Cellular organisms; Eukaryota; Opisthokonta; Fungi; Dikarya; Basidiomycota; Pucciniomycotina; Pucciniomycetes; Pucciniales; Zaghouaniaceae; Hemileia; Hemileia Vastatrix
Description and significance
Hemileia vastatrix is a multicellular fungus that causes the coffee leaf rust disease. This disease is characterized by yellow-colored spots under the coffee leaf, causing the leaves to drop, subsequently killing the coffee plant . Coffee leaf rust has spread across coffee cultivation regions around the world, and damage from coffee leaf rust costs one to two billion U.S. dollars per year. Most notably, H. vastatrix was responsible for epidemics in Central America, Colombia, Peru, and Ecuador . Current H. vastatrix research focuses on controlling the spread of coffee leaf rust and preventing future epidemics .
The size of the Hemileia vastatrix genome is very large (c. 797 Mbp), with moderate diversity and high genome differentiation. The current genome sequencing work based on a draft assembly is reported to account for less than 10% of the predicted genome size. Some studies suggest up to 75% of the assembled genome contains repetitive or non-coding regions.  The majority of sequence-related amplified polymorphism (SRAP) primer fragments exhibited polymorphism markers, which emphasizes the large degree of difference in the whole population.  While the total genome has only been partially identified, recent Hv33 (Hemileia vastatrix race XXXIII) genome assembly and model predictions show that 82% of the 118,162 scaffolds/portions of the genome sequence had repeated elements, and 43.6% of them were transposable. There are around 1,568 unique sequences which include 111 encoded proteins recognized as candidate effectors and 72 secreted proteins without any (NCBI/UNIPROT) database matches identified as potentially novel genes. Overall the genome structure is most similar (at 72.2%) to Puccinia graminis. 
H. vastatrix is a hemicyclic fungus that possesses urediniospores, which are thin-walled spores created during the uredium stage of H. vastatrix’s rust life cycle. These urediniospores of H. vastatrix are 28-36 x 18-28 μm and reniform/kidney-shaped . Their wall is 1 μm thick of hyaline; the urediniospores are composed of warts on its convex side and smooth lining on its concave side. β-1,3-Glucans and chitin are features in the cell wall of the urediniospores as these polymers spread over the pre-penetrative fungal structures for infection of the coffee leaf itself . The teliospores are 20-28 μm in diameter and are sphere-shaped, but they are not perfectly globose. These teliospores also possess a hyaline wall that is about 1 μm thick and smooth throughout .
Hemileia vastatrix spores are unique upon comparison to other rusts due to its suprastomal cluster of sporangia which are shaped like bouquets, the contrasting wall face textures of the urediniospores, and the irregularly angular-spherical teliospores. The hyphae and haustoria, projections that allow the parasitic fungus to enter the coffee leaf host, of H. vastatrix are similar to other rust fungi .
As a rust fungus, H. vastatrix obtains nutrients from its host - the plants of the genus Coffea. Through these host plants, H. vastatrix both reproduce and complete their life cycle. As obligate biotrophs, H. vastatrix utilizes a haustorium, a thin projection from its hyphae, to penetrate its host plant and derive nutrients from it. The haustorium also serves a dual purpose, secreting effectors that target the host plant’s cytoplasm in order to promote the infection of the plant . H. vastatrix has been hypothesized to be heteroecious in nature, meaning it ultimately requires two hosts to complete its disease cycle . At this time, molecular features driving adaptations to an obligate biotrophic relationship with plant hosts remain unknown .
H. vastatrix is an obligate-host specific fungus which requires both temperatures of 10°C to 35°C and liquid water to develop, leading it to proliferate in warmer climates . H. vastatrix acts as a biotrophic fungal pathogen, primarily attacking the plants of the genus Coffea, which is composed of over one hundred species . Today, H. vastatrix affects the leaves of coffee plants in most coffee-growing countries worldwide and is present in almost all regions conducive for growing Arabica coffee . While Coffea arabica originated in the dry climate of Ethiopia and northern Kenya, it is now present globally . The spread of H. vastatrix, and consequently coffee leaf rust, has coevolved alongside the spread of Coffea arabica. Since the first major outbreak of coffee leaf rust caused by H. vastatrix in Sri Lanka in 1869, the majority of the world’s coffee producing regions have reported instances of coffee leaf rust outbreaks . H. vastatrix was most recently responsible for a widespread epidemic of coffee leaf rust throughout Central and South America, resulting in yield losses of up to 35% .
