Coffee rust is a leaf disease caused by the fungus, Hemileia vastatrix. Coffee rust epidemics, with intensities higher than previously observed, have affected a number of countries including: Colombia, from 2008 to 2011; Central America and Mexico, in 2012–13; and Peru and Ecuador in 2013. There are many contributing factors to the onset of these epidemics e.g. the state of the economy, crop management decisions and the prevailing weather, and many resulting impacts e.g. on production, on farmers’ and labourers’ income and livelihood, and on food security. Production has been considerably reduced in Colombia (by 31 % on average during the epidemic years compared with 2007) and Central America (by 16 % in 2013 compared with 2011–12 and by 10 % in 2013–14 compared with 2012–13). These reductions have had direct impacts on the livelihoods of thousands of smallholders and harvesters. For these populations, particularly in Central America, coffee is often the only source of income used to buy food and supplies for the cultivation of basic grains. As a result, the coffee rust epidemic has had indirect impacts on food security. The main drivers of these epidemics are economic and meteorological. All the intense epidemics experienced during the last 37 years in Central America and Colombia were concurrent with low coffee profitability periods due to coffee price declines, as was the case in the 2012–13 Central American epidemic, or due to increases in input costs, as in the 2008–11 Colombian epidemics. Low profitability led to suboptimal coffee management, which resulted in increased plant vulnerability to pests and diseases. A common factor in the recent Colombian and Central American epidemics was a reduction in the diurnal thermal amplitude, with higher minimum/lower maximum temperatures (+0.1 °C/-0.5 °C on average during 2008–2011 compared to a low coffee rust incidence period, 1991–1994, in Chinchiná, Colombia; +0.9 °C/-1.2 °C on average in 2012 compared with prevailing climate, in 1224 farms from Guatemala). This likely decreased the latency period of the disease. These epidemics should be considered as a warning for the future, as they were enhanced by weather conditions consistent with climate change. Appropriate actions need to be taken in the near future to address this issue including: the development and establishment of resistant coffee cultivars; the creation of early warning systems; the design of crop management systems adapted to climate change and to pest and disease threats; and socio-economic solutions such as training and organisational strengthening.

Coffee leaf rust caused by the fungus Hemileia vastatrix is the most damaging disease to coffee worldwide. The pathogen has recently appeared in multiple outbreaks in coffee producing countries resulting in significant yield losses and increases in costs related to its control. New races/isolates are constantly emerging as evidenced by the presence of the fungus in plants that were previously resistant. Genomic studies are opening new avenues for the study of the evolution of pathogens, the detailed description of plant-pathogen interactions and the development of molecular techniques for the identification of individual isolates. For this purpose we sequenced 8 different H. vastatrix isolates using NGS technologies and gathered partial genome assemblies due to the large repetitive content in the coffee rust hybrid genome; 74.4% of the assembled contigs harbor repetitive sequences. A hybrid assembly of 333Mb was built based on the 8 isolates; this assembly was used for subsequent analyses. Analysis of the conserved gene space showed that the hybrid H. vastatrix genome, though highly fragmented, had a satisfactory level of completion with 91.94% of core protein-coding orthologous genes present. RNA-Seq from urediniospores was used to guide the de novo annotation of the H. vastatrix gene complement. In total, 14,445 genes organized in 3,921 families were uncovered; a considerable proportion of the predicted proteins (73.8%) were homologous to other Pucciniales species genomes. Several gene families related to the fungal lifestyle were identified, particularly 483 predicted secreted proteins that represent candidate effector genes and will provide interesting hints to decipher virulence in the coffee rust fungus. The genome sequence of Hva will serve as a template to understand the molecular mechanisms used by this fungus to attack the coffee plant, to study the diversity of this species and for the development of molecular markers to distinguish races/isolates.

Latin America harbors some of the most biodiverse countries in the world, including Colombia. Despite the increasing use of cutting-edge technologies in genomics and bioinformatics in several biological science fields around the world, the region has fallen behind in the inclusion of these approaches in biodiversity studies. In this study, we used data mining methods to search in four main public databases of genetic sequences such as: NCBI Nucleotide and BioProject, Pathosystems Resource Integration Center, and Barcode of Life Data Systems databases. We aimed to determine how much of the Colombian biodiversity is contained in genetic data stored in these public databases and how much of this information has been generated by national institutions. Additionally, we compared this data for Colombia with other countries of high biodiversity in Latin America, such as Brazil, Argentina, Costa Rica, Mexico, and Peru. In Nucleotide, we found that 66.84% of total records for Colombia have been published at the national level, and this data represents less than 5% of the total number of species reported for the country. In BioProject, 70.46% of records were generated by national institutions and the great majority of them is represented by microorganisms. In BOLD Systems, 26% of records have been submitted by national institutions, representing 258 species for Colombia. This number of species reported for Colombia span approximately 0.46% of the total biodiversity reported for the country (56,343 species). Finally, in PATRIC database, 13.25% of the reported sequences were contributed by national institutions. Colombia has a better biodiversity representation in public databases in comparison to other Latin American countries, like Costa Rica and Peru. Mexico and Argentina have the highest representation of species at the national level, despite Brazil and Colombia, which actually hold the first and second places in biodiversity worldwide. Our findings show gaps in the representation of the Colombian biodiversity at the molecular and genetic levels in widely consulted public databases. National funding for high-throughput molecular research, NGS technologies costs, and access to genetic resources are limiting factors. This fact should be taken as an opportunity to foster the development of collaborative projects between research groups in the Latin American region to study the vast biodiversity of these countries using ‘omics’ technologies.

The aim of the present research was to test the transferability of simple sequence repeat (SSR) markers developed in two Uredinales species to Hemileia vastatrix, coffee rust. The development of efficient techniques for the identification of H. vastatrix isolates is imperative, given the continuous development of new races. The transferability of 25 SSR markers developed in the related Uredinales species Puccinia coronata f. sp lolli and Melampsora linii to H. vastatrix was tested. A low level of transferability of SSRs was detected, and only 4 potential markers that can be used to fingerprint the coffee rust races were identified.