Objectives
Transposon insertion break continuity of co-selected traits, can alter gene transcription, lead to chromosomal rearrangements through homologous recombination and to insertional mutations what can have deleterious consequences for target loci. In the last decade remarkable examples of functional impact of transposons on host fate have been described. The phenomena resulting from transposon proximity have been thoroughly studied mainly for model animals and plants but few studies involved fungal genomes despite genomic resource abundance. TE neighborhood within a window of 1 kb had repressive effect on neighboring genes in fungal taxa with functional methylation machinery but had no such effect in Saccharomyces cerevisiae which lacks methylation (Castanera et al. 2016). Castanera and colleagues showed that the proximity of TE clusters leads to stronger gene expression silencing compared to neighbourhood of just a single TE, either upstream or downstream. Genes within 1kb of a Gypsy or hAT transposon have lower expression in Coccidioides immitis (Kirkland, Muszewska, and Stajich 2018). In this organism transposons are often inserted in proximity of phosphorylation related genes.
Methods
Encouraged by experimental screenings showing impact of TEs on gene expression we performed a systematic analysis of genomic location of TEs in 632 publicly available fungal genomes from NCBI database. TEs were predicted de novo with irf and RepeatModeler, and obtained consensus sequences together with RepBase database were used as a library for Repeat Masker search. Identified TEs were scanned against a fixed list of reference protein domains associated with TEs to detect potentially functional copies. Genomic neighborhood was analysed using available genome annotations. Ecological features were extracted from literature.
Results
We found that non autonomous transposons and remnants massively overlap with regions annotated as genes. These results suggest a great contribution of transposon derived sequences to host’s genes. Younger, potentially active transposons cluster together with other transposons. Observed non-random distribution of potentially active transposons might be a sign of selection against insertion of TE in gene proximity and target site preference among some types of TEs. 
The ubiquity of transposon fragments even in areas devoid of functional TEs does not support the hypothesis of insertion bias (omitting genes) as a key player shaping TE genomic placement.
Proteins coded by genes impacted by old transposon insertions have significantly less repeat motifs and protein-protein interaction domains but are more abundant in enzymatic domains. 
Animal related and pathogenic fungi have more TEs inserted into genes than fungi with different lifestyles. The overlapping of transposon derived sequences with genes is particularly common in taxa with compact genomes. 

Conclusions:
Here, we investigate the immediate neighborhood of transposons that contribute to a fast evolving part of the genome, with special focus on genes co-localized with transposons. Our findings show a link between the mobilome and fungal ecology.

6 / Transposable elements contribute to fungal genes and impact fungal lifestyle