H. vastatrix causes coffee leaf rust on C. arabica by acting as an obligate plant pathogen and using urediniospores as its infectious structures . After the pathogen germinates on a leaf of C. arabica, the urediniospore produces a germ tube that utilizes the stomata of the leaf to penetrate the tissue. Hyphae then grow intercellularly and form two different specialized structures: haustoria and uredia . The haustoria take up nutrients from the host plant while simultaneously suppressing plant defense, and the uredia create new urediniospores that, similarly to the original urediniospores, go through the stomata and do not break the host cuticle, completing the life cycle of H. vastatrix. During infection, successive rounds of urediniospores are created and the tissue of the plant is infected multiple times during the growing season, making coffee leaf rust a polycyclic disease .
H. vastatrix only infects living leaves, causing chlorotic lesions on the underside of the leaves around the site of fungal penetration. Additionally, the urediniospores can be seen as orange splotches on the top of the leaf . As the chlorotic lesions grow, they reduce the photosynthetic abilities of the plant by reducing the amount of area on the leaves that can be used for the process. In serious cases, this can lead to defoliation and the death of full branches of C. arabica .
Resistance to H. vastatrix
C. arabica has developed several defenses against H. vastatrix including heightened peroxidase production and a hypersensitive reaction involving multiple genes. When coffee plants are infected by H. vastatrix, a peak in peroxidases and other oxidases is observed, particularly at infection sites. These enzymes have been found to reinforce the cell walls of C. arabica cells and produce hydrogen peroxide as a defense mechanism against the fungus . The increased production of peroxidases is involved in a greater hypersensitivity of naturally resistant coffee plants that occurs upon interaction with H. vastatrix. In this reaction, genes coding for stress-related proteins, disease resistance proteins, and signal transduction pathways are up-regulated to fight off the infection .
These defense responses can be induced by chitosan, a natural polymer with multiple advantages in terms of safety and easy access. Chitosan provides a protective effect when applied to coffee plants, and it increases the production of important resistance proteins including peroxidases, making it effective in improving the resistance of C. arabica to H. vastatrix .
Treatment of Coffee Leaf Rust
Many treatment options, both biological and non-biological, have been explored to limit the effect of the pathogen. The application of chitosan to coffee plants is useful in bolstering the plant’s natural resistance to coffee leaf rust . The use of mycoparasites, organisms that parasitize fungi, is another option to biologically control H. vastatrix. Mycoparasites such as Digitopodium hemileiae, Digitopodium cannae, Hyalocladosporiella tectonae, and Hyalocladosporiella cannae have been found to specifically attack H. vastatrix and are consequently potential treatments for coffee leaf rust . Lecanicillium lecanii is another mycoparasite that could be used to target H. vastatrix; however, its effectiveness depends on a large population of Coccus viridis, a green coffee scale also attacked by L. lecanii. In turn, C. viridis depends on its mutualistic relationship with Azteca instabilis, an ant species, making the use of L. lecanii as a biological control of H. vastatrix a complicated procedure .
Non-biological treatments of coffee leaf rust have also been explored. Along with selective breeding of resistant coffee plants, protectant fungicides such as copper hydroxide are commonly used as a preventative measure against H. vastatrix; other standard fungicides are also frequently applied. Treatments involving salicylic acid have been explored after being validated by their success against other plant pathogens . This salicylic acid treatment was discovered to be of use in reducing both the severity and incidence of coffee leaf rust. In fact, it holds the potential to be more effective than the traditional treatment options of copper hydroxide and other fungicides .
While coffee is a crucial staple of individuals’ lives globally, H. vastatrix is still not as widely studied as other rust fungi due to its complicated mechanisms in pathogenicity and virulence. Current research mostly focuses on the prevention of H. vastatrix spread, with limited emphasis on the specific mechanisms underlying its pathogenicity and virulence. During this time, there have been new rust races found that are able to overcome resistance .
Novel research on the prevention of H. vastatrix was conducted by using chitosan, a natural polymer that has been favored due to its biodegradable, biocompatible, and safe nature. Chitosan has already been widely used in plant defense against pathogenic microorganisms . Results showed a protective effect using practical-grade and commercial food-grade chitosan. These induced the activity of enzymes with β-1,3 glucanase and peroxidase, which effectively inhibited the fungus’ ability to infect Coffea plants.
Additionally, since critical aspects of the disease cycle of H. vastatrix remain unclear and no alternate host has ever been reported, a new hypothetical alternate host ranking (HAHR) method and an automated text mining (ATM) procedure termed HAHR/ATM method was recently developed to discover an alternate plant host of H. vastatrix. Using this new research method, researchers were able to create a list of potential alternate host plants for coffee leaf rust, which included Croton, Euphorbia and Rubus genera .
A study on the gene expression discovered approximately 516 H. vastatrix genes that were putatively encoding secreted proteins; of these genes, more than 50% held no homology to proteins in other rust fungi and were uniquely specific to H. vastatrix . This study worked to prompt the identification of coffee resistant genes encoding target proteins in the early and late defense stages to provide additional tools to advance in the improvement of disease resistance breeding .
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