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Abstract Variations in chromosome number are occasionally observed among oomycetes, a group that includes many plant pathogens, but the emergence of such variations and their effects on genome and virulence evolution remain ambiguous. We generated complete telomere-to-telomere genome assemblies for Phytophthora sojae, Globisporangium ultimum, Pythium oligandrum, and G. spinosum. Reconstructing the karyotype of the most recent common ancestor in Peronosporales revealed that frequent chromosome fusion and fission drove changes in chromosome number. Centromeres enriched with Copia-like transposons may contribute to chromosome fusion and fission events. Chromosome fusion facilitated the emergence of pathogenicity genes and their adaptive evolution. Effectors tended to duplicate in the sub-telomere regions of fused chromosomes, which exhibited evolutionary features distinct to the non-fused chromosomes. By integrating ancestral genomic dynamics and structural predictions, we have identified secreted Ankyrin repeat-containing proteins (ANKs) as a novel class of effectors in P. sojae. Phylogenetic analysis and experiments further revealed that ANK is a specifically expanded effector family in oomycetes. These results revealed chromosome dynamics in oomycete plant pathogens, and provided novel insights into karyotype and effector evolution.

Abstract Plant diseases have significant implications on agriculture and food security. Recent research published in Nature Communications by Hao et al. (Nat Commun 15:3310, 2024) has identified a novel disease-resistant gene, Rpp6907-7, which shows high potential in enhancing resistance to Asian Soybean Rust (ASR), a major threat to soybean production. This discovery provides valuable insights for developing improved soybean varieties with enhanced disease resistance.

Fungal effectors play critical roles in manipulating plant immune responses and promoting colonization. Sphaerulina musiva is a heterothallic ascomycete fungus that causes Septoria leaf spot and stem canker disease in poplar (Populus spp.) plantations. This disease can result in premature defoliation, branch and stem breakage, increased mortality, and plantation failure. However, little is known about the interaction between S. musiva and poplar. Previous work predicted 142 candidate secreted effector proteins in S. musiva (SmCSEPs), 19 of which were selected for further functional characterization in this study. SmCSEP3 induced plant cell death in Nicotiana benthamiana, while 8 out of 19 tested SmCSEPs suppressed cell death. The signal peptides of these eight SmCSEPs exhibited secretory activity in a yeast signal sequence trap assay. Confocal microscopy revealed that four of these eight SmCSEPs target both the cytoplasm and the nucleus, whereas four predominantly localize to discrete punctate structures. Pathogen challenge assays in N. benthamiana demonstrated that the transient expression of six SmCSEPs promoted Fusarium proliferatum infection. The expression of these six SmCSEP genes were induced during infection. SmCSEP2, SmCSEP13, and SmCSEP25 suppressed chitin-triggered reactive oxygen species burst and callose deposition in N. benthamiana. The candidate secreted effector proteins of S. musiva target multiple compartments in the plant cell and modulate different pattern-triggered immunity pathways. [Graphic: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2023.

The petrogenesis and geodynamic setting of the Mesozoic magmatic rocks in the Erguna Block, NE China remains controversial, especially the relationship between magmatism and the subduction history of the Mongol–Okhotsk oceanic plate. Here we present data for the Early Jurassic–Early Cretaceous adakite-like magmatic rocks from Chaoman Farm in the northeastern part of the Erguna Block. Zircon U-Pb dating reveals that the syenogranites crystallized at around 190–180 Ma, while the monzonites, quartz diorite porphyries, and quartz monzonite porphyries were emplaced at around 147–143 Ma. The syenogranites, monzonites, quartz diorite porphyries, and quartz monzonite porphyries are adakite-like rocks. The syenogranites and quartz monzonite porphyries were produced by the partial melting of a thickened ancient mafic lower continental crust and a thickened juvenile lower crust, respectively. Meanwhile, the monzonites and quartz diorite porphyries were formed as a result of partial melting of the oceanic crust. In conclusion, the occurrence of these Early Jurassic magmatic rocks was closely linked to the process of southward subduction of the Mongol–Okhotsk oceanic plate. On the contrary, the Late Jurassic to early Early Cretaceous magmatism (147–143 Ma) occurred in an extensional environment, and was probably triggered by upwelling of the asthenosphere.

To date, the intricacies and efficacy of how periodic seasonal environmental fluctuations affect fish populations in biogeography in the context of profound climate change remain to be elucidated. Collected monitoring data on fish resources in the temperate estuary provide an excellent opportunity to assess the effects of seasonal environmental fluctuations on populations and functional assemblages under climate change. We first developed a framework for predicting habitat suitability under different climate change scenarios (SSP1-2.6 and SSP5-8.5) for 12 fish populations in the Yangtze estuary by examining the seasonal environmental affinities of temperate estuarine fishes. We then summarized the multidimensional habitat suitability responses (HSRs) of populations and functional assemblages and discussed the possible drivers and mechanisms underlying these changes. The results suggest that the acidity of the Yangtze estuary may decline in the future as the climate warms, endangering the ecosystem that many fish species depend on. Prospective climate change may have an impact on fish population HSRs through redistribution, area changes, and centroid migration of suitable habitats; nevertheless, affinity for environmental factors may be limited to distinguishing patterns of population response in the spring. Fish (5 populations) and functional assemblages (11 assemblages) may exhibit robust adaptations or non-adaptations to climate change when seasons change, given their suitable habitat area. Furthermore, projections indicate that the majority of fish habitat centroids exhibit seasonal responses, migrating northeast in the spring and southeast in the autumn. By decentralizing climate risk to seasonal scales, seasonal resilience in the multidimensional HSRs of several fish populations (5/12) and their functional assemblages (11/16) is revealed for the first time. Efforts to mitigate climate risks and safeguard resources should take these seasonal forecasts and indicative information into account.

