Molecular identification and genetic variation of Alternaria species isolated from tomatoes using ITS1 sequencing and inter simple sequence repeat methods

Abstract

Background and Purpose: Alternaria is one of the most abundant fungi that exists in numerous places around the world. This saprophytic fungus causes diseases in plants and accounts for the spoilage of cereals in warehouses. The aim of this study was to identify Alternaria isolates based on their morphological characteristics and internal transcribed spacer ribosomal RNA (ITS rRNA) sequencing method. To this end, genetic diversity in the isolates was also examined using inter simple sequence repeat (ISSR) markers. Materials and Methods: To conduct this research, a total of 60 tomato samples with black spots were collected from supermarkets in Khorramabad City, Iran, in the winter of 2017. The specimens were cultured on a potato dextrose agar medium. After the purification of the fungus by the single-spore method, the identification of the species was carried out using morphological characteristics and ITS rRNA sequencing by polymerase chain reaction. The genetic diversity of the identified species with four primers was evaluated using the ISSR marker. Results: Based on the sequencing of the ITS1 region, all the isolates were identified as A. alternata. Cluster diagrams for the ISSR marker were classified into six distinct groups. The mean polymorphism information content was obtained as 0.35, indicating the effectiveness of the primers in the separation of the isolates. Conclusion: The sequencing of ITS1 led to the identification of Alternaria species that are morphologically similar. The production of various mycotoxins by A . Alternata species leads to the contamination of livestock and human food. Regarding this, the investigation of the genetic diversity of A. alternata species using the ISSR marker would facilitate the identification of suitable and effective strategies for controlling the fungal and mycotoxin contamination of human nutrition.

Morphological and molecular identification study of rose and lantana fungal leaf spot pathogens

“…The phylogenetic tree was drawn using the Neighbor-Joining method of genetic convergences using the nitrogenous bases of the fungi matching with the species under study and the fungi deposited in the NCBI for fungi as in Figures (5, 6 and 7). The high matching rate of A. alternata was similar to what was reached in several similar studies by [14,15,31], as well as what was reached by researchers [11] with the high matching of B. cinerea and F. chlamydosporum [12].…”

The first case report of thorn-induced Alternaria alternata infection of the hand in an immunocompetent host

“…The primers used to amplify and sequence the nuclear ribosomal internal transcribed spacer (ITS) gene for fungus were ITS1, 5′-TCCGTAGGTGAACCTGCGG-3′ and ITS4, 5′TCCTCCGCTTATTGATATGC-3′. The fungus was identified as Alternaria alternata with 100% homology according to the BLAST program ( www.ncbi.nlm.nih.gov/BLAST ) and compared with the similar sequences in the Gene Bank [ 7 ]. A phylogenetic tree was constructed based on ITS gene sequences, using the maximum likelihood method implemented in MEGA 6 [ 8 ] (Fig.…”

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“…Alternaria alternata is one of the most common saprophytes found throughout the world [13]. A. alternata cause a range of diseases with economic impact on a large variety of important agronomic host plants and fruits including potatoes, pomegranate, almond, kiwi, aloe vera, tomato, ginseng , citrus, banana, pepper , water hyacinth, Lantana camara, and Amaranthus spp.…”