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Fruit stones play an important role in fruit development and are closely related to fruit quality. Lignification of the fruit stone (endocarp) is a typical feature of stone fruits. Stoneless jujube is a valuable jujube germplasm resource, and the degree of lignification of its fruit stone is low. However, the underlying mechanisms of lignification in the jujube endocarp remain unclear. In this study, we characterised a novel Class III peroxidase, PRX1, via comparative transcriptome analysis of the jujube endocarp and investigated its potential molecular mechanism in endocarp lignin synthesis. Subcellular localisation analysis revealed that ZjPRX1 was localised to the cytoplasm. According to the results of an in situ hybridisation analysis, the tissue‐specific expression of ZjPRX1 was greatest in the endocarp. Moreover, ZjPRX1 overexpression in jujube fruits and calluses caused significant changes in the amount of lignin that accumulated. Scanning electron microscopy revealed that the cell walls of the stems of ZjPRX1‐OE Arabidopsis lines were significantly thicker than those of WT Arabidopsis. Yeast one‐hybrid, dual‐luciferase reporter and electrophoretic mobility shift assays indicated that ZjbZIP33 activated ZjPRX1 expression by binding specifically to the G‐box element in the ZjPRX1 promoter. IAA and GA3 induced ZjbZIP33‐ZjPRX1 expression and lignin formation. Overall, the results revealed a novel module, that is, ZjbZIP33‐ZjPRX1, that positively regulates lignin formation in the jujube fruit stone. This study contributes to a better understanding of the molecular basis of lignin synthesis in the endocarp of jujube fruits and identifies candidate genes for optimising stone fruit breeding.

Fruit is a key component of a healthy diet. However, it is still not clear whether some classes of fruit may be more beneficial than others and whether all individuals whatever their age, gender, health status, genotype, or gut microbiota composition respond in the same way to fruit consumption. Such questions require further observational and intervention studies in which the intake of a specific fruit can be precisely assessed at the population and individual levels. Within the Food Biomarker Alliance Project (FoodBAll Project) under the Joint Programming Initiative “A Healthy Diet for a Healthy Life”, an ambitious action was undertaken aiming at reviewing existent literature in a systematic way to identify validated and promising biomarkers of intake for all major food groups, including fruits. This paper belongs to a series of reviews following the same BFIRev protocol and is focusing on biomarkers of pome and stone fruit intake. Selected candidate biomarkers extracted from the literature search went through a validation process specifically developed for food intake biomarkers.

In the present work, an effort has been made to utilize Phyllanthus emblica (PE) fruit stone as a potential biomaterial for the sustainable remediation of noxious heavy metals viz. Pb(II) and Cd(II) from the aqueous solution using adsorption methodology. Further, to elucidate the adsorption potential of Phyllanthus emblica fruit stone (PEFS), effective parameters, such as contact time, initial metal concentration, temperature, etc., were investigated and optimized using a simple batch adsorption method. It was observed that 80% removal for both the heavy metal ions was carried out within 60 min of contact time at an optimized pH 6. Moreover, the thermodynamic parameters results indicated that the adsorption process in the present study was endothermic, spontaneous, and feasible in nature. The positive value of entropy further reflects the high adsorbent–adsorbate interaction. Thus, based on the findings obtained, it can be concluded that the biosorbent may be considered a potential material for the remediation of these noxious impurities and can further be applied or extrapolated to other impurities.

Brown rot is the most economically important fungal disease of stone fruits and is primarily caused by Monilinia laxa and Monlinia fructicola. Both species co-occur in European orchards although M. fructicola is considered to cause the most severe yield losses in stone fruit. This study aimed to generate a high-quality genome of M. fructicola and to exploit it to identify genes that may contribute to pathogen virulence. PacBio sequencing technology was used to assemble the genome of M. fructicola. Manual structural curation of gene models, supported by RNA-Seq, and functional annotation of the proteome yielded 10,086 trustworthy gene models. The genome was examined for the presence of genes that encode secreted proteins and more specifically effector proteins. A set of 134 putative effectors was defined. Several effector genes were cloned into Agrobacterium tumefaciens for transient expression in Nicotiana benthamiana plants, and some of them triggered necrotic lesions. Studying effectors and their biological properties will help to better understand the interaction between M. fructicola and its stone fruit host plants.

