Whole Genome Sequencing of Race II and Low Coverage Sequencing of Twelve Additional isolates of the Coffee Rust, Hemileia vastatrix
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB50957 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR8703040.fastq.gz | Fastqsanger.gz | |||
| ERR8703050.fastq.gz | Fastqsanger.gz | |||
| ERR8703060.fastq.gz | Fastqsanger.gz | |||
| ERR8703070.fastq.gz | Fastqsanger.gz | |||
| ERR8703080.fastq.gz | Fastqsanger.gz |
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Project description:Digitopodium hemileiae was described originally in 1930 as Cladosporium hemileiae; growing as a mycoparasite of the coffee leaf rust (CLR), Hemileia vastatrix, in a sample of diseased leaves of Coffea canephora collected in the Democratic Republic of Congo. No cultures from this material exist. More recently, the type material was re-examined and, based on morphological features, considered to be incorrectly placed in Cladosporium. The new genus Digitopodium was erected to accommodate this species. Interest in fungal antagonists of H. vastarix, as potential biocontrol agents of CLR, led to comprehensive surveys for mycoparasites, both in the African centre of origin of the rust, as well as in its South American exotic range. Among the rust specimens from Ethiopia, one was found to be colonized by a fungus congeneric with, and similar to, D. hemileiae. Pure cultures obtained from the Ethiopian material enabled a molecular study and for its phylogenetic position to be elucidated, based on DNA sequence data from the ITS and LSU regions. Molecular data showed that two members of the recently erected genus Hyalocladosporiella (Herpotrichiellaceae: Chaetothyriales) are congeneric with Digitopodium from Ethiopia and morphologically similar to both D. hemileiae and the two Ethiopian isolates. These isolates were found to be morphologically and genetically identical to H. tectonae, described previously from Brazil. Thus, species of Hyalocladosporiella are re-allocated to Digitopodium here; including D. tectonae, and a novel species, D. canescens, recently found in Brazil growing as a mycoparasite of Puccinia thaliae. The potential use of D. hemileiae and D. tectonae for classical biological control of CLR is discussed.
| S-EPMC7784264 | biostudies-literature
Project description:Hawaii has long been one of the last coffee-producing regions of the world free of coffee leaf rust (CLR) disease, which is caused by the biotrophic fungus Hemileia vastatrix. However, CLR was detected in coffee farms and feral coffee on the island of Maui in February 2020 and subsequently on other islands of the Hawaiian archipelago. The source of the outbreak in Hawaii is not known, and CLR could have entered Hawaii from more than 50 coffee-producing nations that harbor the pathogen. To determine the source(s) of the Hawaii inoculum, we analyzed a set of eleven simple sequence repeat markers (SSRs) generated from Hawaii isolates within a dataset of 434 CLR isolates collected from 17 countries spanning both old and new world populations, and then conducted a minimum spanning network (MSN) analysis to trace the most likely pathway that H. vastatrix could have taken to Hawaii. Forty-two multilocus genotypes (MLGs) of H. vastatrix were found in the global dataset, with all isolates from Hawaii assignable to MLG 10 or derived from it. MLG 10 is widespread in Central America and Jamaica, making this region the most probable source of inoculum for the outbreak in Hawaii. An examination of global weather patterns during the months preceding the introduction of CLR makes it unlikely that the pathogen was windborne to the islands. Likely scenarios for the introduction of CLR to Hawaii are the accidental introduction of spores or infected plant material by travelers or seasonal workers, or improperly fumigated coffee shipments originating from Central America or the Caribbean islands.
| S-EPMC8877902 | biostudies-literature
Project description:Calonectria hemileiae, a fungus associated with pustules of the coffee leaf rust (CLR, Hemileia vastatrix) in Brazil, was tested in vitro and in planta to assess its biocontrol potential. The fungus inhibited the germination of rust spores by over 80%. CLR severity was reduced by 93% when Calonectria was applied to coffee leaf discs inoculated with H. vastatrix, whilst a reduction of 70-90% was obtained for in planta experiments. Mycoparasitism was demonstrated through the fulfillment of Koch's postulates. Elucidation of the biochemical interaction between Calonectria and Hemileia on coffee plants indicated that the mycoparasite was able to increase plant resistance to rust infection. Coffee plants sprayed with Calonectria alone showed greater levels of chitinase, β-1,3-glucanase, ascorbate peroxidase and peroxidase. Although effective in controlling the rust, fungicide applications damaged coffee photosynthesis, whereas no harm was caused by Calonectria. We conclude that C. hemileiae shows promise as a biocontrol agent of CLR.
| S-EPMC8044427 | biostudies-literature
Project description:The genus Cryptococcus is well known for its two species -Cryptococcus neoformans and C. gatii- that are etiological agents of cryptococcosis, an important fungal disease of mammals, including humans, and which is particularly common in immunocompromised patients. Nevertheless, Cryptococcus is a large and widely distributed genus of basidiomycetes occupying a broad range of niches, including mycoparasitism. One such mycoparasitic species is Cryptococcus depauperatus, which was firstly mistakenly described as a pathogen of scale insects under the name Aspergillus depauperatus. The "Aspergillus" conidiophores were later shown to be basidia of a Cryptococcus and the new combination C. depauperatus was proposed. Additionally, instead of an entomopathogen, the fungus was found to be a mycoparasite growing on the entomopathogen Akanthomyces (Lecanicillium) lecanii. Recently, during surveys for mycoparasites of coffee leaf rust (Hemileia vastatrix) in the context of a biocontrol project, white colonies covering rust pustules were observed in Cameroon. Upon close examination, instead of a member of the "white colony forming complex" of Ascomycetes, commonly collected growing on H. vastatrix, such colonies were found to represent a basidiomycete fungus with basidia-bearing chains of basidiospores, typical of the genus Cryptococcus. Morphological and molecular evidence was generated supporting the identification of the fungus on rust pustules as C. depauperatus. This is the first record of C. depauperatus from Africa and of its association with coffee leaf rust.