Abstract Extracellular vesicles (EVs) are important for cell-to-cell communication in animals. EVs also play important roles in plant–microbe interactions, but the underlying mechanisms remain elusive. Here, proteomic analyses of EVs from the soybean (Glycine max) root rot pathogen Phytophthora sojae identify the tetraspanin family proteins PsTET1 and PsTET3, which are recognized by Nicotiana benthamiana to trigger plant immune responses. Both proteins are required for the full virulence of P. sojae. The large extracellular loop (EC2) of PsTET3 is the key region recognized by N. benthamiana and soybean cells in a plant receptor-like kinase NbSERK3a/b dependent manner. TET proteins from oomycete and fungal plant pathogens are recognized by N. benthamiana thus inducing immune responses, whereas plant-derived TET proteins are not due to the sequence divergence of sixteen amino acids at the C-terminal of EC2. This feature allows plants to distinguish self and non-self EVs to trigger active defense responses against pathogenic eukaryotes.

Abstract Oomycetes, such as Pythium species, contain numerous devastating plant pathogens that inflict substantial economic losses worldwide. Although CRISPR/Cas9-based genome editing is available, the selection markers available for genetic transformation in these species are limited. In this study, a mutated version of the Phytophthora capsici oxysterol-binding protein-related protein 1 (PcMuORP1), known to confer oxathiapiprolin resistance, was introduced into the CRISPR/Cas9 system for in situ complementation in Pythium ultimum. We targeted PuLLP, which encodes a loricrin-like protein, and showed significant downregulation when the Puf RNA-binding protein-encoding gene PuM90 was knocked out. The PuLLP knockout mutants could not produce oospores, indicating a similar biological function as PuM90. The reintroduction of PuLLP into the knockout mutant using PcMuORP1 as a selection marker restored oospore production. Further comparisons with the conventional selection marker NPTII indicated that PcMuORP1 could be applied at a lower concentration and cost, resulting in a higher screening efficiency. Successive subculturing in the absence of selective pressure showed that PcMuORP1 had little long-term effect on the fitness of transformants. Hence, it could be reused as an alternative selection marker. This study demonstrates the successful implementation of the PcMuORP1 gene as a selection marker in the genetic transformation of Py. ultimum and reveals the loricrin-like protein PuLLP as a sexual reproduction-related factor downstream of the Puf RNA-binding protein PuM90. Overall, these results will help accelerate the functional genomic investigation of oomycetes.

Abstract Phytopathogenic fungi secrete chitin deacetylase (CDA) to escape the host’s immunological defense during infection. Here, we showed that the deacetylation activity of CDA toward chitin is essential for fungal virulence. Five crystal structures of two representative and phylogenetically distant phytopathogenic fungal CDAs, VdPDA1 from Verticillium dahliae and Pst_13661 from Puccinia striiformis f. sp. tritici, were obtained in ligand-free and inhibitor-bound forms. These structures suggested that both CDAs have an identical substrate-binding pocket and an Asp-His-His triad for coordinating a transition metal ion. Based on the structural identities, four compounds with a benzohydroxamic acid (BHA) moiety were obtained as phytopathogenic fungal CDA inhibitors. BHA exhibited high effectiveness in attenuating fungal diseases in wheat, soybean, and cotton. Our findings revealed that phytopathogenic fungal CDAs share common structural features, and provided BHA as a lead compound for the design of CDA inhibitors aimed at attenuating crop fungal diseases.

Abstract Soybean rust caused by the fungus Phakopsora pachyrhizi is one of the most destructive diseases to soybean production worldwide. For the rapid diagnosis and the control of soybean rust, we developed a loop-mediated isothermal amplification (LAMP) assay that targets a P. pachyrhizi-specific gene (Phapa_6409908) identified from a comparative genomic analysis of 61 Pucciniomycotina strains. Using a set of screened primers and the optimized reaction conditions of 62°C for 70 min, the LAMP assay can detect P. pachyrhizi while excluding other plant pathogens. The assay consistently showed high sensitivity in detecting low contents of P. pachyrhizi DNA (10 pg). We confirmed the practical application of this LAMP assay in diagnosing soybean rust using soybean leaf samples collected from fields in four cities of Sichuan Province, China, in 2020 and 2021. The developed LAMP assay provides a specific, sensitive, and rapid method for the diagnosis of soybean rust caused by P. pachyrhizi, which can assist in the prediction, prevention, and control of this major soybean disease.

Abstract In recent years, the emergence of soybean stay-green syndrome (SGS), also referred to as ‘zhengqing’, in the Huang-Huai-Hai region of China has resulted in significant yield losses. SGS is a phenomenon characterized by the delayed senescence of soybean, resulting in stay-green leaves, flat pods, and stunted seed development at harvest. We previously identified a distinct geminivirus, named soybean stay-green associated geminivirus (SoSGV), as the causative agent of SGS by fulfilling Koch’s postulates. To further understand the epidemiology of SoSGV, in this study, we collected 368 stay-green samples from 17 regions in 8 provinces including the Huang-Huai-Hai region and surrounding areas. The results showed that 228 samples tested positive for SoSGV (61.96%), and 96.93% of these positive samples showed severe pod deflation. Our epidemiological assessment reveals that SGS caused by the SoSGV is prevalent in the fields, and it is undergoing geographical expansion and genetic differentiation. Additionally, we determined other natural hosts grown in the Huang-Huai-Hai region. By capturing insects in the field and conducting laboratory vector transmission tests, we confirmed that the common brown leafhopper (Orosius orientalis) is the transmission vector of SoSGV. With a better understanding of the transmission and epidemiology of SoSGV, we can develop more effective strategies for managing and mitigating its impact on soybean yields.

Abstract Although the functions of most protein effectors secreted by fungi are not predictable, they are known to modulate host immunity and facilitate infection. Fusarium graminearum is one of the 10 most abundant plant pathogenic fungi worldwide. To date, few effector proteins secreted by F. graminearum have been identified. In this study, we screened a putative effector protein Fg62 from proteins that contain signal peptides and unknown functional domains in F. graminearum secretome. Fg62 expression was highly upregulated during the early stages of F. graminearum infection, and its deletion reduced F. graminearum virulence in wheat and soybean. Transient expression of Fg62 or the recombinant protein led to plant cell death in Nicotiana benthamiana, and the signal peptide of Fg62 was required for cell death activation. Fg62 homologs are distributed in two species of the F. sambucinum species complex, which are also able to induce cell death in N. benthamiana. Fg62 activated plant immunity by increasing the expression of defense-related genes, and the recombinant Fg62 protein induced plant resistance to various pathogens. Overall, our results revealed that the extracellular effector Fg62 contributes to both pathogen virulence and plant immunity induction, providing new avenues for the development of environmentally friendly crop disease control strategies utilizing nonpolluting immune-inducing factors.

