Introduction: Valsa canker, caused by Cytospora mali, is a destructive disease in apple production. However, the mechanism by which apple defend against C. mali infection remains unclear.Methods: In this study, the integrative transcriptional and metabolic analysis were used to investigate the responses of the ‘Jin Hong’ apple branches to the invasion of C. mali.Results and Discussion: Results showed that the differentially expressed genes were mainly enriched in the pathways of carbon metabolism, photosynthesis-antenna proteins, and biosynthesis of amino acids pathways. Additionally, the differentially accumulated metabolites were significantly enriched in aminoacyl-tRNA biosynthesis, fructose and mannose metabolism, and alanine, aspartate, and glutamate metabolism pathways. Conjoint analysis revealed that C. mali infection significantly altered 5 metabolic pathways, 8 highly relevant metabolites and 15 genes of apples. Among which the transcription factors WRKY and basic domain leucine zipper transcription family were induced, the α-linolenic acid and betaine were significantly accumulated in C. mali infected apple stems. This work presents an overview of the changes in gene expression and metabolic profiles in apple under the inoculation of C. mali, which may help to further screen out the mechanism of plant-pathogen interaction at the molecular level.

Blue mold caused by Penicillium expansum is one of the most common apple diseases, and it is becoming a serious threat in apple production. The strain Bacillus amyloliquefaciens Ba168 showed high levels of antimicrobial activity in our previous study. To analyze the antimicrobial protein of Ba168, a high-resolution LC-MS/MS proteomic analysis was performed. A total of 1155 proteins were identified from 5233 unique peptides. A total of 16 potential antimicrobial-activity-related proteins were identified; 10 of these proteins have direct antimicrobial effects, while 6 of these proteins are associated with the formation of antimicrobial substances. Then, an antifungal protein of Ba168 was isolated and purified by the sequential chromatography of DEAE Bio-sep FF anion exchange and Sephadex G-75. The single protein, named BP8-2, showed antifungal activity towards Penicillium expansum. The peptide mass fingerprinting of the protein band of BP8-2 had a high similarity with the amino acid sequences of flagellin protein. The results showed that BP8-2 significantly inhibited the growth of P. expansum and slowed the spread of apple blue mold. The results indicated that flagellin is one of the important antimicrobial substances from Ba168.

White clover (Trifolium repens L.) is an important perennial legume forage and ornamental plant, and is widely distributed and cultivated in the world. Recently, white clover plants showing symptoms of leaf mosaic and redding were observed in Hohhot, Inner Mongolia of China. In this work, flexuous filamentous viral particles of about 700 × 13 nm in size were observed in the symptomatic leaf samples. The infection of clover yellow vein virus (ClYVV) was confirmed by small RNA sequencing and RT-PCR validation. Mechanical inoculation assays showed that this ClYVV isolate (ClYVV-IM) can infect a range of herbaceous species, including Nicotiana benthamiana, N. occidentalis, Chenopodium quinoa, C. amaranticolor, Vicia faba, Vigna unguiculata, and Solanum lycopersicum, causing various symptoms. The complete genome sequence of ClYVV-IM consists of 9565 nt and shared sequence identities, ranging from 83.05% to 96.30%, with those of the other ClYVV isolates published in GenBank. Phylogenetic analyses based on the polyprotein nucleotide and amino acid sequences clustered 15 ClYVV isolates into two groups and ClYVV-IM located in Group I. Two potential recombination events located at 914–2970 nt and 5153–5694 nt were detected in the genome of ClYVV-IM. To our knowledge, this is the first report of occurrence and complete genome of ClYVV infecting white clover in China.

Apple geminivirus 1 (AGV) in the genus Maldovirus of the family Geminiviridae was first identified infecting apple trees in the year 2015 in China. In this work, we characterized three isolates of the AGV in the Chinese pearleaf crabapple (Malus asiatica) in Inner Mongolia Autonomous Region. The viruses were detected by Illumina sequencing and its existence was confirmed by reverse transcription-polymerase chain reaction (RT-PCR) amplification of an AGV fragment. Between the three AGV isolates and the initially characterized AGV isolate PL2015, the nucleotide sequence identities of the complete genome ranged from 91.2 to 91.7%, of the coat protein gene (V1) ranged from 95.4% to 97.3%, and of the replicase gene (C1) ranged from 87.3% to 88.0%. Phylogenetic analysis indicated that the three isolates formed a monophyletic group together with the AGV, separated from the current genera in the family Geminiviridae. This is the first description of the AGV infecting crabapples.

In July 2022, root rot was observed in several goji (Lycium barbarum) orchards located in Qinghai Province, China. Approximately 40% of the goji plants were affected in the orchards. Morphology of fungi isolated from affected plant, phylogenetic analyses, using internal transcribed spacer (ITS), translation elongation factor 1-alpha (TEF), and trichothecene (Tri5) sequences, as well as pathogenicity assays, were conducted to characterize and identify the causing agent of goji root rot. Isolate GQGF1-3 caused typical symptoms of L. barbarum root rot. Fungal colony characteristics and conidium morphology, combined with ITS, TEF, and Tri5 sequences showed that isolate GQGF1-3 was Fusarium sambucinum. This is the first report of F. sambucinum causing root rot of goji.