Yuqiang Zhao

• Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen)

Erwinia amylovora , the causal agent of fire blight disease, is a destructive agricultural plant pathogen in the Rosaceae family. The disease was first described in North America and has now spread to more than 50 countries. The disease has recently been reported in China’s neighboring countries, including Russia, South Korea, Kyrgyzstan, and Kazak...

The σ ⁵⁴ factor (RpoN), a significant transcriptional regulatory factor, plays crucial roles in regulating virulence, motility, biofilm formation, and the utilization of carbon and nitrogen sources in pathogenic bacteria. However, the function of RpoN has not been identified in Paracidovorax citrulli (formerly Acidovorax citrulli ). To investigate...

Background and aims Ectomycorrhizal (ECM) symbiosis can alter root tip structures; but the detailed mechanisms behind these changes and their impact on overall root architecture remain unclear. This study aimed to investigate the effects of ECM inoculation with Cenococcum geophilum (Cg) and Pisolithus orientalis (Po) on root growth, nutrient levels...

Carya illinoinensis is an economically important nut tree, and its chloroplast (cp.) genome has been reported; however, its mitochondrial (mt) genome remains unknown. In the present study, we assembled the first mt genome of C. illinoinensis. The circular mt genome of C. illinoinensis is 495,205 bp long, with 37 protein-coding genes(PCGs), 24 tRNA...

This study delved into the larval development and the morphological and anatomical transformations that occur in the galls of chestnut trees (Castanea mollissima BL.) and are induced by the chestnut gall wasp Dryocosmus kuriphilus Yasumatsu (GWDK) across various stages: initial, growth, differentiation, maturity, and lignification. Chestnut galls i...

Xylanases derived from fungi, including phytopathogenic and nonpathogenic fungi, are commonly known to trigger plant immune responses. However, there is limited research on the ability of bacterial‐derived xylanases to trigger plant immunity. Here, a novel xylanase named CcXyn was identified from the myxobacterium Cystobacter sp. 0969, which displa...

Carya illinoinensis, is a highly valuable nut plant that is cultivated worldwide. As a precious pecan pollination resource, C. illinoinensis cv. Xinxuan-4 is protandrous, with a very early bud break in China. In this study, the chloroplast (cp) genome of 'Xinxuan-4' was sequenced and compared with closely related cultivars. The cp genome was found...

Pecan (Carya illinoinensis) is an important economic forest crops widely cultivated in China. From June to September in both 2021 and 2022, severe leaf disease resembling anthracnose was observed in 6.6-ha pecan orchard in Jintan (31°42′23.84″ N, 119°21′22.90″ E), Jiangsu Province. The disease severity was about 15 to 25% with 5 to 12% incidence on...

Public metabolites such as vitamins play critical roles in maintaining the ecological functions of microbial community. However, the biochemical and physiological bases for fine-tuning of public metabolites in the microbiome remain poorly understood. Here, we examine the interactions between myxobacteria and Phytophthora sojae , an oomycete pathoge...

Pecan (Carya illinoinensis) is one of the important economic forest crops widely cultivated in Jiangsu Provinces, China. From August to September in both 2021 and 2022, a foliar blight was observed in 7-ha and 6-ha pecan orchards in Changzhou (31°58'9.6″ N, 119°48'33.84″ E), and Jurong (31°52'15.46″ N, 119°9'24.62″ E), Jiangsu Province. The disease...

Chaste-tree (Vitex agnus-castus Linn.) is a perennial ornamental shrub that is native to Europe, which has been widely distributed in China. Since 2021, a serious leaf spot on chaste-tree leaves was observed in Nanjing Botanical Garden, Jiangsu Province, China (31°14'6″N, 118°22'12″E). The disease incidence on the leaves ranged from 20 to 40%. The...

Fungal cell wall decomposition enzymes exhibit great potential for the development of efficient antifungal agents. However, their practical application is restricted due to incomplete understanding of the action mode. In our previous study, we identified that a novel outer membrane (OM) β-1,6-glucanase GluM is deployed by predatory myxobacteria to...

As social micropredators, myxobacteria are studied for their abilities to prey on bacteria and fungi. However, their predation of oomycetes has received little attention. Here, we show that Archangium sp. AC19 secretes a carbohydrate-active enzyme (CAZyme) cocktail during predation on oomycetes Phytophthora. These enzymes include three specialized...

