Molecular identification and genetic variation of Alternaria species isolated from leaves of ornamental plants using Internal transcribed spacer (ITS) sequencing

Abstract

Alternaria species are pathogens that cause significant economic losses in ornamental plants. The present study focused on the molecular identification and genetic diversity of Alternaria species, a common fungal genus that includes pathogens causing plant diseases. Accurate identification and understanding of the genetic relationships of Alternaria species are important for managing plant diseases. This study included 100 samples collected from several plant species: Ivy plant (Convolvulus), Chrysanthemum plant  (Chrysanthemum), Infernal (Bougainville), Rubber plant (Ficus),  Cardina flower (Gardenia) infected with fungi. All samples cultured on PDA medium and purified with the single-spore method, followed by Polymerase Chain Reactions PCR identification through internal transcribed spacer ITS1 and ITS4 gene and sanger or next-generation sequencing of positive samples to construct a phylogenetic tree. Preliminary results showed the presence of Alternaria in 23 of the 100 samples, which were confirmed by PCR. Genetic sequencing revealed 10 newly recorded isolates, which were registered with National Center for Biotechnolo gy Information  (NCBI) under the following names: A.infectoria strainWS1-iqOR053817.1, strainWS3-iqOR064285.1,strainWS5-iqOR064342.1,strainWS9-iqOR083596.1,strainWS10-iqOR083599.1, A.angustivoidea  strainWS4-iqOR064286.1, A. tenuissima strainWS2-iqOR053945.1 , strainWS7-iq OR083592.1, Alternaria burnsii strainWS8-iq , OR088248.1 , A. alternate strain WS6-iqOR072637.1. These species were classified into groups based on their genetic patterns. This molecular study confirmed the association of various Alternaria species with ornamental plants and revealed the importance of ITS for diagnosing and identifying genetic diversity within the genus Alternaria.