Phytophthora species are oomycete plant pathogens that cause great economic and ecological impacts. The Phytophthora genus includes over 180 known species, infecting a wide range of plant hosts, including crops, trees, and ornamentals. We sequenced the genomes of 31 individual Phytophthora species and 24 individual transcriptomes to study genetic relationships across the genus. De novo genome assemblies revealed variation in genome sizes, numbers of predicted genes, and in repetitive element content across the Phytophthora genus. A genus-wide comparison evaluated orthologous groups of genes. Predicted effector gene counts varied across Phytophthora species by effector family, genome size, and plant host range. Predicted numbers of apoplastic effectors increased as the host range of Phytophthora species increased. Predicted numbers of cytoplasmic effectors also increased with host range but leveled off or decreased in Phytophthora species that have enormous host ranges. With extensive sequencing across the Phytophthora genus, we now have the genomic resources to evaluate horizontal gene transfer events across the oomycetes. Using a machine-learning approach to identify horizontally transferred genes with bacterial or fungal origin, we identified 44 candidates over 36 Phytophthora species genomes. Phylogenetic reconstruction indicates that the transfers of most of these 44 candidates happened in parallel to major advances in the evolution of the oomycetes and Phytophthora spp. We conclude that the 31 genomes presented here are essential for investigating genus-wide genomic associations in genus Phytophthora. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

The pathogenic fungus Phomopsis longicolla causes numerous plant diseases, such as Phomopsis seed decay, pod and stem blight, and stem canker, which seriously affect the yield and quality of soybean production worldwide. Because of a lack of technology for efficient manipulation of genes for functional genomics, understanding of P. longicolla pathogenesis is limited. Here, we developed an efficient polyethylene glycol–mediated protoplast transformation system in P. longicolla that we used to characterize the functions of two genes involved in the cell wall integrity (CWI) pathway of the mitogen-activated protein kinase (MAPK) cascade, including PlMkk1, which encodes MAPK kinase, and its downstream gene PlSlt2, which encodes MAPK. Both gene knockout mutants ΔPlMkk1 and ΔPlSlt2 displayed a reduced growth rate, fragile aerial hyphae, abnormal polarized growth and pigmentation, defects in sporulation, inadequate CWI, enhanced sensitivity to abiotic stress agents, and significant deficiencies in virulence, although there were some differences in degree. The results suggest that PlMkk1 and PlSlt2 are crucial for a series of growth and development processes as well as pathogenicity. The developed transformation system will be a useful tool for additional gene function research and will aid in the elucidation of the pathogenic mechanisms of P. longicolla. [Graphic: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Nucleosome-free open chromatin often harbors transcription factor (TF)-binding sites that are associated with active cis-regulatory elements. However, analysis of open chromatin regions has rarely been applied to oomycete or fungal plant pathogens. In this study, we performed the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to identify open chromatin and cis-regulatory elements in Phytophthora sojae at the mycelial stage. We identified 10,389 peaks representing nucleosome-free regions (NFRs). The peaks were enriched in gene-promoter regions and associated with 40% of P. sojae genes; transcription levels were higher for genes with multiple peaks than genes with a single peak and were higher for genes with a single peak than genes without peak. Chromatin accessibility was positively correlated with gene transcription level. Through motif discovery based on NFR peaks in core promoter regions, 25 candidate cis-regulatory motifs with evidence of TF-binding footprints were identified. These motifs exhibited various preferences for location in the promoter region and associations with the transcription level of their target genes, which included some putative pathogenicity-related genes. As the first study revealing the landscape of open chromatin and the correlation between chromatin accessibility and gene transcription level in oomycetes, the results provide a technical reference and data resources for future studies on the regulatory mechanisms of gene transcription.[Graphic: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Oomycetes are filamentous microorganisms easily mistaken as fungi but vastly differ in physiology, biochemistry, and genetics. This commonly-held misconception lead to a reduced effectiveness by using conventional fungicides to control oomycetes, thus it demands the identification of novel functional genes as target for precisely design oomycetes-specific microbicide. The present study initially analyzed the available transcriptome data of the model oomycete pathogen, Phytophthora sojae, and constructed an expression matrix of 10,953 genes across the stages of asexual development and host infection. Hierarchical clustering, specificity, and diversity analyses revealed a more pronounced transcriptional plasticity during the stages of asexual development than that in host infection, which drew our attention by particularly focusing on transcripts in asexual development stage to eventually clustered them into 6 phase-specific expression modules. Three of which respectively possessing a serine/threonine phosphatase (PP2C) expressed during the mycelial and sporangium stages, a histidine kinase (HK) expressed during the zoospore and cyst stages, and a bZIP transcription factor (bZIP32) exclusive to the cyst germination stage were selected for down-stream functional validation. In this way, we demonstrated that PP2C, HK, and bZIP32 play significant roles in P. sojae asexual development and virulence. Thus, these findings provide a foundation for further gene functional annotation in oomycetes and crop disease management.

Abstract While conventional chemical fungicides directly eliminate pathogens, plant immunity inducers activate or prime plant immunity. In recent years, considerable progress has been made in understanding the mechanisms of immune regulation in plants. The development and application of plant immunity inducers based on the principles of plant immunity represent a new field in plant protection research. In this review, we describe the mechanisms of plant immunity inducers in terms of plant immune system activation, summarize the various classes of reported plant immunity inducers (proteins, oligosaccharides, chemicals, and lipids), and review methods for the identification or synthesis of plant immunity inducers. The current situation, new strategies, and future prospects in the development and application of plant immunity inducers are also discussed.

