This work was carried out during two successive seasons (2016 and 2017) on cucumber fruits from a plastic greenhouse and from open field cultivation in El Gharbeia and El Giza Governorates, Egypt. Isolation trials from spoilage fruit samples of plastic greenhouse cultivation recorded high frequency of Alternaria tenusinium, Fusarium spp. and Pleospora alli. The most common fungi of rotten cucumber fruits from an open field were Galactomyces spp. and Fusarium spp. Pathogenicity tests proved that, Fusarium solani from El-Gharbeia followed by A. tenusinium from El-Giza were the most frequent isolates responsible for rot of cucumber fruits from plastic greenhouse cultivation. Moreover, the most frequent isolates causing postharvest disease of cucumber fruits of the open field were Galactomyces candidium from El-Giza followed by Geotrichum sp. and F. fujikuroi from El-Gharbeia Governorates, respectively. This is the first report of several fungi causing postharvest fruit rot disease of cucumber i.e., G. candidium, Geotrichum sp., A. tenusinium, P. alli and Fusarium spp. (F. fujikuroi, F. verticiolides, F. solani, F. geraminearium and Fusarium incarnatum). Fungal isolates were identified according to cultural, morphological and molecular characterization based on sequencing of internal transcribed spacer1 (ITS1). All the ITS nucleotide sequences of fungi were applied and conserved in GenBank.

Genetically modified Bt cotton (Gossypium hirsutum) leaves with typical symptoms of Alternaria early blight disease resembling that of tomato and potato were observed in the main cotton growing schemes in Sudan. Symptoms on leaves appeared as either brown 2leaf spot with gray centers or leaf blight with concentric rings. Pathogenicity tests using isolates with both symptoms showed that the isolated fungi were highly pathogenic to both G. hirsutum and G. barbadense cotton varieties. Alternaria alternata isolated from infected tomato and potato leaves with early blight symptoms was included for comparison. Microscopic examination showed that the mean length of conidia from cotton, tomato and potato isolates ranged from 26.25 to 45.45 μm, while the width ranged from 9.56 to 13.64 μm. The mean number of transverse septa among all isolates was 3.4 to 5.7 and the peak length ranged from 3.75 to 7.8 μm. Based on morphological characteristics the two isolates from cotton were identified as A. alternata. Genomic DNA was extracted directly from fungal cultures grown on potato dextrose agar (PDA) plates using a Zymo Research Quick DNA kit. A species-specific primer using the internal transcribed spacer ribosomal DNA (ITS rDNA) PCR scoring indicated the presence of A. alternata using primer pair ITS4/ITS5. Amplifications of the internal transcribed spacer region of 600 bp revealed 100% identity of the isolated fungus from cotton with A. alternata from tomato and potato. These data oblige us to reconsider the presence of A. alternata in the four main cotton growing schemes in Sudan while these symptoms have always been described for tomato and potato early blight disease.