- BioISI - BioSystems & Integrative Sciences Institute, FCUL University of Lisbon, Lisbon, Portugal

The fungal pathogen Hemileia vastatrix (Hv), causing the devastating coffee leaf rust (CLR) disease, has been the major constraint to Arabica coffee production for more than one and a half centuries. Since the 19^th century historical first outbreak, the disease gained a worldwide distribution, becoming practically endemic in all regions of the world where coffee is grown. Although the deployment of coffee resistant varieties has successfully contributed to control the disease, the dynamic system of host-pathogen co-evolution have been leading to the recurrent resurgence of severe epidemics, causing heavy yield and revenue losses. This scenario is expected to be aggravated by the pronounced climate changes that are predicted to occur, particularly in tropical environments. In fact, during the last decade, a cluster of epidemic outbreaks bursted out across the Americas, extending both the temporal and spatial range of the disease, and thus conferring to CLR the status of natural disaster in the tropics. The impact of such cash crop diseases on sustainable production and global food security has catalyzed a change towards focusing on pathogen research, and using integrative genomics to probe pathogen population dynamics and evolutionary potential, host adaptation and virulence evolution, with the practical goal of guiding disease control strategies. In this communication, we will take a look into the power of pathogenomics to bring new and important findings with direct implications in disease control, by presenting our previous results on Hv population genomics and the follow-up approach devised under the recently approved project PATHOmics (02/SAICT/2017_29189). The integrated strategy provided by this project relies on the combination of comparative genomics, genome-wide association and transcriptomic analyses to identify SNPs, genomic changes and candidate effector genes that can be linked to virulence profiles of coffee pathogens, and thus provide insights on the mechanisms of pathogen evolution underlying virulence differentiation. With such approach we aim at uncovering genetic determinants underpinning virulence that at the same time can be used as markers to track pathotypes at international level through diagnostic assays, promoting the establishment of a web platform for coffee disease surveillance.

Oral communication