Transposable Element Analysis in Pleurotus ostreatus

Overview

• End-to-end bioinformatics pipeline for discovery and characterization of transposable elements (TEs) in Pleurotus ostreatus (oyster mushroom)
• Integrates sequence alignment, RNA-seq mapping, ORF prediction, differential expression, and functional annotation
• Goal: characterize TE structure, expression patterns, and putative function across biological conditions

Pipeline Components

• Sequence alignment — Filtered TE sequences by length (±20% of median), applied MAFFT multiple sequence alignment, and generated consensus sequences for Gypsy and Copia TE subfamilies
• Scaffold analysis — Focused analysis of Scaffold 81, a primary TE-containing genomic region; identified open reading frames, start codons, and reading frames across the sequence
• RNA-seq integration — Mapped reads from three conditions (Healthy, HC, Alpha/Beta variants) to TE sequences using SAMtools; extracted high-coverage regions of interest (ROIs) with depth threshold of 10
• Differential expression — DESeq2-based statistical comparison of TE expression across conditions; output includes p-values and fold changes per ROI
• Functional annotation — BLAST-based remote annotation of predicted protein sequences against NCBI

Key Findings

• Multiple ORFs identified on Scaffold 81 ranging from ~5,600–7,900 bp; protein translations of 1,800–2,600+ amino acids
• Condition-dependent expression differences detected across Healthy, HC, and variant conditions
• High-expression ROIs identified (e.g. ROI_18597: 1,690 reads; ROI_20640: 1,580 reads)
• Consensus sequences generated for Gypsy_1 subfamily with pairwise identity comparisons across variants

Tools & Technologies

• Python, R, BioPython, MAFFT
• SAMtools, DESeq2, BLAST/NCBI, ORFfinder