Bacterial canker is one of the most important diseases of stone fruit trees in various locations of Kurdistan province, Iran. Genetic diversity and evolutionary relationships among 20 fluorescent pseudomonads isolated from stone fruit trees with symptoms similar to bacterial canker were investigated using a polyphasic approach by means of phenotypic characterizations, repetitive PCR using the REP and ERIC primers and multilocus sequence typing (MLST) of four housekeeping genes (gapA, rpoD, gyrB and gltA). The pathogenicity of strains was carried out under greenhouse conditions. Twelve strains produced an expected amplified DNA fragment of about 752-bp which indicated the presence of the syrB gene. Based on MLST, these strains belonged to P. syringae species complex and included in the genomospecies 1, phylogroup 2b and 2d. Phylogenetic analysis of the other eight fluorescent pseudomonad strains by using gyrB and rpoD sequences allowed the identification of strains into P. fluorescens, P. putida and P. lutea groups. Unweighted pair group method analysis (UPGMA) of genomic fingerprints obtained by rep-PCR revealed 17 different patterns which grouped P. syringae strains into three clusters clearly separated from other fluorescent pseudomonads. MLST confirmed the genetic variability among strains obtained by rep-PCR. Grouping identified of P. syringae strains by both rep-PCR and MLST was related to geographic locations of strains.

“Candidatus Phytoplasma prunorum” (CPp) is a highly destructive phytopathogenic agent in many stone fruit-growing regions in Europe and the surrounding countries. In this work, we focused on documenting entire bacterial community in the phloem tissues of 60 stone fruit trees. Nested PCR and two real-time PCR assays were used to select CPp-positive (group A) and CPp-negative samples (group B). Afterwards, high-throughput amplicon sequencing was performed to assess bacterial community compositions in phloem tissues. The bacterial composition in phloem tissue consisted of 118 distinct genera, represented mainly by Pseudomonas, Acinetobacter, Methylobacterium, Sphingomonas, and Rhizobium. Statistics showed that CPp influenced the bacterial composition of infected plants (group A) and that the bacterial community depended on the geographical origin of the sample. This is the first work focusing on an analysis of the influence of CPp on the bacteria coexisting in the phloem tissues of stone fruit trees.

Specific primers were developed to detect the causal agent of stone fruit bacterial canker using conventional and real-time polymerase chain reaction (PCR) methods. PCR melting profile (PCR MP) used for analysis of diversity of Pseudomonas syringae strains, allowed to pinpoint the amplified fragments specific for P. syringae pv. morsprunorum race 1 (Psm1) and race 2 (Psm2), which were sequenced. Using obtained data, specific sequence characterised amplified region (SCAR) primers were designed. Conventional and real-time PCRs, using genomic DNA isolated from different bacterial strains belonging to the Pseudomonas genus, confirmed the specificity of selected primers. Additionally, the specificity of the selected DNA regions for Psm1 and Psm2 was confirmed by dot blot hybridisation. Conventional and real-time PCR assays enabled accurate detection of Psm1 and Psm2 in pure cultures and in plant material. For conventional PCR, the detection limits were the order of magnitude ~10⁰ cfu/reaction for Psm1 and 10¹ cfu/reaction for Psm2 in pure cultures, while in plant material were 10⁰–10¹ cfu/reaction using primers for Psm1 and 3 × 10² cfu/reaction using primers for Psm2. Real-time PCR assays with SYBR Green I showed a higher limit of detection (LOD) − 10⁰ cfu/reaction in both pure culture and in plant material for each primer pairs designed, which corresponds to 30–100 and 10–50 fg of DNA of Psm1 and Psm2, respectively. To our knowledge, this is the first PCR-based method for detection of the causal agents of bacterial canker of stone fruit trees.

