J Basic Microbiol. 2020;1–9. www.jbm-journal.com © 2020 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim | 1 Received: 5 September 2019 | Revised: 27 February 2020 | Accepted: 1 March 2020 DOI: 10.1002/jobm.201900487 RESEARCH PAPER Genetic differentiation and phylogenetic potential of Ty3/Gypsy LTR retrotransposon markers in soil and plant pathogenic fungi Sonia Chadha 1,2 | Mradul Sharma 3 1 Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India 2 Life Sciences, Homi Bhabha National Institute, Mumbai, India 3 Astrophysical Sciences Division, Bhabha Atomic Research Centre, Mumbai, India Correspondence Sonia Chadha, Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India. Email: schadha@barc.gov.in Abstract Genetic diversity studies are crucial for understanding the genetic structure and evolutionary dynamics of fungal species and communities. Fungal gen- omes are often reshaped by their repetitive components such as transposable elements. These elements are key players in genomic rearrangements and are ideal targets for genetic diversity and evolutionary studies. Herein, we used three Ty3/Gypsy long terminal repeat retrotransposons, Grasshopper, Maggy, and Pyret, for genetic differentiation and diversity in soil and plant pathogenic fungi, representing diverse species, order, and phyla. Pyret DNA markers showed the highest gene diversity and Shannon's information indices, followed by Maggy and Grasshopper. The observed high levels of multilocus poly- morphism indicate the continuous mobility of these elements after their transfer in the new host. In conclusion, this study presents novel markers for genetic differentiation and evolutionary studies of fungi, and sheds light on the prevalence of gene acquisition phenomenon in field fungi. KEYWORDS fungi, genetic differentiation, genotyping, horizontal gene transfer, LTR retrotransposons 1 | INTRODUCTION Fungi are diverse and cryptic organisms that assemble into complex and dynamic communities [1]. The fungal king- dom includes numerous species that affect plants, hu- mans, and animals in both beneficial and detrimental ways [2]. Their exposure to diverse ecological and evolu- tionary factors, and survival under these surroundings involve adaptive genomic rearrangements [3]. In such genomic responses, repetitive DNA elements including transposable elements (TEs) play a key role, as these ele- ments can influence the evolutionary potential and fitness of an organism [4]. Generally, the classification of TEs depends on their transpositional mode [5], where class I elements or retroelements use reverse transcriptase to transpose using copy and paste mechanisms via RNA intermediates. These elements include long and short in- terspersed elements, and long terminal repeat (LTR) ret- rotransposons (RTNs). Class II elements or DNA transposons move directly from DNA to DNA by cut and paste mode. LTR‐RTNs contain direct LTRs flanking the internal regions of retrotransposons. In fungi, LTR‐RTNs are further classified as Ty1/Copia and Ty3/Gypsy ele- ments, with Gypsy being the most dominant TE in fungi. The majority of the detected Ty3/Gypsy representatives belong to Chromoviridae [6]. The insertion of TEs to new genomic locations leads to the expansion and diversifica- tion of the genomes [6,7]. RTNs are detected in more than 60 analyzed fungal genomes, and around 66,000 retroelements are identified