To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the tes...

The β-1,6-glucan is the key linker between mannoproteins in the outermost part of the cell wall and β-1,3-glucan/chitin polysaccharide to maintain the rigid structure of the cell wall. The β-1,6-glucanase GluM, which was purified from the fermentation supernatant of Corallococcus sp. EGB, was able to inhibit the germination of Fusarium oxysporum f....

Pecan (Carya illinoinensis) is one of the important economic forest crops which has been widely cultivated in Anhui and Jiangsu Provinces, China. Since 2019, symptoms resembling anthracnose disease had been observed in 5-ha and 6.6-ha pecan orchards in Quanjiao ( 32°5′7.08″ N, 118°16′2.91″ E), Anhui Province, and Jintan (31°42′23.84″ N, 119°21′22.9...

The chestnut is widely cultivated fruit tree enriched with nutrients and has pleasant tasting fruit. The starch properties of kernels greatly influence the nutritional quality of chestnuts. Although various studies have examined the production and accumulation of starch in chestnuts, the transcription alteration linked with starch properties in the...

Chitosanases hydrolyze chitosan into chitooligosaccharides (COSs) with various biological activities, which are widely employed in many areas including plant disease management. In this study, the novel chitosanase AqCsn1 belonging to the glycoside hydrolase family 46 (GH46) was cloned from Aquabacterium sp. A7-Y and heterologously expressed in Esc...

Pecan (Carya illinoinensis) is a world-famous nut tree that is widely cultivated in China, especially in Jiangsu Province (Zhang et al. 2015). In April 2022, cankers on trunks were recorded in pecan (cv. Pawnee) fields located in Taizhou (32°27'58″ N, 120°0'49″ E), Jiangsu. Cankers on the trunks resulted in wilt of the plants. Usually, the color of...

Pecan (Carya illinoinensis) is a world-famous nut tree which widely cultivated in China. Quanjiao County, located in Anhui province, is reputed to be the capital of pecan production in China. Since 2019, typical scab symptoms were observed on most pecan cultivars in orchards located in the regions of Quanjiao (32°5'7.08″ N, 118°16'2.91″ E). In Apri...

In many bacteria, OxyR acts as a transcriptional regulator that facilitates infection via degrading hydrogen peroxide (H2O2) generated by the host defense response. Previous studies showed that OxyR also plays an important role in regulating biofilm formation, cell motility, pili relate-genes expression, and surface polysaccharide production. Howev...

Bacterial fruit blotch, caused by seed-borne pathogen Acidovorax citrulli , poses a serious threat to the production of cucurbits globally. Although the disease can cause substantial economic losses, limited information is available about the molecular mechanisms of virulence. This study identified that, a random transposon insertion mutant impaire...

Maltogenic amylase CoMA from Corallococcus sp. strain EGB catalyzes the hydrolysis and transglycosylation of maltooligosaccharides and soluble starch into maltose, the sole hydrolysate. This process yields pure maltose with potentially wide applications. Here, we identified and evaluated the role of Phenylalanine 314 (F314), a key amino acid locate...

In our previous study, the chitosanase AqCoA and the chitooligosaccharides it produced were found to exhibit significant protective effects against fungal diseases. In this study, we enhanced the expression of AqCoA using the novel pMC-GAP that enables stable transformation of Escherichia coli, and built an integrated model based on the gene copy n...

Corallococcus sp. strain EGB is a Gram-negative myxobacteria isolated from saline soil, and has considerable potential for the biocontrol of phytopathogenic fungi. However, the detailed mechanisms related to development and predatory behavior are unclear. To obtain a comprehensive overview of genetic features, the genome of strain EGB was sequenced...

Some microbial-associated molecular patterns (MAMPs), like glucan oligosaccharides, can be recognized by pattern recognition receptors (PRRs) of plant to elicit further immunity response. In this study, a novel glycoside hydrolase family 55 β-1,3-glucanase (AcGluA) from Archangium sp. strain AC19 was cloned and expressed in Escherichia coli. Among...

The process of raw starch conversion has attracted extensive attention in recent years due to its high energy conversion efficiency and saving of operational costs. In this study, extensive hydrolysis of raw starch by α-amylase AmyM from Corallococcus sp. EGB was investigated with robust substrate and products tolerance. AmyM showed broad substrate...