The soilborne oomycete Phytophthora capsici is the most destructive pathogen of vegetable crops and is responsible for substantial economic losses worldwide. Here, we present an improved genome assembly of P. capsici generated by Oxford Nanopore long-read sequencing (for de novo assembly) and Illumina short-read sequencing (for polishing). The genome of P. capsici is 100.5 Mb in length (GC content = 50.8%) and contains 26,069 predicted protein-coding genes. The whole genome of P. capsici is assembled into 194 scaffolds, 90% of which are larger than 300 kb. The N50 scaffold length and maximum scaffold length are 1.0 and 4.1 Mb, respectively. The whole-genome sequence of P. capsici will broaden our knowledge of this pathogen and enhance our understanding of the molecular basis of its pathogenicity, which will facilitate the development of effective management strategies.[Graphic: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Ustilaginoidea virens is a fungal pathogen that infects rice via the panicles. Here, the authors show that U. virens SGP1, a conserved Ser-Thr-rich glycosyl-phosphatidyl-inositol-anchored protein, elicits immune responses in rice leaves while contributing to virulence in panicles.

Abstract The basic leucine zipper (bZIP) transcription factor family, one of the largest and most diverse transcription factor families in eukaryotes, is associated with the development and stress responses of many eukaryotic organisms. However, their biological functions in oomycete plant pathogens are unclear. A genome-wide analysis of bZIP transcription factors in Phytophthora sojae showed that PsBZP32, which has a unique bZIP-PAS domain structure, exhibited a high transcription level during the early stages of P. sojae infection. We silenced PsBZP32 in P. sojae and found that the transformants showed defective cyst germination and pathogenicity. The transformants could not eliminate host-derived reactive oxygen species during infection and were more sensitive to oxidative stress. Their response to oxidative stress was independent of the PsBZP32 transcription level; however, subcellular localization and phosphorylation of PsBZP32 were affected by H2O2 stress. These results indicate that PsBZP32 is involved in regulation of P. sojae cyst germination, oxidative stress response, and pathogenicity.

Diaporthe-Phomopsis disease complex causes considerable yield losses in soybean production worldwide. As one of the major pathogens, Phomopsis longicolla T. W. Hobbs (syn. Diaporthe longicolla) is not only the primary agent of Phomopsis seed decay but is also one of the agents of Phomopsis pod and stem blight and Phomopsis stem canker. We performed both PacBio long-read sequencing and Illumina short-read sequencing and obtained a genome assembly for the strain P. longicolla YC2-1, which was isolated from soybean stem with Phomopsis stem blight disease. The 63.1 Mb genome assembly contains 87 scaffolds, with a minimum, maximum, and N50 scaffold length of 20 kb, 4.6 Mb, and 1.5 Mb respectively, and a total of 17,407 protein-coding genes. The high-quality data expand the genomic resource of P. longicolla species and will provide a solid foundation for a better understanding of their genetic diversity and pathogenic mechanisms.[Graphic: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

This article is part of the Top 10 Unanswered Questions in MPMI invited review series.The past few decades have seen major discoveries in the field of molecular plant-microbe interactions. As the result of technological and intellectual advances, we are now able to answer questions at a level of mechanistic detail that we could not have imagined possible 20 years ago. The MPMI Editorial Board felt it was time to take stock and reassess. What big questions remain unanswered? We knew that to identify the fundamental, overarching questions that drive our research, we needed to do this as a community. To reach a diverse audience of people with different backgrounds and perspectives, working in different areas of plant-microbe interactions, we queried the more than 1,400 participants at the 2019 International Congress on Molecular Plant-Microbe Interactions meeting in Glasgow. This group effort resulted in a list of ten, broad-reaching, fundamental questions that influence and inform our research. Here, we introduce these Top 10 unanswered questions, giving context and a brief description of the issues. Each of these questions will be the subject of a detailed review in the coming months. We hope that this process of reflecting on what is known and unknown and identifying the themes that underlie our research will provide a framework to use going forward, giving newcomers a sense of the mystery of the big questions and inspiring new avenues and novel insights.[Graphic: see text] Copyright © 2020 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.

Phytophthora sojae is a model species for the study of plant pathogenic oomycetes. The initial research on gene function using Phytophthora was mainly based on gene silencing technology. Recently, the CRISPR/Cas9-mediated genome editing technology was successfully established in P. sojae and widely used in oomycetes. In this protocol, we describe the operating procedures for the use of CRISPR/Cas9-based genome editing technology and PEG-mediated stable transformation of P. sojae protoplasts. Two plasmids were co-transformed into P. sojae: pYF515 expressing Cas9 and the single guide RNA, and the homologous replacement vector of the candidate gene. Finally, the ORF of candidate gene were replaced with the ORF of the entire hygromycin B phosphotransferase gene (HPH), to achieve precise knockout.

In recent years, the proportion and economic value of Lophius litulon (family Lophiidae) in the coastal fishery off Shandong Province, China has increased. In this study, we mapped the distribution of L. litulon abundance [catch per unit effort (CPUE)] and applied a generalized additive model (GAM) to explore the relationship between CPUE and environmental factors. Two data-limited methods (the BSM related to the CMSY method and the AMSY method) were used to evaluate the stock status and relevant fishery reference points of L. litulon. The results showed that the L. litulon stock was concentrated in the central Yellow Sea, at 34.0°–37.0° N and 121.0°–124.0° E, and the highest average CPUE of L. litulon in this area occurred in winter. The three most significant environmental factors affecting species abundance were bottom temperature, bottom salinity, and depth. L. litulon was most abundant when bottom temperature ranged from 5.8 to 10.6°C, depth was > 18 m, and bottom salinity varied from 31.0 to 33.2‰. The BSM and AMSY models indicated that the L. litulon stock was unhealthy and had been overfished in recent years, as its biomass remained below the level that can support maximum sustainable yield. The relative exploitation ratios were also high. These results provide the basic data for improving sustainability of the exploitation of L. litulon in the Yellow and Bohai Seas.

