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BACKGROUND: Phytophthora spp. represent a pivotal genus of plant pathogens with a global distribution, exerting significant deleterious effects on food safety and forestry ecosystems. Numerous pathogenic and invasive Phytophthora species, introduced through imported fruits, have been frequently detected at Chinese ports. With the rise in global trade activities, the plant quarantine of imported fruits is becoming increasingly important but challenging. Fast, simple, and labor‐saving techniques are necessary and anticipated. RESUITS: A polymerase chain reaction restriction fragment length polymorphism capillary electrophoresis (PCR‐RFLP‐CE) technology‐based quarantine approach was developed for 16 Phytophthora species associated with the imported fruits in China. The Ypt1 gene, exhibiting abundant interspecific variations, was selected as the marker gene for PCR. The restriction endonuclease AluI was proven to be capable and compatible in simultaneously separating different Phytophthora species during CE. By combining with a fast and efficient DNA extraction kit, the developed PCR‐RFLP‐CE technique was successfully applied to identify Phytophthora species in artificially infested fruits. CONCLUSION: We provide a quick, practical, and high‐throughput detection approach for hazardous and invasive Phytophthora species associated with imported fruits in China. This strategy can give good convenience and technological support for carrying out massive quarantine activities at Chinese ports. © 2024 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The poor fidelity of T4 DNA ligase has always limited the simple detection of single-nucleotide polymorphisms (SNPs) and is only applicable to some special SNP types. This study developed a highly sensitive and specific detection method for SNPs based on high-fidelity single-stranded circularisation. It used T4 DNA ligase and rolling circle amplification (RCA) plus loop-mediated isothermal amplification (LAMP). Surprisingly, the cyclisation stage's efficiency greatly improved. The ligation fidelity was almost perfect via the unique pairing pattern between a long-paired base at the 5′ terminus and only five bases at the 3′ terminus on linear single-stranded DNA (l-DNA). Subsequently, LR-LAMP was performed and combined with the circularisation step for the simple detection of SNPs. The results showed that even 100 aM targets could be detected correctly and that a mutation rate of 0.1% or even 0.01% could be analysed via naked-eye visualisation or fluorescence detection, respectively. In addition, genomic DNA samples were used to evaluate the method, which indicated that it could effectively distinguish the SNPs of RPA190-T1145A in Phytophthora infestans. This strategy may play an important role in both circularisation of single-stranded DNA and detecting arbitrary SNPs. [ABSTRACT FROM AUTHOR]

Members of the Fusarium graminearum species complex are known to cause head blight of wheat. A natural nonpathogenic mutant, strain Fa0233007, was found in the strain collection of the Japanese F. graminearum species complex. In addition, this strain cannot form perithecia. Complete linkage of these deficiencies in the progenies obtained from crossing a wild‐type strain and the mutant strain suggested that a single genomic locus was responsible for deficiencies in both traits. The locus was mapped to chromosome 1 using sequence‐tagged markers. An NADPH oxidase gene (NoxA, FGSG00739) was identified in the mapped region, and a 2‐bp deletion that results in premature termination of the open reading frame was detected in the gene. Both pathogenicity and perithecium formation were recovered by FGSG00739 complementation in the mutant strain. [ABSTRACT FROM AUTHOR]

Correction for 'High-efficiency and high-fidelity ssDNA circularisation via the pairing of five 3′-terminal bases to assist LR-LAMP for the genotyping of single-nucleotide polymorphisms' by Taiwen Li et al., Analyst, 2022, https://doi.org/10.1039/d2an01042a. [ABSTRACT FROM AUTHOR]

