Screening of grapevine red blotch virus in two European ampelographic collections

Grapevine red blotch virus (GRBV) is a recently identified virus that infects grapevine and has a severe impact on the grape industry in North America. Since the first description of the virus 8 years ago, clear progress has been made regarding our understanding of the GRBV pathosystem. However, questions remain regarding the origin of this pathogen and its spread outside North America, especially in Europe. In this study, we present the results of a large-scale GRBV survey in two European repositories; we targeted Vitis spp. accessions with diverse geographical origins. Of 816 accessions from different origins (50 different countries around the world), six accessions were infected by GRBV, all of which originated from the United States. We investigated the DNA virome of 155 grapevine accessions from the Swiss grapevine collection using high-throughput sequencing. We observed that virome of the Swiss grapevine collection was composed of several RNA viruses. In contrast, we did not detect any DNA viruses in the 155 Swiss grapevine accessions. This finding suggests that the abundance of DNA viruses infecting grapevines in Switzerland is either very low or non-existent. Our results and the findings of studies published since 2008 show that GRBV most likely originated in North America and subsequently spread to other viticultural areas in the world via unintentional movement of infected cuttings. According to our data, the most plausible scenario for the origin of GRBV is that the virus evolved from non-Vitis vinifera hosts and underwent a host jump to Vitis vinifera after its introduction to North America in the 1600s.

Regressive evolution of an effector following a host jump in the Irish Potato Famine Pathogen Lineage

In order to infect a new host species, the pathogen must evolve to enhance infection and transmission in the novel environment. Although we often think of evolution as a process of accumulation, it is also a process of loss. Here, we document an example of regressive evolution in the Irish potato famine pathogen (Phytophthora infestans) lineage, providing evidence that a key sequence motif in the effector PexRD54 has degenerated following a host jump. We began by looking at PexRD54 and PexRD54-like sequences from across Phytophthora species. We found that PexRD54 emerged in the common ancestor of Phytophthora clade 1b and 1c species, and further sequence analysis showed that a key functional motif, the C-terminal ATG8-interacting motif (AIM), was also acquired at this point in the lineage. A closer analysis showed that the P. mirabilis PexRD54 (PmPexRD54) AIM appeared unusual, the otherwise-conserved central residue mutated from a glutamate to a lysine. We aimed to determine whether this PmPexRD54 AIM polymorphism represented an adaptation to the Mirabilis jalapa host environment. We began by characterizing the M. jalapa ATG8 family, finding that they have a unique evolutionary history compared to previously characterized ATG8s. Then, using co-immunoprecipitation and isothermal titration calorimetry assays, we showed that both full-length PmPexRD54 and the PmPexRD54 AIM peptide bind very weakly to the M. jalapa ATG8s. Through a combination of binding assays and structural modelling, we showed that the identity of the residue at the position of the PmPexRD54 AIM polymorphism can underpin high-affinity binding to plant ATG8s. Finally, we conclude that the functionality of the PexRD54 AIM was lost in the P. mirabilis lineage, perhaps owing to as-yet-unknown pressure on this effector in the new host environment.Author SummaryPathogens evolve in concert with their hosts. When a pathogen begins to infect a new host species, known as a “host jump,” the pathogen must evolve to enhance infection and transmission. These evolutionary processes can involve both the gain and loss of genes, as well as dynamic changes in protein function. Here, we describe an example of a pathogen protein that lost a key functional domain following a host jump, a salient example of “regressive evolution.” Specifically, we show that an effector protein from the plant pathogen Phytopthora mirabilis, a host-specific lineage closely related to the Irish potato famine pathogen Phytopthora infestans, has a derived amino acid polymorphism that results in a loss of interaction with certain host machinery.

