Genome-Wide Analysis of Microsatellites in Alternaria arborescens and Elucidation of the Function of Polyketide Synthase (PksJ)

Abstract

Microsatellites or simple sequence repeats (SSRs) have been the most widely applied class of molecular markers used in genetic studies, having applications in genetic conservation, population studies, as well as diagnostics of fungi. Mining and analysis of SSRs of the whole genome sequence have been carried out in this study for the fungus Alternaria arborescens causing early blight of tomato and well known for producing mycotoxins like alternariol (AOH), alternariol monomethyl ether (AME), etc. A total of 4097 microsatellites were identified in A. Arborescens genome. Contig 1 was identified as the most SSR-rich region which was further analyzed to correlate the presence of SSRs with different biological processes. A total of 246 putative genes were predicted in this study and KEGG pathway analysis of 155 predicted genes indicated that SSRs can be linked with important metabolic pathways, molecular functioning, signal transduction, and cellular processes. The prediction of fungal mycotoxin inducer gene Polyketide synthase (PksJ) linked with SSR in this study may be a potential candidate participating in oncogenic signal transduction in human. Our study is the first report of PksJ gene in A. arborescens, a precursor of AOH and AME.

Identification of Novel Microsatellite Markers to Assess the Population Structure and Genetic Differentiation of Ustilago hordei Causing Covered Smut of Barley

“…However, the current study was performed on the complete genome assembly of Uh4857-4 and Uh364 isolates and non-coding sequences were also included. As a consequence, it permits to report a huge number of microsatellites (100239 in Uh364 and 137442 in Uh4857-4) compared to earlier reports in phytopathogenic fungi (Kumar et al, 2012;Singh et al, 2014a;Zhang et al, 2015;Mahfooz et al, 2017;Choudhary et al, 2018;Varady et al, 2018). In the present study, the relative abundance of microsatellites in the whole genome of Uh4857-4 (5246.27 microsatellites per Mb) and Uh364 (5125.14 microsatellites per Mb) is quite similar, suggesting the highly homogeneous genomic structure of these two U. hordei isolates.…”

Outcomes of Gallic Acid on Alternariol Induced Cyto-Morphic and Genotoxic In Vivo Changes in Parotid Gland: 4-HNE Incorporated

“…Fleck et al [47] reported that AOH-induced reactive catechols react covalently with DNA forming depurinating adducts at the N-7 of guanine and the N-3 of adenine. Tiessen et al [48] added that AOH exposure induced complex distributions of γH2AX histones which are paramount biomarkers of DNA double strand breaks (DSBs) and strong indicator that AOH-induced DSBs are important triggering signals for G2 arrest and autophagy [49]. AOH has been proved as a DNA topoisomerase poison with certain selectivity for its IIa isoform [50].…”

Comparative analysis of nine Tilletia indica genomes for the development of novel microsatellite markers for genetic diversity and population structure analysis

“…These methods also lack precision and accuracy. There are a flood of research reports that illustrate the potential of nucleic acid-derived markers for unzipping the variation among fungal pathogens at the genome level ( Kumar et al, 2013 ; Kashyap et al, 2015 , 2019b ; Goswami et al, 2017 ; Choudhary et al, 2018 ; Jiménez-Becerril et al, 2018 ; Prasad et al, 2018 ). For instance, genetic markers such as inter simple sequence repeats (ISSR) and random amplified polymorphic DNA (RAPD) have been extensively utilized to understand the genetic diversity of T. indica isolates ( Avinash et al, 2000 ; Seneviratne et al, 2009 ; Aggarwal et al, 2010 ; Parveen et al, 2015 ; Aasma et al, 2022 ).…”