Genome-wide Landscaping of Repetitive Elements in the Genome of Neurospora crassa

Objectives: Repetitive elements are ubiquitous in eukaryotes and have contributed in expression of genes and maintaining the architecture of genome. Fungi although being a eukaryote, repeat sequences are typically limited due to small genome size and typical genome defense mechanisms which fights against expansion of repeats and maintains streamlined genome. Methods/Findings: Despite, the presence of such mechanisms Tad element was found to be active in Adiopodoume strain of N. crassa. This is one of the most enigmatic discoveries made in Neurospora. From this perspective, we have analyzed the genome of N. crassa OR74A (NC12) by in silico tools for the identification of repeats. The comprehensive analysis of these elements suggests that about six (PuntRIP) DNA transposons and 2 Tad1 (Non-Long Terminal Repeat) elements share highest homology with known repeats from RepBase. The presence of DNA binding and transposase domain in the protein sequence of NCU02991 indicates that the element identified is a DNA transposon. Application: The results also suggest that among the identified six PuntRIP sequences four of them share homology, which indicates that similar sequence is repeated four times within the genome. The promoters identified in the dataset of identified repeats in the upstream and downstream regions indicate that these repeats may play certain role in the regulation of genes. Keywords: DNA Transposons, Non-LTR, Repetitive Elements, Tad1