In our previous study, the chitosanase Aq CoA and its products chitooligosaccharides exhibited significant application in fungal disease protection. In this study, to enhance the expression of Aq CoA, we obtained various strains with multi-copy by a novel plasmid pMC-GAP with stable transformation ability in Pichia pastoris and built an integrated...

Nutraceuticals containing modified starch with increased content of slowly-digestible starch (SDS) may reduce the prevalence of obesity, diabetes and cardiovascular diseases due to its slow digestion rate. Enzymatic methods for the preparation of modified starch have attracted increasing attention because of their low environmental impact, safety a...

The Castanea mollissima ‘Chuizhili’ is an important variety of C. mollissima in breeding for dwarf chestnut and ornamental trees due to the weeping characteristic in China. In this study, the complete chloroplast genome of C. mollissima ‘Chuizhili’ was identified and sequenced by using Illumina sequencing data. The genome size is 160,799 bp, with a...

Castanea sativa Mill. is mainly grown in the temperate regions of continental Europe, and it has a considerable economic value. In this study, the complete chloroplast genome sequence of Castanea sativa was characterized. Leaves were collected from the National Botanical Garden of Latvia. The chloroplast genome was determined to be 160,938 bp in le...

Background Biological nitrogen fixation (BNF) and nitrogenous fertilizers are two crucial ways for nitrogen input in the rice paddy system. Little is known about the effect of nitrogenous fertilizers on root-associated diazotrophs. Here, we investigated the succession of total and active diazotrophs in rhizosphere soil and rice roots under four fer...

Myxobacteria have excellent biocontrol activity against various phytopathogens due to their rich spectrum of secondary metabolites and active predatory characteristics. In this study, the mycelial growth of Fusarium oxysporum f. sp. cucumerinum (FOC) was found to be significantly inhibited by volatile compounds (VOCs) produced by Corallococcus sp....

Structural modification of starch using efficient α-amylases to improve its properties is an established method in the starch industry. In our previous research, the novel maltogenic α-amylase CoMA that catalyzes multi-molecular reactions has been identified. In this study, the impact of CoMA on the structure and retrogradation properties of potato...

Pecan [Carya illinoinensis (Wangenh.) K. Koch] is a famous high grade dry fruit, oil tree species and excellent tree species for both timber and fruit. Pecan is a monoecious plant, and the formation and number of female flowers directly determine the pecan yield. In this work, to illuminate the molecular mechanism of floral formation in pecan, scan...

Abstract Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to commercial watermelon and melon crop production worldwide. Ferric Uptake Regulator (Fur) is a global transcription factor that affects a number of virulence-related functions in phytopathogenic bacteria; however, the role of furA has not been deter...

Acidovorax citrulli is the causal agent of bacterial fruit blotch (BFB), a serious threat to cucurbit fruit and seed production worldwide. In recent years, the BFB has spread to many areas of China, mainly via the inadvertent distribution of contaminated commercial seeds. To assess the prevalence of seedborne A. citrulli in commercial watermelon an...

Myxobacterial predation on bacteria has been investigated for several decades. However, their predation on fungi has received less attention. Here, we show that a novel outer membrane β-1,6-glucanase GluM from Corallococcus sp. strain EGB is essential for initial sensing and efficient decomposition of fungi during predation. GluM belongs to an unst...

Starch modification by amylolytic enzymes has been proved feasible in restraining aging behavior during the starchy food storage. The objective of this study was to determine the contribution of a maltohexaose (G6) producing α-amylase AmyM to the anti-staling properties of bread. Hydrolyzed wheat starch with different degree of hydrolysis (DH) was...

Chinese Chestnut (Castanea mollissima) is an economically valuable tree in China. More than 300 wild and cultivated varieties were reported. In this study, we reported and characterized the complete chloroplast genome sequence of Chinese Chestnut cultivar ‘Hongli’, variant dominant strain with high yield, good quality of nuts, especially with red c...

Chinese chestnut (Castanea mollissima Blume) can be infested by Dryocosmus kuriphilus Yasumatsu, resulting in gall formation and yield losses. Research on the control of gall wasps using genomics approaches is rarely reported. We used RNA-seq to investigate the dynamic changes in the genes of a chestnut species (C. mollissima B.) during four gall-f...