We applied Catch and Maximum Sustainable Yield (CMSY), Bayesian Schaefer model (BSM), and Abundance Maximum Sustainable Yield (AMSY) methods to estimate the status of Platycephalus indicus stocks in the Bohai and Yellow Seas, assessed model performance, and determined the impact of priors derived from expert knowledge on the performance of each model. Results showed that P. indicus stock in the Bohai Sea had collapsed, while that in the Yellow Sea stock was recovering. With the input of an expert prior derived from the length-based Bayesian biomass (LBB) estimation method, the CIs of each model narrowed, but the changes in biomass trajectory were not significant, and the estimates of B/BMSY were differed compared with model results using default rules. These three models can be used to evaluate data-limited stocks to reflect stock dynamics when reliable inputs are available. However, the ranges of priors, which are preferably obtained from other stock assessment tools, should be carefully established.

In plants, the apoplast is a critical battlefield for plant-microbe interactions. Plants secrete defense-related proteins into the apoplast to ward off the invasion of pathogens. How microbial pathogens overcome plant apoplastic immunity remains largely unknown. In this study, we reported that an atypical RxLR effector PsAvh181 secreted by Phytophthora sojae, inhibits the secretion of plant defense-related apoplastic proteins. PsAvh181 localizes to plant plasma membrane and essential for P. sojae infection. By co-immunoprecipitation assay followed by liquid chromatography-tandem mass spectrometry analyses, we identified the soybean GmSNAP-1 as a candidate host target of PsAvh181. GmSNAP-1 encodes a soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein, which associates with GmNSF of the SNARE complex functioning in vesicle trafficking. PsAvh181 binds to GmSNAP-1 in vivo and in vitro. PsAvh181 interferes with the interaction between GmSNAP-1 and GmNSF, and blocks the secretion of apoplastic defense-related proteins, such as pathogenesis-related protein PR-1 and apoplastic proteases. Taken together, these data show that an atypical P. sojae RxLR effector suppresses host apoplastic immunity by manipulating the host SNARE complex to interfere with host vesicle trafficking pathway.

Sexual reproduction is an essential stage of the oomycete life cycle. However, the functions of critical regulators in this biological process remain unclear due to a lack of genome editing technologies and functional genomic studies in oomycetes. The notorious oomycete pathogen Pythium ultimum is responsible for a variety of diseases in a broad range of plant species. In this study, we revealed the mechanism through which PuM90, a stage-specific Puf family RNA-binding protein, regulates oospore formation in P. ultimum. We developed the first CRISPR/Cas9 system-mediated gene knockout and in situ complementation methods for Pythium. PuM90-knockout mutants were significantly defective in oospore formation, with empty oogonia or oospores larger in size with thinner oospore walls compared with the wild type. A tripartite recognition motif (TRM) in the Puf domain of PuM90 could specifically bind to a UGUACAUA motif in the mRNA 3' untranslated region (UTR) of PuFLP, which encodes a flavodoxin-like protein, and thereby repress PuFLP mRNA level to facilitate oospore formation. Phenotypes similar to PuM90-knockout mutants were observed with overexpression of PuFLP, mutation of key amino acids in the TRM of PuM90, or mutation of the 3'-UTR binding site in PuFLP. The results demonstrated that a specific interaction of the RNA-binding protein PuM90 with the 3'-UTR of PuFLP mRNA at the post-transcriptional regulation level is critical for the sexual reproduction of P. ultimum.

The status of fishery resources in the Yangtze estuary and its adjacent waters is still unclear for the effective implementation of fishery management strategies. To help address this gap, a new method especially for data-limited fish stocks (LBB) was applied to assess seven commercially and ecotrophically important fish stocks. Fish specimens were collected in the estuary by bottom trawling quarterly from May 2018 to February 2019. Two historical datasets were collected with the same method in the same area for Indian perch (Jaydia lineata) and sickle pomfret (Pampus echinogaster). To explore the growth features and resilience of fish stocks, auximetric plots and growth performance indices (Φ′) were used. Results showed that common hairfin anchovy (Setipinna tenuifilis) in 2018 and Indian perch in 2018 showed a healthy stock biomass status with complete length structures under a sustainable fishing pressure. The others were outside of safe biological limits or overfished. The Lmean/Lopt < 0.9 in six (67%) of nine LBB models for seven fish stocks suggested that most of the stocks were truncated in length structures. This contribution provides the main fishery reference points regarding stock status that can inform managers and form the basis for various management strategies.

Abstract Phytophthora sojae is a destructive pathogen of soybean that is widely distributed in the world. The interaction between P. sojae and soybean follows the gene-for-gene model. The use of resistant soybean cultivars is the primary and most effective method to combat the disease. However, variation in the Avr genes of the pathogen enables it to evade host defenses. We collected 81 isolates from four major soybean-production areas in China to analyze the polymorphism of Avr genes in P. sojae field population. The virulence of these isolates towards 14 differential soybean lines indicated complex pathotypes in P. sojae field population in China. In this study we found that Rps1c, which is cognate with Avr1c, could be deployed in Heilongjiang, Shandong, and Jiangsu Provinces but not in Anhui Province. To determine the mechanism by which Avr1c escapes recognition by Rps1c, we analyzed the polymorphism of Avr1c gene in 50 isolates of a field population of P. sojae and found multiple novel genotypes related to virulence and avirulence. By performing infection assays and gene co-bombardment, we showed that the K105 amino-acid residue was under strong positive selection and was a determinant of the avirulence of Avr1c. Structural analysis showed that K105 was exposed on the surface of the protein, suggesting it to be a critical site for interacting with Rps genes or their associated proteins.