Ophiocordyceps salganeicola, a parasite of social cockroaches in Japan and insights into the evolution of other closely-related Blattodea-associated lineages

The entomopathogenic genus Ophiocordyceps includes a highly diverse group of fungal species, predominantly parasitizing insects in the orders Coleoptera, Hemiptera, Hymenoptera and Lepidoptera. However, other insect orders are also parasitized by these fungi, for example the Blattodea (termites and cockroaches). Despite their ubiquity in nearly all environments insects occur, blattodeans are rarely found infected by filamentous fungi and thus, their ecology and evolutionary history remain obscure. In this study, we propose a new species of Ophiocordyceps infecting the social cockroaches Salganea esakii and S. taiwanensis, based on 16 years of collections and field observations in Japan, especially in the Ryukyu Archipelago. We found a high degree of genetic similarity between specimens from different islands, infecting these two Salganea species and that this relationship is ancient, likely not originating from a recent host jump. Furthermore, we found that Ophiocordyceps lineages infecting cockroaches evolved around the same time, at least twice, one from beetles and the other from termites. We have also investigated the evolutionary relationships between Ophiocordyceps and termites and present the phylogenetic placement of O. cf. blattae. Our analyses also show that O. sinensis could have originated from an ancestor infecting termite, instead of beetle larvae as previously proposed.

Sirolpidium bryopsidis, a parasite of green algae, is probably conspecific with Pontisma lagenidioides, a parasite of red algae

The genus Sirolpidium (Sirolpidiaceae) of the Oomycota includes several species of holocarpic obligate aquatic parasites. These organisms are widely occurring in marine and freshwater habitats, mostly infecting filamentous green algae. Presently, all species are only known from their morphology and descriptive life cycle traits. None of the seven species classified in Sirolpidium, including the type species, S. bryopsidis, has been rediscovered and studied for their molecular phylogeny, so far. Originally, the genus was established to accommodate all parasites of filamentous marine green algae. In the past few decades, however, Sirolpidium has undergone multiple taxonomic revisions and several species parasitic in other host groups were added to the genus. While the phylogeny of the marine rhodophyte- and phaeophyte-infecting genera Pontisma and Eurychasma, respectively, has only been resolved recently, the taxonomic placement of the chlorophyte-infecting genus Sirolpidium remained unresolved. In the present study, we report the phylogenetic placement of Sirolpidium bryopsidis infecting the filamentous marine green algae Capsosiphon fulvescens sampled from Skagaströnd in Northwest Iceland. Phylogenetic reconstructions revealed that S. bryopsidis is either conspecific or at least very closely related to the type species of Pontisma, Po. lagenidioides. Consequently, the type species of genus Sirolpidium, S. bryopsidis, is reclassified to Pontisma. Further infection trials are needed to determine if Po. bryopsidis and Po. lagenidioides are conspecific or closely related. In either case, the apparently recent host jump from red to green algae is remarkable, as it opens the possibility for radiation in a largely divergent eukaryotic lineage.

Codon pattern reveals SARS-CoV-2 to be a monomorphic strain that emerged through recombination of replicase and envelope alleles of bat and pangolin origin

Viruses are dependent on the host tRNA pool, and an optimum codon usage pattern (CUP) is a driving force in its evolution. Systematic analysis of CUP of replicase (rdrp), spike, envelope (E), membrane glycoprotein (M), and nucleocapsid (N) encoding genes of SARS-CoV-2 from reported diverse lineages to suggest one-time host jump of a SARS-CoV-2 isolate into the human host. In contrast to human isolates, a high degree of variation in CUP of these genes suggests that bats, pangolins, and dogs are natural reservoirs of diverse strains. At the same time, our analysis suggests that dogs are not a source of SARS-CoV-2. Interestingly, CUP of rdrp displays conservation with two bat SARS isolates RaTG13 and RmYN02. CUP of the SARS-CoV-2 E gene is also conserved with bat and pangolin isolates with variations for a few amino acids. This suggests role allele replacement in these two genes involving SARS strains of least two hosts. At the same time, a relatively conserved CUP pattern in replicase and envelope across hosts suggests them it to be an ideal target in antiviral development for SARS-CoV-2.

