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Since the discovery of the Pleurocordyceps/ "Polycephalomyces" clade unaffiliated with the clades of Clavicipitaceae s. str., Ophiocordycipitaceae, and Cordycipitaceae of clavicipitaceous fungi, some taxa have been published and more fungal material relevant to the group have become available for further study. Here, a multigene phylogeny using nrSSU, nrLSU, tef1, rpb1, and rpb2 was constructed with some of the recently discovered additional taxa using maximum likelihood and Bayesian analyses (BI) to test and refine the current phylogenetic framework for Cordyceps s. lat. and other clavicipitaceous fungi. In addition to the well supported major Pleurocordyceps/"Polycephalomyces" clade revealed previously, another clade with newly added taxa referred to as "Polycephalomyces formosus‐like" from Japan was found to be sister to the Pleurocordyceps/"Polycephalomyces" clade. Extensive investigation revealed that strains named "P. formosus‐like" grouped in this new clade and do indeed represent the true P. formosus and that species previously included in the genus Polycephalomyces required a new generic name. Based on the phylogenetic analyses and morphological characteristics, including both sexual and asexual morphs when available, the new generic name Pleurocordyceps is introduced and relevant new combinations are made. A newly designated lectotype and a supporting epitype for P. formosus is selected and the circumscription of Polycephalomyces is discussed. [ABSTRACT FROM AUTHOR]

Biological control is a promising approach to reduce plant diseases caused by nematodes to ensure high productivity in agricultural production. Large‐scale analyses of genetic variation in fungal species used for biocontrol can generate knowledge regarding interaction mechanisms that can improve efficacy of biocontrol applications. In this study, we performed a genome‐wide association study (GWAS) for in vitro antagonism against the root lesion nematode Pratylenchus penetrans in 53 previously genome re‐sequenced strains of the biocontrol fungus Clonostachys rosea. Nematode mortality in C. rosea potato dextrose broth (PDB) culture filtrates was highly variable and showed continuous variation (p <.001) between strains, indicating a polygenic inheritance. Twenty‐one strains produced culture filtrates with higher (p ≤.05) nematode mortality compared with the PDB control treatment, while ten strains lowered (p ≤.05) the mortality. The difference in in vitro antagonism against P. penetrans correlated with antagonism against the soybean cyst nematode Heterodera glycines, indicating lack of host specificity in C. rosea. An empirical Bayesian multiple hypothesis testing approach identified 279 single nucleotide polymorphism markers significantly (local false sign rate < 10–10) associated with the trait. Genes present in the genomic regions associated with nematicidal activity included several membrane transporters, a chitinase and genes encoding proteins predicted to biosynthesize secondary metabolites. Gene deletion strains of the predicted nonribosomal peptide synthetase genes nps4 and nps5 were generated and showed increased (p ≤.001) fungal growth and conidiation rates compared to the wild type. Deletion strains also exhibited reduced (p <.001) nematicidal activity and reduced (p ≤.05) biocontrol efficacy against nematode root disease and against fusarium foot rot on wheat. In summary, we show that the GWAS approach can be used to identify biocontrol factors in C. rosea, specifically the putative nonribosomal peptide synthetases NPS4 and NPS5. [ABSTRACT FROM AUTHOR]

Gene gain/loss in the context of gene family dynamics plays an important role in evolutionary processes as organisms, particularly invasive species, adapt to new environments or niches. One notable example of this is the duplication of digestive proteases in some parasitic insects and helminths to meet nutritional requirements during animal parasitism. However, whether gene family expansion participates in the adaptation of a plant parasite nematode to its host remains unknown. Here, we compared the newly sequenced genomes of the pinewood nematode, Bursaphelenchus xylophilus, with the genomes of free‐living, animal‐parasitic and plant‐parasitic nematodes. The results showed gene expansions occurring in 51 gene families in B. xylophilus, especially in xenobiotic detoxification pathways, including flavin monooxygenase (FMO), cytochrome P450 (CYP450), short chain dehydrogenase (SDR), alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), UDP‐glucuronosyltransferase (UGT) and glutathione S‐transferase (GST). Although a majority of these expansions probably resulted from gene duplications, nine ADH genes were potentially acquired by horizontal gene transfer (HGT) from fungi. From the transcriptomes of B. xylophilus treated with pine saplings and terpenes, candidate xenobiotic detoxification genes were identified. We propose that host defence chemicals led to gene family expansions of xenobiotic detoxification pathways in B. xylophilus facilitating its survival in pine resin ducts. This study contributes to a better understanding of how a parasitic nematode adapts to its host. [ABSTRACT FROM AUTHOR]

Emerald ash borer (EAB, Agrilus planipennis) is an invasive killer of ash trees (Fraxinus spp.) in North America and Europe. Ash species co‐evolved with EAB in their native range in Asia are mostly resistant, although the precise mechanism(s) remain unclear. Very little is also known about EAB or ash tree microbiomes. We performed the first joint comparison of phloem mycobiome and metabolites between a native and a nonnative ash species, infested and uninfested with EAB, in conjunction with investigation of larval mycobiome. Phloem mycobiome communities differed between the tree species, but both were unaffected by EAB infestation. Several indicator taxa in the larval gut shared a similarly high relative abundance only with the native host trees. Widely targeted metabolomics revealed 24 distinct metabolites in native trees and 53 metabolites in nonnative trees, respectively, that differed in relative content between infested and uninfested trees only in one species. Interestingly, four metabolites shared a strong relationship with the phloem mycobiomes, majority of which affected only the native trees. Collectively, our results demonstrate a complex interplay between host tree chemistry and mycobiome, and suggest the shared relationships between the mycobiomes of the native host tree and EAB may reflect their shared co‐evolution. [ABSTRACT FROM AUTHOR]

Identifying cryptic species poses a substantial challenge to both biologists and naturalists due to morphological similarities. Bemisia tabaci is a cryptic species complex containing more than 44 putative species; several of which are currently among the world's most destructive crop pests. Interpreting and delimiting the evolution of this species complex has proved problematic. To develop a comprehensive framework for species delimitation and identification, we evaluated the performance of distinct data sources both individually and in combination among numerous samples of the B. tabaci species complex acquired worldwide. Distinct datasets include full mitogenomes, single‐copy nuclear genes, restriction site‐associated DNA sequencing, geographic range, host speciation, and reproductive compatibility datasets. Phylogenetically, our well‐supported topologies generated from three dense molecular markers highlighted the evolutionary divergence of species of the B. tabaci complex and suggested that the nuclear markers serve as a more accurate representation of B. tabaci species diversity. Reproductive compatibility datasets facilitated the identification of at least 17 different cryptic species within our samples. Native geographic range information provides a complementary assessment of species recognition, while the host range datasets provide low rate of delimiting resolution. We further summarized different data performances in species classification when compared with reproductive compatibility, indicating that combination of mtCOI divergence, nuclear markers, geographic range provide a complementary assessment of species recognition. Finally, we represent a model for understanding and untangling the cryptic species complexes based on the evidence from this study and previously published articles. [ABSTRACT FROM AUTHOR]