Transposable elements with long terminal direct repeats (LTR TEs) are one of the 
best studied groups of mobile elements. They are ubiquitous elements present in 
almost all eukaryotic genomes. Their number and state of conservation can be a 
highlight of genome dynamics. We searched all published fungal genomes for 
LTR-containing retrotransposons, including both complete, functional elements 
and remnant copies. We identified a total of over 66,000 elements, all of which 
belong to the Ty1/Copia or Ty3/Gypsy superfamilies. Most of the detected Gypsy 
elements represent Chromoviridae, i.e. they carry a chromodomain in the pol ORF. 
We analyzed our data from a genome-ecology perspective, looking at the abundance 
of various types of LTR TEs in individual genomes and at the highest-copy 
element from each genome. The TE content is very variable among the analyzed 
genomes. Some genomes are very scarce in LTR TEs (<50 elements), others 
demonstrate huge expansions (>8000 elements). The data shows that transposon 
expansions in fungi usually involve an increase both in the copy number of 
individual elements and in the number of element types. The majority of the 
highest-copy TEs from all genomes are Ty3/Gypsy transposons. Phylogenetic 
analysis of these elements suggests that TE expansions have appeared 
independently of each other, in distant genomes and at different taxonomical 
levels. We also analyzed the evolutionary relationships between protein domains 
encoded by the transposon pol ORF and we found that the protease is the fastest 
evolving domain whereas reverse transcriptase and RNase H evolve much slower and 
in correlation with each other.