A rapid, sensitive and visual loop‐mediated isothermal amplification (LAMP) method for detecting Acidovorax citrulli in cucurbit seed was developed in this study. The LAMP primers were designed to recognize the non‐ribosomal peptide synthetase (NRPS) gene (locus tag: Aave_4658) from A. citrulli. The LAMP assay was conducted at 64°C in 1 hr with cal...

Tongcheng (TC) and Yorkshire (YK) are two pig breeds with distinctive muscle morphology. Porcine microRNAome (miRNAome) of the longissimus muscle during five developmental stages (40, 55, 63, 70, and 90 days post coitum (dpc)) was explored by Solexa sequencing in the present study to find miRNAs involved in the different regulation of skeletal musc...

The number of differentially expressed miRNAs among different developmental stages. Number of differentially expressed miRNAs. TC: Tongcheng, YK: Yorkshire,DE: differentially expressed. (A) All stage-DE miRNA in TC and YK. The numbers marked in the overlapping areas show the stage-DE miRNAs in common. (B)The numbers of stage-DE miRNA in every compa...

Interaction network of breed-DE miRNAs and breed-DE mRNAs. The network was constructed using 464 pairs of breed-DE miRNAs with breed-DE mRNAs. The green diamonds represent miRNA and the red circles represent mRNA. The nodes with bigger size had higher degree. TC: Tongcheng, YK: Yorkshire. Stages: 40, 55, 63, 70, and 90 days post coitum (dpc). (PDF)

Target genes of miRNAs. (XLSX)

The topological property of the networks with the breed-DE miRNAs and breed-DE mRNAs between TC and YK. (XLSX)

Diagram depicting how to obtain the breed-DE miRNA & breed-DE mRNA pairs. (A) Breed-specific DE miRNAs found at any of the five developmental stages were respectively paired with their software-predicted gene/mRNA targets, based on the negative correlation (Spearman’s correlation coefficient<0.5) between the expression trends of the miRNA and the g...

Sequence length distribution of small RNA. TC: Tongcheng, YK: Yorkshire. Stages: 40, 55, 63, 70, and 90 days post coitum (dpc) (TIF)

Overview of sequencing data. (XLSX)

Primers for plasmid construction and point mutation. (XLSX)

Functional annotation of the miRNAs belonging to cluster 0 in STEM. Ranked in an order of descending TPM value (average). (XLSX)

Differentially expressed (DE) miRNAs among different developmental stages. (XLSX)

Breed-DE miRNAs between TC and YK. (XLSX)

Chromosomal location of small RNA. Chromosomal locations of small RNAs are displayed across 20 chromosomes and mitochondrial DNA (MT). TC: Tongcheng, YK: Yorkshire. (PDF)

Expression profiles of miRNAs divided into three categories. (XLSX)

Highly expressed miRNAs for cluster analysis. (XLSX)

Functional annotation of stage-DE miRNAs. (XLSX)

Data for building interaction network of breed-DE miRNAs and breed-DE mRNAs between TC and YK. (XLSX)

Bacterial soft rot caused by Pectobacterium carotovorum subsp. carotovorum is a devastating plant disease in calla lily (Zantedeschia spp.). Considering the economic value of calla lily in the cut flower industry, effective means for controlling this disease are urgently needed. A screening of 12 isolates yielded strain BS as the best antagonist ag...

Peach (Prunus persica (L.) Batsch) is produced locally in Yangshan, Wuxi City, China. In recent years, a widespread shoot blight has been observed in many peach orchards of Yangshan that kills the twigs and results in high losses in fruit production. Disease incidences ranged from 10 to 20% in the affected orchards and, in extreme cases, 40% of the...

Dickeya fangzhongdai DSM 101947 T was isolated from pear trees ( Pyrus pyrifolia ) in Zhejiang Province, China, and is the causal agent of bleeding canker, a devastating disease of pear trees. Here, we provide the complete genome sequence of this bacterium, which has a 5,027,163-bp-long genome, including 4,375 protein-coding genes and 100 RNA genes...

Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, an...

Tongcheng pigs (TC) and Yorkshire (YK) are two pig breeds with distinguished morphologies in muscle. A comprehensive study of porcine microRNAome (miRNAome) in longissimus muscle during 5 developmental stages (40, 55, 63, 70 and 90 dpc (days post coitum)) using Solexa sequencing technology, was carried out in order to compare miRNA expression invol...