Abstract Background Filamentous plant pathogen genomes often display a bipartite architecture with gene-sparse, repeat-rich compartments serving as a cradle for adaptive evolution. The extent to which this two-speed genome architecture is associated with genome-wide DNA modifications is unknown. Results We show that the oomycetes Phytophthora infestans and Phytophthora sojae possess functional adenine N6-methylation (6mA) methyltransferases that modulate patterns of 6mA marks across the genome. In contrast, 5-methylcytosine could not be detected in these species. Methylated DNA IP sequencing (MeDIP-seq) of each species reveals 6mA is depleted around the transcription start sites (TSSs) and is associated with lowly expressed genes, particularly transposable elements. Genes occupying the gene-sparse regions have higher levels of 6mA in both genomes, possibly implicating the methylome in adaptive evolution. All six putative adenine methyltransferases from P. infestans and P. sojae, except PsDAMT2, display robust enzymatic activities. Surprisingly, single knockouts in P. sojae significantly reduce in vivo 6mA levels, indicating that the three enzymes are not fully redundant. MeDIP-seq of the psdamt3 mutant reveals uneven 6mA methylation reduction across genes, suggesting that PsDAMT3 may have a preference for gene body methylation after the TSS. Furthermore, transposable elements such as DNA elements are more active in the psdamt3 mutant. A large number of genes, particularly those from the adaptive genomic compartment, are differentially expressed. Conclusions Our findings provide evidence that 6mA modification is potentially an epigenetic mark in Phytophthora genomes, and complex patterns of 6mA methylation may be associated with adaptive evolution in these important plant pathogens.

The catch-maximum sustainable yield (CMSY) method and a closely related Bayesian state-space Schaefer surplus production model (BSM) were combined with published catch data and catch per unit effort (CPUE) time series or spawning stock biomass (SSB) data to evaluate fisheries reference points for exploited resources of the Japan Sea. Eleven fish and invertebrate stocks were assessed; outcomes obtained through this analysis were the carrying capacity, biomass trajectory, maximum sustainable yield, and related parameters of each stock. Results showed that the stock of Arctoscopus japonicus was slightly overfished; the stocks of Cleisthenes pinetorum, Hippoglossoides dubius, Paralichthys olivaceus, and Chionoecetes opilio were overfished; and the stocks of Eopsetta grigorjewi, Pagrus major, Gadus chalcogrammus, and Glossanodon semifasciatus were grossly overfished; Pseudopleuronectes herzensteini was proved to be severely depleted; only Pandalus eous was in good condition. These results are consistent with the few previous studies on the status of fish species around the Japan Sea, where overfishing is becoming increasingly apparent. These assessments provide a basis for guiding the use, management, and rebuilding of fishery resources in the Japan Sea.

Roots hold complex microbial communities at the soil–root interface, which can affect plant nutrition, growth, and health. Although the composition of plant microbiomes has been extensively described for various plant species and environments, little is known about the effect of wheat straw return (WSR) on the soybean root microbiota. We used Illumina-based 16S rRNA and ITS amplicon sequencing to track changes in bacterial and fungal microbiota in bulk soil and soybean rhizosphere, rhizoplane, s1and endosphere during the third and fourth years after implementing WSR in a wheat–soybean rotation system. The results revealed that WSR had a greater impact on fungal communities than bacterial communities, particularly in bulk soil, rhizosphere, and rhizoplane. WSR enriched the relative abundance of cellulose-degrading fungi (e.g., Acremonium, Trichoderma, and Myrmecridium, among which Trichoderma also had antimicrobial activity), saprotroph (e.g., Exophiala), and nitrogen cycling bacteria (e.g., Chryseolinea). Furthermore, WSR depleted the relative abundance of pathogenic fungi (e.g., Fusarium and Alternaria). These data revealed for the first time that WSR had diverse effects on soybean root-associated microbial community composition, not only in soil but also in the rhizosphere, rhizoplane, and endosphere.

This contribution presented stock assessments for 10 fish and 2 squid populations exploited by Chinese, South Korean, and Japanese fishing fleets in the Tsushima Warm Current region, i.e., Southwest Japan and East China. The methods used were a Monte Carlo method (CMSY) and a Bayesian state-space implementation of the Schaefer model (BSM), based on published time series of catch and abundance data (SSB and CPUE). Results showed that 2 fish stocks, Japanese jack mackerel (Trachurus japonicus) and yellowback sea-bream (Dentex hypselosomus), had a healthy status, while daggertooth pike conger (Muraenesox cinereus) appeared to have collapsed. The other 9 stocks showed varying degrees of overfishing. The cooperation of several countries would be required to recover the fishery resources in the Tsushima Warm Current region.

We assessed 12 marine fish species in the Northwestern Pacific exploited by Japanese fisheries, using published catch time series, CPUE data and the CMSY and BSM methods. The results showed that one stock was severely depleted, three stocks were outside of safe biological limits, three stocks were fully/overfished, three stocks were recovering, while the other two stocks were in good condition. These results match those of previous research on the status of fish species in the Northwestern Pacific, where overfishing is becoming increasingly apparent. We used the CMSY/BSM assessments as a basis for suggestions to assist in the management and rebuilding of fishery resources in this area.

Nitrogen is a major constituent of proteins, chlorophyll, nucleotides, and hormones and has profound effects on plant growth and productivity. RWP-RK family transcription factors (TFs) are key regulators that bind to cis-acting elements in the promoter regions of nitrogen use efficiency-related genes and genes responsible for gametogenesis and embryogenesis. The proteins share a conserved RWPxRK motif; have been found in all vascular plants, green algae, and slime molds; and are considered to be a plant-specific TF family. In this study, we show that RWP-RK proteins are also widely present in the Stramenopila kingdom, particularly among the oomycetes, with 12–15 members per species. These proteins form three distinct phylogenetic subgroups, two of which are relatively closely related to the nodule inception (NIN)-like protein (NLP) or the RWP-RK domain protein (RKD) subfamilies of plant RWP-RK proteins. The donor for horizontal gene transfer of RWP-RK domains to slime molds is likely to have been among the Stramenopila, predating the divide between brown algae and oomycetes. The RWP-RK domain has secondary structures that are conserved across plants and oomycetes, but several amino acids that may affect DNA-binding affinity differ. The transcriptional activities of orthologous RWP-RK genes were found to be conserved in oomycetes. Our results demonstrate that RWP-RK family TF genes are present in the oomycetes and form specific subgroups with functions that are likely conserved. Our results provide new insights for further understanding the evolution and function of this TF family in specific eukaryotic organisms.