A population of Xiphinema americanum-group was recovered in association with stone fruit trees in Isfahan province, center of Iran. A reverse taxonomic approach based upon the large subunit ribosomal DNA (LSU rDNA D2-D3) and the mitochondrial cytochrome c oxidase subunit I (COI mtDNA) gene sequences in integration with morphological studies, revealed that the recovered population belongs to Xiphinema santos. The Iranian population was mainly characterized by 1240–1868 μm long females with 60–84 μm long odontostyle, a = 37.2–51.9 and c = 42.8–54.6. It is further characterized by a lip region having a depression in junction with the body, presence of visible endosymbiont bacteria in ovaries under light microscope, dorsally convex and ventrally slightly concave conical tail with a blunt tip and three juvenile developmental stages. This population was similar to the type population in its morphology; however overlapped and extended morphometric data ranges, as well as differences in some indexes were observed. Compared to a Spanish population of this species, the Iranian population had a close morphology, similar morphometric data ranges and identical LSU and COI sequences. In LSU phylogeny, the relationship between the present and some previously sequenced isolates of the species and some isolates of three species X. georgianum, X. laevistriatum and X. citricolum was not resolved. In COI phylogeny, the clade of the Iranian and Spanish populations appeared as an independent lineage inside an unsupported clade including several species. The comparison with other populations of the species was reported and discussed. A second species, X. primum, that is native to Iran, was recovered from a new locality and characterized molecularly.

Over the years, real-time PCR outflanked endpoint PCR in phytopathogen diagnostics, mainly because of the increase in sensitivity and timesaving aspects of the technique. However, a time consuming 16S rRNA-based nested PCR method is still the gold standard for phytoplasma diagnosis. This is also the case for phytoplasma detection in Malus , Pyrus and Prunus , the three main host plants of apple proliferation (AP), pear decline (PD) and European stone fruit yellows (ESFY) phytoplasma, respectively. The last decade, loop-mediated isothermal amplification (LAMP) (Notomi et al. 2000 ) is gaining a lot in significance and is also for phytoplasmas expected to become a widely used reliable diagnostic tool. High specificity and sensitivity which also requires a less stringent need for DNA purification, and the short analysis time and the limited equipment requirements makes the LAMP method a fast and affordable alternative with great point-of-care diagnostic potential. In this paper, we present a LAMP primer set for the ribosomal group 16SrX, containing the important fruit tree phytoplasmas AP, PD and ESFY. The primers were developed and validated for fast and sensitive detection and general use for diagnosis. We foresee that the LAMP technique will also have its application in on-site diagnosis of the fruit tree phytoplasmas during inspections and surveys.

Monilinia fructicola and Monilinia laxa are causal agents of brown rot, the most serious fungal disease of stone fruit (Prunus species). The disease is controlled primarily by applying fungicides. It was hypothesised that Monilinia isolates exposed to a regime of fungicidal sprays would exhibit greater tolerance to those compounds than isolates that had not been subjected at all to such fungicide sprays. Sixty-six M. fructicola and 52 M. laxa isolates were collected from fungicide-sprayed and unsprayed commercial and domestic orchards. The fungicides propiconazole, iprodione, and a mixture of fluopyram and trifloxystrobin were used regularly on all the sprayed orchards tested, and these were used to challenge all Monilinia isolates in vitro. We found that isolates collected from sprayed orchards were on average more tolerant to the fungicides, as measured by effective concentration of fungicide reducing mycelial growth by 50% (EC50). This trend was evident for both fungal species tested, but it was statistically significant only for M. fructicola. Monilinia laxa isolates were on average more tolerant to propiconazole than were M. fructicola isolates irrespective of orchard type, while average responses to iprodione and fluopyram + trifloxystrobin were similar for both species. Although tolerant and sensitive isolates were identified under both sprayed and unsprayed regimes, there was a greater range of responses to all three fungicides by isolates from sprayed orchards. Isolates with tolerance to two fungicides were not exclusively from sprayed orchards, but occurred more frequently there.