| S-EPMC8578230 | biostudies-literature
Project description: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.
| S-EPMC4215621 | biostudies-literature
Project description:Hemileia vastatrix is the causal agent of coffee leaf rust, the most important disease of coffee Arabica. In this work, a 454-pyrosequencing transcriptome analysis of H. vastatrix germinating urediniospores (gU) and appressoria (Ap) was performed and compared to previously published in planta haustoria-rich (H) data. A total of 9234 transcripts were identified and annotated. Ca. 50% of these transcripts showed no significant homology to international databases. Only 784 sequences were shared by the three conditions, and 75% were exclusive of either gU (2146), Ap (1479) or H (3270). Relative transcript abundance and RT-qPCR analyses for a selection of genes indicated a particularly active metabolism, translational activity and production of new structures in the appressoria and intense signaling, transport, secretory activity and cellular multiplication in the germinating urediniospores, suggesting the onset of a plant-fungus dialogue as early as at the germ tube stage. Gene expression related to the production of carbohydrate-active enzymes and accumulation of glycerol in germinating urediniospores and appressoria suggests that combined lytic and physical mechanisms are involved in appressoria-mediated penetration. Besides contributing to the characterization of molecular processes leading to appressoria-mediated infection by rust fungi, these results point toward the identification of new H. vastatrix candidate virulence factors, with 516 genes predicted to encode secreted proteins.
| S-EPMC3953675 | biostudies-literature
Project description:A number of genes that confer resistance to coffee leaf rust (SH 1-SH 9) have been identified within the genus Coffea, but despite many years of research on this pathosystem, the complementary avirulence genes of Hemileia vastatrix have not been reported. After identification of H. vastatrix effector candidate genes (HvECs) expressed at different stages of its lifecycle, we established an assay to characterize HvEC proteins by delivering them into coffee cells via the type-three secretion system (T3SS) of Pseudomonas syringae pv. garcae (Psgc). Employing a calmodulin-dependent adenylate cyclase assay, we demonstrate that Psgc recognizes a heterologous P. syringae T3SS secretion signal which enables us to translocate HvECs into the cytoplasm of coffee cells. Using this Psgc-adapted effector detector vector (EDV) system, we found that HvEC-016 suppresses the growth of Psgc on coffee genotypes with the SH 1 resistance gene. Suppression of bacterial blight symptoms in SH 1 plants was associated with reduced bacterial multiplication. By contrast, HvEC-016 enhanced bacterial multiplication in SH 1-lacking plants. Our findings suggest that HvEC-016 may be recognized by the plant immune system in a SH 1-dependent manner. Thus, our experimental approach is an effective tool for the characterization of effector/avirulence proteins of this important pathogen.
| S-EPMC6079635 | biostudies-literature
Project description:Coffee leaf miner is an important plague in coffee crops. Using subtracted cDNA libraries and nylon filter arrays, we analyzed the expression profile of 1536 expressed sequence tags (ESTs) of coffee plants from an hybrid progeny (C. arabica x C. racemosa), containg resistant (R) and susceptible plants (S) to the infestation of coffee leaf miner. Leaf discs were collected from non-infested plants (R control - RC; S control - SC), infested plants after moth oviposition (R oviposition - Ro; S oviposition - So) and infested after larvar eclosion (R eclosion - Re; S eclosion - Se). Isolation and characterization of Coffea genes induced during coffee leaf miner (Leucoptera coffeella) infestation. Plant Science 169(2):351-360 Keywords: ordered
2005-08-15 | GSE2045 | GEO
Project description:Population genetic studies of Hemileia vastatrix have been conducted in order to describe the evolutionary dynamics of the pathogen and the disease epidemiology as consequence of changes in disease management and host distribution occurred in Peru after the 2013 epidemic. These analyses were performed by sequencing the internal transcribed spacers of the nuclear ribosomal DNA (rDNA-ITS) of H. vastatrix collected from two coffee growing areas in 2014 and 2018. H. vastatrix population showed high haplotype diversity (Hd = 0.9373 ± 0.0115) with a low nucleotide diversity (π = 0.00322 ± 0.00018). Likewise, AMOVA indicated that fungus population has behaved as a large population without structuring by geographical origin and sampling years (FST = 0.00180, P = 0.20053 and FST = 0.00241, P = 0.19693, respectively). Additionally, the haplotype network based on intraspecific phylogenetic analysis of H. vastatrix using Peruvian and NCBI sequences revealed that Peruvian ancestral haplotypes, which were maintained in time and space, would correspond to the reported sequences of the races II and XXII. This result suggests that no substantial changes have occurred through time in Peruvian Hemileia vastatrix population.
| S-EPMC8200579 | biostudies-literature
Project description:Hemileia vastatrix isolate:Race I Genome sequencing and assembly
| PRJNA912191 | ENA