A set of diseases caused by fungi and oomycetes are responsible for large losses in annual world cocoa production. Managing the impact caused by these diseases is very complex because a common solution has yet to be found for different pathogens. In this context, the systematic knowledge of Theobroma cacao L. pathogens\' molecular characteristics may help researchers understand the possibilities and limitations of cocoa disease management strategies. This work systematically organized and summarized the main findings of omics studies of T. cacao eukaryotic pathogens, focusing on the plant-pathogen interaction and production dynamics. Using the PRISMA protocol and a semiautomated process, we selected papers from the Scopus and Web of Science databases and collected data from the selected papers. From the initial 3169 studies, 149 were selected. The first author\'s affiliations were mostly from two countries, Brazil (55%) and the USA (22%). The most frequent genera were Moniliophthora (105 studies), Phytophthora (59 studies) and Ceratocystis (13 studies). The systematic review database includes papers reporting the whole-genome sequence from six cocoa pathogens and evidence of some necrosis-inducing-like proteins, which are common in T. cacao pathogen genomes. This review contributes to the knowledge about T. cacao diseases, providing an integrated discussion of T. cacao pathogens\' molecular characteristics, common mechanisms of pathogenicity and how this knowledge is produced worldwide.

The oomycetes of the genus Phytophthora have the most aggressive species for agriculture and forestry, such as Phytophthora sojae which is responsible for soybean root rot, Phytophthora infestans responsible for the potato downy mildew that caused the diaspora in Ireland in the nineteenth-century, and Phytophthora cinnamomi that affects a wide variety of tree species, from avocado in America, trees in Oceania to European chestnut trees. P. cinnamomi reproduces either sexually or asexually and asexual zoospores can live as saprotrophs and subsist in the soil long after death and removal of host plants. Controlling this organism is very challenging for researchers due to the limited range of effective chemical inhibitors. In this work, we present a systematic review of alternatives for biocontrol of Phytophthora in general and P. cinnamomi in particular. Our literature review indicates that Trichoderma spp., mainly Trichoderma harzianum, T. virens, and T. asperellum are very promising fungal species in the control of different Phytophthora spp. The Bacillus genus is also very promising in the control and inhibition of several Phytophthoras spp.

Phytophthora spp. are the causal agents of gummosis or foot rot, fibrous root rot, and fruit brown rot diseases that affect the roots, trunk, and fruits of citrus trees, causing severe economic losses. This work presents an updated systematic review addressing the defence responses in citrus against Phytophthora and the strategies to manage Phytophthora diseases. Applying a new method of search based on an explicit, rigorous, and transparent methodology. For this purpose, a systematic literature review was conducted using the databases available for academic research. The main plant defence mechanisms reported in the cited papers are the hypersensitivity response, cell wall reinforcement, production of pathogenesis-related proteins, and expression of defence-related genes. Moreover, the main strategies to manage Phytophthora root rot are organic compounds in the soil and biological control with fungi and bacteria. In addition, inhibition of Phytophthora gummosis or canker by applying new oomycota fungicides and reducing the incidence of brown fruit rot through the application of potassium phosphite have also been reported. Moreover, modern plant biotechnology techniques can help to accelerate the selection of resistant rootstocks in breeding programs, as controlled crossings for the generation of hybrids, somatic hybridisation, transgenic citrus plants, mapped genomic regions of Quantitative Trait Loci (QTLs), candidate genes, metabolic markers and comparative transcriptomic. These innovative techniques represent a suitable tool to breed new Phytophthora resistant rootstocks, which is widely recognised as the best strategy to face gummosis or foot rot, fibrous root rot and ultimately minimise the expensive use of pesticides in crop protection.

The Phytophthora genus is composed, mainly, of plant pathogens. This genus belongs to the Oomycete class, also known as \"pseudo-fungi\", within the Chromista Kingdom. Phytophthora spp. is highlighted due to the significant plant diseases that they cause, which represents some of the most economically and cultural losses, such as European chestnut ink disease, which is caused by P. cinnamomi. Currently, there have been four genome assemblies placed at the National Center for Biotechnology Information (NCBI), although the progress to understand and elucidate the pathogenic process of P. cinnamomi by its genome is progressing slowly. In this review paper, we aim to report and discuss the recent findings related to P. cinnamomi and its genomic information. Our research is based on paper databases that reported probable functions to P. cinnamomi proteins using sequence alignments, bioinformatics, and biotechnology approaches. Some of these proteins studied have functions that are proposed to be involved in the asexual sporulation and zoosporogenesis leading to the host colonization and consequently associated with pathogenicity. Some remarkable genes and proteins discussed here are related to oospore development, inhibition of sporangium formation and cleavage, inhibition of flagellar assembly, blockage of cyst germination and hyphal extension, and biofilm proteins. Lastly, we report some biotechnological approaches using biological control, studies with genome sequencing of P. cinnamomi resistant plants, and gene silencing through RNA interference (iRNA).

Human-induced global change is expected to amplify the disease risk for marine biota. However, the role of disease in the rapid global decline of seagrass is largely unknown. Global change may enhance seagrass susceptibility to disease through enhanced physiological stress, while simultaneously promoting pathogen development. This review outlines the characteristics of disease-forming organisms and potential impacts of global change on three groups of known seagrass pathogens: labyrinthulids, oomycetes and Phytomyxea. We propose that hypersalinity, climate warming and eutrophication pose the greatest risk for increasing frequency of disease outbreaks in seagrasses by increasing seagrass stress and lowering seagrass resilience. In some instances, global change may also promote pathogen development. However, there is currently a paucity of information on these seagrass pathosystems. We emphasise the need to expand current research to better understand the seagrass-pathogen relationships, serving to inform predicative modelling and management of seagrass disease under future global change scenarios.

Various aspects, mechanisms and functions of the oxidative burst with generation of O2- superoxide anions in plant cells, which is stimulated by active defence-inducing agents such as fungal infection or elicitor treatment, were reviewed mainly on the basis of experimental evidence obtained in a system of Solanaceae plants and Phytophthora spp. The oxidative burst may be due to an O(2-)generating NADPH oxidase in the plasma membrane, which is activated with combinations of cytosolic proteins, Ca2+, calmodulin and protein kinase, following stimulation by elicitor molecules. The oxidative burst may play the role of an internal emergency signal for induction of the metabolic cascade for active defence.