Abstract
BackgroundDNA transposons are ubiquitous components of eukaryotic genomes. Academ superfamily of DNA transposons is one of the least characterized DNA transposon superfamilies in eukaryotes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease.ResultsSystematic searches on Repbase and BLAST searches against publicly available genome sequences revealed that several species of fungi and animals contain multiple Academ transposon families encoding a helicase. These AcademH families generate 9 or 10-bp target site duplications (TSDs) while Academ families lacking helicase generate 3 or 4-bp TSDs. Phylogenetic analysis clearly shows two lineages inside of Academ, designated here as AcademH and AcademX for encoding helicase or XPG nuclease, respectively. One sublineage of AcademH in animals encodes plant homeodomain (PHD) finger in its transposase, and its remnants are found in several fish genomes.ConclusionsThe AcademH lineage of TEs is widely distributed in animals and fungi, and originated early in the evolution of Academ DNA transposons. This analysis highlights the structural diversity in one less studied superfamily of eukaryotic DNA transposons.
Highlights
Transposable elements (TEs), or transposons are ubiquitous components of genomes in all three domains of life [1, 2]
Proteins related to AcademH transposases were found from three subdivisions (Agaricomicotina, Pucciniomycotina, Ustilaginomycotina) within Basidiomycota, one subdivision (Pezisomycotina) within Ascomycota, and one subdivision (Mortierellomycotina) within Mucoromycota
Despite the report that Academ transposons are widely distributed in fungi [11], no other fungal group was revealed to contain AcademH transposons in this analysis
Summary
Transposable elements (TEs), or transposons are ubiquitous components of genomes in all three domains of life [1, 2]. TEs are traditionally classified into 2 classes: Class I retrotransposons and Class II DNA transposons [3]. DDE transposase or integrase is the most ubiquitous enzyme that functions as transposase of DNA transposons, as well as of long terminal repeat (LTR) retrotransposons and of retroviruses [6]. Eukaryotic DNA transposons are classified into around 20 superfamilies [1]. Most of these superfamilies, such as Mariner/Tc1 and Harbinger/PIF1, are known to encode a DDE transposase. DNA transposons are ubiquitous components of eukaryotic genomes. DNA transposons belonging to the Academ superfamily have been reported from various animals, one red algal species Chondrus crispus, and one fungal species Puccinia graminis. Six Academ families from P. graminis encode a helicase in addition to putative transposase, while some other families encode a single protein which contains a putative transposase and an XPG nuclease
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