Coffee leaf rust, caused by the fungus Hemileia vastatrix
, is the most damaging disease of coffee worldwide. The pathogen has caused yield reductions of up to 30% in susceptible varieties of Coffea arabica
in recent epidemics associated with climate change in Colombia and several Central American countries. We have sequenced de novo
the genome and transcriptome of H. vastatrix
race II using next-generation sequencing platforms: 454 Roche and Illumina. The H. vastatrix
genome is over 250 Mb, one of the largest fungal genomes to date. The assembled genome has 92% coverage, a GC content of 32%, and a very large proportion of repeated sequences; over 74% of the H. vastatrix
genome is composed of repeats, with prevalence of LTR retro-transposons. We predicted a set of 14,445 proteins encoded by the coffee rust genome, and 44 secreted proteins that might be involved in pathogenesis. Three transcriptome assemblies from different isolates/races were obtained with 44,297, 55,791 and 64,752 contigs with average contig size of 675, 716 and 828 bp. Most H. vastatrix
race II transcripts (84%) were mapped to the assembled genome. H. vastatrix
isolate/race diversity at the transcriptome level is significant, since they only share 76-78% of expressed sequences.
Only 36% to 44% H. vastatrix
transcriptome sequences had homology with Puccinia
proteins showing the high level of genetic diversity present in rust fungi. We have also developed molecular markers for H. vastatrix
that are being used for genetic diversity studies.
In addition, we have developed molecular markers for host derived resistance against this pathogen that are linked to the introgression of C. canephora (rust resistant genotype) in breeding F5 lines of C. arabica, particularly in the resistant components of the Castillo variety of Colombia. These markers have high potential to accelerate development of rust resistant varieties through marker-assisted selection in coffee breeding programs.
Note: This abstract will have two presenters Marco Cristancho and Huver Posada