Bacterial leaf blight (BLB) has caused severe yield losses in cantaloupe (Cucumis melo L.) in the major melon-growing regions of China since the beginning of the twentieth century. Historically, Pseudomonas syringae pv. lachrymans was considered to be the causal agent of BLB of cantaloupe and angular leaf spot of cucumber. In the process of charact...

Tea (Camellia sinensis L.) is an economically important crop widely cultivated for leaves in China. Leaf and young shoot blights were observed on some commercial gardens of tea (cv. Yinghong IX) in April from 2013 to 2015, Guangzhou, China. The disease occurred initially on the young leaves, producing water-soaked spots. When the disease further de...

The type VI secretion system (T6SS) plays a major role in mediating interbacterial competition and might contribute to virulence in plant pathogenic bacteria. However, the role of T6SS in Erwinia amylovora remains unknown. In this study, 33 deletion mutants within three T6SS clusters were generated in E. amylovora strain NCPPB1665. Our results show...

A method was developed using a Loop-mediated isothermal amplification assay (LAMP) for detecting Didymella bryoniae in cucurbit seeds. The LAMP primers were designed based on the DNA-dependent RNA polymerase II RPB140 gene (RPB2) from D. bryoniae. Calcein was used as an indicator for the endpoint visual detection of DNA amplification. The LAMP assa...

Gram-negative, pectinolytic bacteria were repeatedly isolated from pear trees displaying symptoms of bleeding canker in China. Three strains, JS5T, LN1 and QZH3, had identical 16S rRNA sequences which shared 99% sequence similarity to Dickeya dadantii. Phylogentic analysis of JS5T, LN1 and QZH3 with isolates representing all species of genus Dickey...

The growth and development of skeletal muscle directly impacts the quantity and quality of pork production. Chinese indigenous pig breeds and exotic species vary greatly in terms of muscle production and performance traits. We present transcriptome profiles of 110 skeletal muscle samples from Tongcheng (TC) and Yorkshire (YK) pigs at 11 development...

ABSTRACT Based on 16S-23S internal transcribed spacer ribosomal DNA sequence data, two padlock probes (PLPs), P-Xoo and P-Xoc, were designed and tested to detect Xanthomonas oryzae pv. oryzae and X. oryzae pv. oryzicola, respectively. These PLPs were combined with dot-blot hybridization to detect X. oryzae pv. oryzae and X. oryzae pv. oryzicola ind...

The type VI protein secretion system (T6SS) is essential for virulence of several Gram-negative bacteria. In this study, we identified a T6SS gene cluster in Acidovorax citrulli, a plant pathogenic bacterium that causes bacterial fruit blotch (BFB) of cucurbits. One T6SS cluster, approximately 25 kb in length, and comprised of 17 genes was found in...

A method was developed using a padlock probe (PLP) and dot-blot hybridization for detecting Acidovorax citrulli in cucurbit seed. The PLP was designed based on the 16S-23S internal transcribed spacer ribosomal DNA sequence from A. citrulli. The detection threshold for the PLP assay was 100 fg of genomic DNA, and A. citrulli was detected in 100% of...

Bacterial fruit blotch (BFB) is a devastating disease caused by Acidovorax citrulli, which was first observed in the United States in 1988 (3). A. citrulli can cause severe infection on a wide range of cucurbits, including watermelon, cantaloupe, and pumpkin. Cotyledon symptoms are brown, angular, necrotic spots or large necrotic lesions. The disea...

Acidovorax citrulli (Ac) is an important bacterium that occurs in watermelon, melon and other cucurbits. It mainly damages watermelon and melon, and can cause leaf blight, fruit rot, and even mortality. To verify the relationship between defects in the synthesis of histidine and the pathogenicity of Ac. We generated a transposon (Tn5) mutant librar...

Acidovorax avenae subsp. citrulli is a Gram-negative bacterium and is the causal agent of bacterial fruit blotch (BFB) in cucurbits. In this study, the role played by the acyl-homoserine lactone (AHL)-type quorum sensing (QS) system in growth, swimming motility and virulence was characterized in A. avenae subsp. citrulli strain XJL12. The AHL synth...