Members of the Phytophthora genus are responsible for many important diseases in agricultural and natural ecosystems. Phytophthora ramorum causes devastating diseases of oak, and tanoak stands in US forests and larch in the UK. The four evolutionary lineages involved express different virulence phenotypes on plant hosts, and characterization of gene content is foundational to understanding the basis for these differences. Recent discovery of P. ramorum at its candidate center of origin in Asia provides a new opportunity for investigating the evolutionary history of the species. We assembled, high-quality genome sequences of six P. ramorum isolates representing three lineages from Asia and three causing epidemics in western US forests. The six genomes were assembled into 13 putative chromosomes. Analysis of structural variation revealed multiple chromosome fusion and fission events. Analysis of putative virulence genes revealed variations in effector gene composition among the sequenced lineages. We further characterized their evolutionary history and inferred a contraction of crinkler-encoding genes in the subclade of Phytophthora containing P. ramorum . There were losses of multiple families and a near complete loss of paralogs in the largest core crinkler family in the ancestor of P. ramorum and sister species P. lateralis . Secreted glycoside hydrolase enzymes showed a similar degree of variation in abundance among genomes of P. ramorum lineages as that observed among several Phytophthora species. We found plasticity among genomes from multiple lineages in a Phytophthora species and provide insights into the evolutionary history of a class of anciently conserved effector genes.

Pythium amaminum sp. nov. was isolated from river and reservoir water on Amami island, Kagoshima Prefecture, Japan. The species can grow at temperatures between 10 °C and 35 °C. At the optimum temperature of 25 °C, the radial growth rate is 22.5 mm per day. Pythium amaminum produces filamentous sporangia consisting of branched, lobulate or digitate elements forming large complexes. Zoospores form inside the vesicle, which is discharged through a long tube at least 320 μm. Globose oogonia are ornamented with conical blunt spines. Oospores are aplerotic and globose. Antheridia twine around the oogonia or stick to them. These features having a both of the long discharge tube from sporangium and oogonia with spines are not observed in any other species of the genus Pythium , and thus we conclude that P. amaminum is a new Pythium species., (2024, by The Mycological Society of Japan.)

Aconitum carmichaelii Debeaux is a traditional Chinese medicinal herb that has been utilized for approximately 2,000 years. However, as cultivation has increased, there have been more reports of A. carmichaelii infections caused by four major pathogenic fungal species, Fusarium oxysporum , F. solani , Mucor circinelloides , and Sclerotium rolfsii , resulting in increased disease incidences and limited production and quality. To detect these infections, we developed a LAMP-based toolbox in this study. The cytochrome c oxidase subunit 1 ( cox1 ) gene, translation elongation factor-1α ( EF-1α ), internal transcribed spacer (ITS) regions of rDNA, and alcohol dehydrogenase 1 ( ADH1 ) gene, respectively, were used to design species-specific LAMP primer sets for F. oxysporum , F. solani , S. rolfsii , and M. circinelloides . The results showed that the LAMP-based toolbox was effective at detecting pathogens in soil and plant materials. We also used this toolbox to investigate pathogen infection in the main planting regions of A. carmichaelii . Before harvesting, F. oxysporum , M. circinelloides , and S. rolfsii were commonly found in the planting fields and in infected A. carmichaelii plants. Therefore, the toolbox we developed will be useful for tracking these infections, as well as for disease control in A. carmichaelii .

China has the largest area of kiwifruit production in the world. Pathogens associated with root diseases of kiwi trees have not been investigated extensively. In this research, three Phytophthora species, Phytophthora cactorum , Phytophthora cinnamomi , and Phytophthora lateralis , which are pathogenic to kiwi trees in the main planting areas of China, were studied. The population densities of these species in 128 soil samples from 32 kiwi orchards in 2017 and 2018 were measured using multiplex real-time quantitative PCR based on the ras-related protein gene Ypt1 . P. cactorum was the most widely distributed of the three species in orchards of the Zhouzhi and Meixian prefectures. We used redundancy analysis to examine soil factors in the kiwi orchards to understand their effects on the population densities of the Phytophthora species. The redundancy analysis indicated that soil temperature and pH were significantly correlated with the abundance of P. cactorum and P. cinnamomi . In addition, two loop-mediated isothermal amplification detection systems for P. cactorum were developed based on the tigA gene. The color-change detection system proved to be accurate, sensitive, and faster than quantitative PCR. The results of this study, along with the loop-mediated isothermal amplification detection systems, will be of great use in the control of Phytophthora diseases for the production of kiwifruits in China.