A Duplex-Droplet Digital PCR Assay for Simultaneous Quantitative Detection of Monilinia fructicola and Monilinia laxa on Stone Fruits

AcOTApks Gene-Based Molecular Tools to Improve Quantitative Detection of the Mycotoxigenic Fungus Aspergillus carbonarius

Ochratoxin A (OTA) is a mycotoxin, a common contaminant of grapes and their derivatives, such as wine, and classified as possible human carcinogen (group 2B) by the International Agency for Research on Cancer (IARC). Aspergillus carbonarius is the main producer of OTA in grapes. The stability of the molecule and the poor availability of detoxification systems makes the control of A. carbonarius in vineyards the main strategy used to reduce OTA contamination risk. Several molecular methods are available for A. carbonarius detection, but the correlation between the abundance of fungal population and OTA contamination needs to be improved. This study aimed at the development of innovative quantitative PCR (qPCR) and digital droplet PCR (ddPCR) tools to quantify the mycotoxigenic fractions of A. carbonarius strains on grapes, based on the key gene AcOTApks in the pathway of OTA biosynthesis. Different primers/probe sets were assessed, based on their specificity and sensitivity. This method allowed to quantify up to 100 fg∙µL-1 [cycle of quantification (Cq) = 37] and 10 fg∙µL-1 (0.38 copies∙µL-1) of genomic DNA (gDNA) from A. carbonarius mycelium in qPCR and ddPCR, respectively. The sensitivity as to artificially contaminated must samples was up to 100 conidia (Cq = 38) and 1 conidium (0.13 copies∙µL-1) with qPCR and ddPCR, respectively. Finally, the methods were validated on naturally infected must samples, and the quantification of the fungus was in both cases highly correlated (r = +0.8) with OTA concentrations in the samples. The results showed that both analytical methods can be suitable for improving the sustainable management of OTA contamination in grapes and their derivatives.

Development of the duplex droplet digital PCR for quantitative monitoring of mixed infections of Meloidogyne incognita and M. enterolobii

BACKGROUND

Root-knot nematodes (RKN, Meloidogyne spp.) are economically significant pests that cause immense damage to a wide range of crops. Among them, M. incognita and M. enterolobii are of particular concern, as their high virulence and broad host range. RKN are challenging for detection due to their subterranean lifestyle underground. Also, the mixed infection of nematodes in field crops complicates the need for more accurate diagnostic and quantification technologies.

RESULTS

To address this challenge, we developed and optimized a novel duplex droplet digital PCR (ddPCR) method, using primer/probe sets targeting M. incognita and M. enterolobii, to simultaneously identify and quantify both species within a single assay. The innovative ddPCR diagnostic demonstrated excellent performance in terms of sensitivity, precision and reproductivity when quantifying the eggs and soil samples containing juveniles of both species. Moreover, the application of the duplex ddPCR method enables the monitoring of population dynamics of M. incognita and M. enterolobii under competitive environmental conditions. Our results indicated that the reproduction factor of M. incognita possibly inhibited when in mixed populations of M. enterolobii.

CONCLUSION

In this study, we first applied duplex ddPCR technique for differentiating mixed infections of M. incognita and M. enterolobii, offering a valuable tool for species detection and quantification. It enables the monitoring of population dynamics for both species, which is crucial for providing theoretical guidance for the implementation of timely and effective control measures. © 2024 Society of Chemical Industry.

Early Detection of Both Pyrenophora teres f. teres and f. maculata in Asymptomatic Barley Leaves Using Digital Droplet PCR (ddPCR)

Efficient early pathogen detection, before symptom apparition, is crucial for optimizing disease management. In barley, the fungal pathogen Pyrenophora teres is the causative agent of net blotch disease, which exists in two forms: P. teres f. sp. teres (Ptt), causing net-form of net blotch (NTNB), and P. teres f. sp. maculata (Ptm), responsible for spot-form of net blotch (STNB). In this study, we developed primers and a TaqMan probe to detect both Ptt and Ptm. A comprehensive k-mer based analysis was performed across a collection of P. teres genomes to identify the conserved regions that had potential as universal genetic markers. These regions were then analyzed for their prevalence and copy number across diverse Moroccan P. teres strains, using both a k-mer analysis for sequence identification and a phylogenetic assessment to establish genetic relatedness. The designed primer-probe set was successfully validated through qPCR, and early disease detection, prior to symptom development, was achieved using ddPCR. The k-mer analysis performed across the available P. teres genomes suggests the potential for these sequences to serve as universal markers for P. teres, transcending environmental variations.

What are the 100 most cited fungal genera?

