Annotation of a hybrid partial genome of the coffee rust (Hemileia vastatrix) contributes to the gene repertoire catalog of the Pucciniales.
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 333 Mb 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 3921 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.
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
Marco A
MA
Cristancho
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.
David Octavio
DO
Botero-Rozo
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
William
W
Giraldo
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia ; Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.
Javier
J
Tabima
Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.
Diego Mauricio
DM
Riaño-Pachón
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
Carolina
C
Escobar
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
Yomara
Y
Rozo
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
Luis F
LF
Rivera
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
Andrés
A
Durán
Departamento de Ciencias Biológicas, Universidad de los Andes Bogotá, Colombia.
Silvia
S
Restrepo
Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv, Israel.
Tamar
T
Eilam
Institute for Cereal Crops Improvement, Tel Aviv University Tel Aviv, Israel.
Yehoshua
Y
Anikster
Plant Pathology, National Center for Coffee Research - CENICAFÉ Chinchiná, Colombia.
Alvaro L
AL
Gaitán
RNA-seq; coffee; coffee rust; genetic variants; genome; plant pathogens diversity