Eight common and commercially important marine fishes from coastal and offshore areas of Shandong Province, China, were assessed using the “Length-based Bayesian Biomass” estimator (LBB) method. These species were Scomber japonicus (chub mackerel), Sebastiscus marmoratus (false kelpfish), Hexagrammos otakii (fat greenling), Thryssa kammalensis (kammal thryssa), Gadus macrocephalus (Pacific cod), Setipinna taty (scaly hairfin anchovy), Sillago sihama (silver sillago), and Lophius litulon (yellow goosefish). LBB is a new and powerful, yet simple, approach to evaluate a fisheries’ status using length and frequency data. Shandong Province’s coastal areas, adjacent to the Yellow and Bohai Seas, are an important fishing ground of China, where the 2018 catch of three of these species, yellow goosefish, chub mackerel, and Pacific cod, yielded up to 57,200, 21,100, and 1330 tons, respectively. The ratios of current relative to unexploited biomass (B/B0) is smaller than the relative biomass that can produce MSY (BMSY/B0) in eight stocks save for silver sillago, indicating overfishing. Also, the sizes at first capture were well below the optimal, suggesting that larger mesh sizes would be beneficial. Our study provides evidence that LBB is an efficient method to evaluate the fishery resources in the Yellow and Bohai Seas, especially when length frequencies are the only available data. Also, LBB provided evidence useful for the management of the costal fishery resources of Shandong Province.

Eukaryotic heterotrimeric guanine nucleotide-binding proteins consist of α, β, and γ subunits, which act as molecular switches to regulate a number of fundamental cellular processes. In the oomycete pathogen Phytophthora sojae, the sole G protein α subunit (Gα; encoded by PsGPA1) has been found to be involved in zoospore mobility and virulence, but how it functions remains unclear. In this study, we show that the Gα subunit PsGPA1 directly interacts with PsYPK1, a serine/threonine protein kinase that consists of an N-terminal region with unknown function and a C-terminal region with a conserved catalytic kinase domain. We generated knockout and knockout-complemented strains of PsYPK1 and found that deletion of PsYPK1 resulted in a pronounced reduction in the production of sporangia and oospores, in mycelial growth on nutrient poor medium, and in virulence. PsYPK1 exhibits a cytoplasmic-nuclear localization pattern that is essential for sporangium formation and virulence of P. sojae. Interestingly, PsGPA1 overexpression was found to prevent nuclear localization of PsYPK1 by exclusively binding to the N-terminal region of PsYPK1, therefore accounting for its negative role in sporangium formation. Our data demonstrate that PsGPA1 negatively regulates sporangium formation by repressing the nuclear localization of its downstream kinase PsYPK1.

[This corrects the article DOI: 10.1371/journal.ppat.1001302.].

Due to the monocultural basis of agricultural crops, mutated plant microbes with increased pathogenicity can easily spread in the field and lead to serious yield losses. As a major threat to a wide range of crop plants, oomycete pathogens continuously undergo adaptive evolution to overcome plant defense barriers. However, the genetic basis of their evolution at the molecular level remains largely unknown. Here, we investigated the nature variation and the population genomics of the soybean pathogen Phytophthora sojae by high-throughput genome re-sequencing. Genomic variation analysis revealed uneven “two-speed” evolutionary pattern with genes in gene-sparse regions (GSRs) showing higher rates of structural polymorphisms and positive selection. GSRs are enriched in effector genes and transposase-related genes. Our results also suggested that the NADH oxidase and MIP transporter gene families undergo rapid and diversifying selection. Furthermore, we demonstrated that P. sojae isolates possess varying numbers of RxLR effectors with diverse sequences, totaling 471 members. Among them, 42 core RxLR effectors are assumed to be important for infection. Finally, we observed that Avr genes exhibit abundant sequence variation in P. sojae isolates. Several novel variants lead to the evading of host resistance, including a complete deletion in Avr3c and amino acid mutations in Avr1a. Taken together, our results provide an adaptive landscape of P. sojae at single-nucleotide resolution, as well as resources for further resistance breeding and disease prevention against this important plant pathogen.

The role of most plant leucine-rich repeat (LRR) receptors in innate immunity is unknown. Here, the authors develop virus-based constructs to silence LRR receptor-like genes in the Nicotiana benthamiana genome and identify Response to XEG1 that specifically recognizes the glycoside hydrolase 12 protein XEG1.

The apoplastic space between the plant cell wall and the plasma membrane constitutes a major battleground for plant-pathogen interactions. To survive in harsh conditions in the plant apoplast, pathogens must cope with various immune responses. During infection, plant pathogens secrete an arsenal of effector proteins into the apoplast milieu, some of which are detected by the plant surveillance system and, thus, activate plant innate immunity. Effectors that evade plant perception act in modulating plant apoplast immunity to favor successful pathogen infection. The concerted actions of apoplastic effectors often determine the outcomes of plant-pathogen interactions. In this review, we summarize current advances on the understanding of apoplastic effectors and highlight the strategies employed by pathogens to counter host apoplastic defense.

Various effectors of plant pathogens modulate host cell biology. Here, Huang et al. show PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, can reprogram host pre-mRNA splicing for immune modulation.

The airborne area camera has received broad application in aerial reconnaissance, land resource surveying, environmental monitoring, photogrammetry mapping, and natural disaster information acquisition. A three-axis, inertially stabilized platform with a large rotation range for the roll axis is designed, which is based on the cantilever structure, in order to realize a large-angle sweep imaging function for airborne area cameras. An image attitude control algorithm in the inertial space is proposed, which can regulate the line of sight (LOS) as well as the image orientation. The area camera image motion calculation model and image motion compensation residual computing method are proposed, utilizing space position and velocity vector transformation mathematics and derivations. The variation of linear velocity of the image motion in the sensor frame is analyzed, and the changing laws of the maximum deviation of image motion with the image attitude are studied. Flight tests imply that the vertical imaging technique correctly regulates the LOS along the local geodetic vertical. The along-flight overlap rate is greater than 65%, which meets the stereo mapping requirement. The sweep imaging technique considerably enlarges the cross-flight angle of view. The LOS and image orientation during sweep imaging are correctly controlled, and gap-free coverage of the survey area is maintained. The image’s azimuth or roll deviation is less than 0.1°, and the image pitch deviation is less than 0.35°. The quality of the test images is superior. Black and white line pairs for evaluation can be clearly distinguished. The image’s motion is well compensated, and the image motion compensation residual is well constrained. These verify the validity of the proposed imaging technique and the image motion analysis model.