The global diversity of fungi has been estimated between 2 to 11 million species, of which only about 155 000 have been named. Most fungi are invisible to the unaided eye, but they represent a major component of biodiversity on our planet, and play essential ecological roles, supporting life as we know it. Although approximately 20 000 fungal genera are presently recognised, the ecology of most remains undetermined. Despite all this diversity, the mycological community actively researches some fungal genera more commonly than others. This poses an interesting question: why have some fungal genera impacted mycology and related fields more than others? To address this issue, we conducted a bibliometric analysis to identify the top 100 most cited fungal genera. A thorough database search of the Web of Science, Google Scholar, and PubMed was performed to establish which genera are most cited. The most cited 10 genera are Saccharomyces, Candida, Aspergillus, Fusarium, Penicillium, Trichoderma, Botrytis, Pichia, Cryptococcus and Alternaria. Case studies are presented for the 100 most cited genera with general background, notes on their ecology and economic significance and important research advances. This paper provides a historic overview of scientific research of these genera and the prospect for further research. Citation: Bhunjun CS, Chen YJ, Phukhamsakda C, Boekhout T, Groenewald JZ, McKenzie EHC, Francisco EC, Frisvad JC, Groenewald M, Hurdeal VG, Luangsa-ard J, Perrone G, Visagie CM, Bai FY, Błaszkowski J, Braun U, de Souza FA, de Queiroz MB, Dutta AK, Gonkhom D, Goto BT, Guarnaccia V, Hagen F, Houbraken J, Lachance MA, Li JJ, Luo KY, Magurno F, Mongkolsamrit S, Robert V, Roy N, Tibpromma S, Wanasinghe DN, Wang DQ, Wei DP, Zhao CL, Aiphuk W, Ajayi-Oyetunde O, Arantes TD, Araujo JC, Begerow D, Bakhshi M, Barbosa RN, Behrens FH, Bensch K, Bezerra JDP, Bilański P, Bradley CA, Bubner B, Burgess TI, Buyck B, Čadež N, Cai L, Calaça FJS, Campbell LJ, Chaverri P, Chen YY, Chethana KWT, Coetzee B, Costa MM, Chen Q, Custódio FA, Dai YC, Damm U, de Azevedo Santiago ALCM, De Miccolis Angelini RM, Dijksterhuis J, Dissanayake AJ, Doilom M, Dong W, Alvarez-Duarte E, Fischer M, Gajanayake AJ, Gené J, Gomdola D, Gomes AAM, Hausner G, He MQ, Hou L, Iturrieta-González I, Jami F, Jankowiak R, Jayawardena RS, Kandemir H, Kiss L, Kobmoo N, Kowalski T, Landi L, Lin CG, Liu JK, Liu XB, Loizides M, Luangharn T, Maharachchikumbura SSN, Makhathini Mkhwanazi GJ, Manawasinghe IS, Marin-Felix Y, McTaggart AR, Moreau PA, Morozova OV, Mostert L, Osiewacz HD, Pem D, Phookamsak R, Pollastro S, Pordel A, Poyntner C, Phillips AJL, Phonemany M, Promputtha I, Rathnayaka AR, Rodrigues AM, Romanazzi G, Rothmann L, Salgado-Salazar C, Sandoval-Denis M, Saupe SJ, Scholler M, Scott P, Shivas RG, Silar P, Souza-Motta CM, Silva-Filho AGS, Spies CFJ, Stchigel AM, Sterflinger K, Summerbell RC, Svetasheva TY, Takamatsu S, Theelen B, Theodoro RC, Thines M, Thongklang N, Torres R, Turchetti B, van den Brule T, Wang XW, Wartchow F, Welti S, Wijesinghe SN, Wu F, Xu R, Yang ZL, Yilmaz N, Yurkov A, Zhao L, Zhao RL, Zhou N, Hyde KD, Crous PW (2024). What are the 100 most cited fungal genera? Studies in Mycology 108: 1-411. doi: 10.3114/sim.2024.108.01.

Biodiversity Evaluation and Preservation of Italian Stone Fruit Germplasm (Peach and Apricot) in Southern Italy

The Prunus genus encompasses a group of economically important and closely related crops, sharing an essentially common genome and, thereby, a high level of conserved and transferable microsatellite (SSR) loci. In Southern Italy, many of the local and/or neglected varieties are abandoned and at risk of extinction due to the high degree of urbanization and agricultural intensification, despite their value as genetic resources for crop improvement. This research aimed to genetically and morphologically characterize the traditional apricot (P. armenica) and peach (P. persica) germplasms collected in old family orchards. Most of the official descriptor categories were scored, thus revealing a rather high level of phenotypic variation in both collections. Genetic data allowed the discovery of diversity masked by morphological traits. Genotyping in 15 and 18 SSRs, eight of which were transferable across both species, showed an average polymorphic informativeness (PIC) of 0.44 and 0.59 for apricot and peach, respectively, and a total of 70 and 144 alleles. A reliable identification of each genotype was achieved, and the presence of possible mislabeling and/or erroneous denominations was solved. These results are encouraging for the valorization of the still poorly explored Italian Prunus germplasm, with significant economic consequences for bioresource conservation and management.

Development of real-time PCR and droplet digital PCR based marker for the detection of Tilletia caries inciting common bunt of wheat

This is the first study reporting droplet digital PCR and quantitative real time PCR for detection of Tilletia caries (syn. T. tritici), which causes common bunt of wheat and leads to yield losses of 80% in many wheat growing areas worldwide. To establish an accurate, rapid and quantifiable detection method, we tested 100 inter simple sequence repeats (ISSR) primers and obtained a species-specific fragment (515 bp) generated by ISSR 827. Then, a specific 266 bp band for the sequence characterized amplified region (SCAR) marker was produced from T. caries. The detection limit reached 50 pg/μL. Based on the SCAR marker, we further developed a higher sensitivity of quantitative real time-polymerase chain reaction (qRT-PCR) with a detection limit of 2.4 fg/μL, and droplet digital PCR (ddPCR) with a detection limit of 0.24 fg/μL. Both methods greatly improved the detection sensitivity of T. caries, which will be contribute a lot for quickly and accurately detection of T. caries, which causes wheat common bunt.