Insights into the Ecology and Evolution of Blattodea-associated Ophiocordyceps

Entomopathogenic fungi are ubiquitous inhabitants of forests worldwide, remarkably in tropical regions. Among these fungi, one of the most abundant and diverse is the genus Ophiocordyceps. These fungi are particularly diverse and more commonly found parasitizing coleopteran, lepidopteran, hymenopteran and hemipteran insects. However, other insect orders are also parasitized by these fungi, for example the blattodeans (termites and cockroaches). Despite their ubiquity in nearly all environments insects occur, blattodeans are rarely found infected by filamentous fungi and thus, their ecology and evolutionary history remains obscure. In this study, we propose a new species of Ophiocordyceps infecting the social cockroaches Salganea esakii and S. taiwanensis, based on 16 years of collections and field observations, especially the Ryukyu Archipelago. We found a high degree of genetic similarity between specimens from different islands, infecting two Salganea species and that this relationship is ancient, likely not originated from a recent host jump. Furthermore, we found that Ophiocordyceps lineages infecting cockroaches evolved around the same time, at least twice, one from beetles and the other from termites. We have also investigated the evolutionary relationships between Ophiocordyceps and termites and present the phylogenetic placement of O. blattae for the first time.

A Review of Current Knowledge on Staphylococcus agnetis in Poultry

This review aims to summarize recent discoveries and advancements regarding the characteristics of Staphylococcus agnetis (S. agnetis) and its role in poultry pathology. S. agnetis is an emerging pathogen that was primarily associated with mastitis in dairy cattle. After a presumed host jump from cattle to poultry, it was identified as a pathological agent in broiler chickens (Gallus gallus domesticus), causing lameness induced by bacterial chondronecrosis with osteomyelitis (BCO), septicemia, and valvular endocarditis. Economic and welfare losses caused by lameness are global problems in the poultry industry, and S. agnetis has been shown to have a potential to induce high incidences of lameness in broiler chickens. S. agnetis exhibits a distinct repertoire of virulence factors found in many different staphylococci. It is closely related to S. hyicus and S. chromogenes, hence infections caused by S. agnetis may be misdiagnosed or even undiagnosed. As there are very few reports on S. agnetis in poultry, many facts about its pathogenesis, epidemiology, routes of transmission, and the potential impacts on the poultry industry remain unknown.

Two Is Better Than One: Studying Ustilago bromivora–Brachypodium Compatibility by Using a Hybrid Pathogen

Pathogenic fungi can have devastating effects on agriculture and health. One potential challenge in dealing with pathogens is the possibility of a host jump (i.e., when a pathogen infects a new host species). This can lead to the emergence of new diseases or complicate the management of existing threats. We studied host specificity by using a hybrid fungus formed by mating two closely related fungi: Ustilago bromivora, which normally infects Brachypodium spp., and U. hordei, which normally infects barley. Although U. hordei was unable to infect Brachypodium spp., the hybrid could. These hybrids also displayed the same mating-type bias that had been observed in U. bromivora and provide evidence of a dominant spore-killer-like system on the sex chromosome of U. bromivora. By analyzing the genomic composition of 109 hybrid strains, backcrossed with U. hordei over four generations, we identified three regions associated with infection on Brachypodium spp. and 75 potential virulence candidates. The most strongly associated region was located on chromosome 8, where seven genes encoding predicted secreted proteins were identified. The fact that we identified several regions relevant for pathogenicity on Brachypodium spp. but that none were essential suggests that host specificity, in the case of U. bromivora, is a multifactorial trait which can be achieved through different subsets of virulence factors.

A novel phyllosphere residentProtomycesspecies that interacts with theArabidopsisimmune system

ABSTRACTWe describe the genome contents of sixProtomycesspp. that are pathogenic within the typical host range of the genus and a novelProtomycesstrain (SC29) that was previously isolated from the phylloplane of wildArabidopsis thaliana(Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinctProtomycessp. Analysis of gene family expansions, gene retention, and gene loss patterns among theseProtomycesspp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle ofProtomycesspp. was previously unknown. Genomic changes in SC29 and all otherProtomycesspp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease onArabidopsisas a single strain, but could persist in its phylloplane, while the closely relatedP. inouyeidoes not. SC29 treatedArabidopsisexhibited enhanced immunity againstBotrytis cinereainfection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novelProtomycessp. able to survive in theArabidopsisphylloplane and that phylloplane residency is an important element in the lifecycle ofProtomycesspp.