Returning straw to soil is an effective way to sustain or improve soil quality and crop yields. However, a robust understanding of the impact of straw return on the composition of the soil microbial communities under field conditions has remained elusive. In this study, we characterized the effects of wheat straw return on soil bacterial and fungal communities in a wheat–soybean rotation system over a 3-year period, using Illumina-based 16S rRNA, and internal transcribed region (ITS) amplicon sequencing. Wheat straw return significantly affected the α-diversity of the soil bacterial, but not fungal, community. It enhanced the relative abundance of the bacterial phylum Proteobacteria and the fungal phylum Zygomycota, but reduced that of the bacterial phylum Acidobacteria, and the fungal phylum Ascomycota. Notably, it enriched the relative abundance of nitrogen-cycling bacterial genera such as Bradyrhizobium and Rhizobium. Preliminary analysis of soil chemical properties indicated that straw return soils had significantly higher total nitrogen (TN) contents than no straw return soils. In addition, the relative abundance of fungal genera containing pathogens was significantly lower in straw return soils relative to control soils, such as Fusarium, Alternaria, and Myrothecium. These results suggested a selection effect from the 3-year continuous straw return treatment and the soil bacterial and fungal communities were moderately changed.

Perception of pathogen-associated molecular patterns (PAMPs) often triggers various innate immune responses in plants. The transcriptional changes of defense-related genes are often used as a marker to assay PAMP-triggered plant immune response. Here we described a protocol to monitor the relative expression level of marker genes in Nicotiana benthamiana upon treatment with PAMPs. The procedure includes leaf treatment using PAMPs, total RNA isolation, cDNA synthesis, quantitative real-time PCR and data analysis. This protocol is applicable to monitor marker gene expression triggered by different PAMPs in N. benthamiana.

Phytophthora sojae, the causal agent of soybean root and stem rot, is responsible for enormous economic losses in soybean production. P. sojae secrets various effectors to reprogram host immunity. The plant apoplastic space is a major battleground in plant-pathogen interactions. Here we describe a protocol for purification and isolation of secreted proteins from P. sojae, including precipitation of secreted proteins from P. sojae culture filtrate, chromatographic purification of the secreted proteins and analysis of the proteins by Mass spectrometry. With this protocol, it will be easier to identify potential apoplastic effectors in Phytophthora and will benefit our understanding of plant-microbe interactions.

Oomycete pathogens secrete host cell-entering effector proteins to manipulate host immunity during infection. We previously showed that PsAvh52, an early-induced RxLR effector secreted from the soybean root rot pathogen, Phytophthora sojae, could suppress plant immunity. Here, we found that PsAvh52 is required for full virulence on soybean and binds to a novel soybean transacetylase, GmTAP1, in vivo and in vitro. PsAvh52 could cause GmTAP1 to relocate into the nucleus where GmTAP1 could acetylate histones H2A and H3 during early infection, thereby promoting susceptibility to P. sojae. In the absence of PsAvh52, GmTAP1 remained confined to the cytoplasm and did not modify plant susceptibility. These results demonstrate that GmTAP1 is a susceptibility factor that is hijacked by PsAvh52 in order to promote epigenetic modifications that enhance the susceptibility of soybean to P. sojae infection.

In order to improve the performance in the practical engineering applications including so called low-speed video tracking and large-angle swing scanning imaging at the same time for a three-axis universal inertially stabilized platform (UISP), we propose an adaptive nonsingular fast terminal sliding mode control (ANFTSMC) strategy subjected to the uncertain disturbances and input saturation constraints. First of all, a second-order dynamic model is established with uncertain disturbances and input saturation constraints. Secondly, a nonsingular fast terminal sliding mode controller (NTSMC) is constructed to ensure the system error converges to zero fast in a finite time; meanwhile, a novel reaching law based on a modified normal distribution function is designed to adjust the control gain. Thirdly, an adaptive control law is designed to online estimate the parameters of the lumped uncertain disturbances. Additionally, the stability of the control system is proved by Lyapunov theory. Finally, extensive comparative simulations and experiments are carried out, the results comprehensively show the effectiveness and superiority of the proposed control method, which can accelerate convergence, weaken the chattering, and has the better control accuracy and robust performance both in the low-speed tracking and large-angle swing scanning applications. Moreover, the exact dynamic model and the prior knowledge of the upper bounds of the disturbances are not required during the procedure of the controller design, which make it have more extensive application value in practical engineering.

On the basis of its downy mildew–like morphology, the litchi downy blight pathogen was previously named Peronophythora litchii. Recently, however, it was proposed to transfer this pathogen to Phytophthora clade 4. To better characterize this unusual oomycete species and important fruit pathogen, we obtained the genome sequence of Phytophthora litchii and compared it to those from other oomycete species. P. litchii has a small genome with tightly spaced genes. On the basis of a multilocus phylogenetic analysis, the placement of P. litchii in the genus Phytophthora is strongly supported. Effector proteins predicted included 245 RxLR, 30 necrosis-and-ethylene-inducing protein-like, and 14 crinkler proteins. The typical motifs, phylogenies, and activities of these effectors were typical for a Phytophthora species. However, like the genome features of the analyzed downy mildews, P. litchii exhibited a streamlined genome with a relatively small number of genes in both core and species-specific protein families. The low GC content and slight codon preferences of P. litchii sequences were similar to those of the analyzed downy mildews and a subset of Phytophthora species. Taken together, these observations suggest that P. litchii is a Phytophthora pathogen that is in the process of acquiring downy mildew–like genomic and morphological features. Thus P. litchii may provide a novel model for investigating morphological development and genomic adaptation in oomycete pathogens.