Non-canonical Helitrons in Fusarium oxysporum.

Peter van Dam,Like Fokkens,Ben J. C. Cornelissen,Martijn Rep,Biju Vadakkemukadiyil Chellapan

doi:10.1186/s13100-016-0083-7

Peter van Dam, Like Fokkens + Show 3 more

Open Access

https://doi.org/10.1186/s13100-016-0083-7

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Journal: Mobile DNA	Publication Date: Dec 1, 2016
Citations: 13	License type: cc-by

Affiliation: University of Amsterdam, University of Kerala

Abstract

BackgroundHelitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. They occur widely in plants and animals, and have thus far been relatively little investigated in fungi.ResultsHere, we comprehensively survey Helitrons in several completely sequenced genomes representing the F. oxysporum species complex (FOSC). We thoroughly characterize 5 different Helitron subgroups and determine their impact on genome evolution and assembly in this species complex. FOSC Helitrons resemble members of the Helitron2 variant that includes Helentrons and DINEs. The fact that some Helitrons appeared to be still active in FOSC provided the opportunity to determine whether Helitrons occur as a circular intermediate in FOSC. We present experimental evidence suggesting that at least one Helitron subgroup occurs with joined ends, suggesting a circular intermediate. We extend our analyses to other Pezizomycotina and find that most fungal Helitrons we identified group phylogenetically with Helitron2 and probably have similar characteristics.ConclusionsFOSC genomes harbour non-canonical Helitrons that are characterized by asymmetric terminal inverted repeats, show hallmarks of recent activity and likely transpose via a circular intermediate. Bioinformatic analyses indicate that they are representative of a large reservoir of fungal Helitrons that thus far has not been characterized.Electronic supplementary materialThe online version of this article (doi:10.1186/s13100-016-0083-7) contains supplementary material, which is available to authorized users.

Highlights

Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements
F. oxysporum species complex (FOSC) Helitrons divide into two groups and 5 subgroups Most software designed to identify Helitrons are based on the DNA motifs of the Helitron1 variant and will overlook instances of Helitron2 because these have different termini [5, 18, 20, 38,39,40]
DNA sequence similarity can be hard to recognize over long evolutionary distances and very few ascomycete Helitron sequences were available at the start of our studies

Summary

Introduction

Helitrons are eukaryotic rolling circle transposable elements that can have a large impact on host genomes due to their copy-number and their ability to capture and copy genes and regulatory elements. Autonomous TEs contain one or more sequences coding for proteins that are involved in transposition, combined with TE-specific DNA motifs such as terminal inverted repeats. Helitrons are a family of TEs that encode an Y2transposase consisting of an N-terminal rolling circle replication initiator (Rep) domain and a C-terminal helicase (Hel) domain They were first characterized in an in silico analysis of the genomes of A. thaliana, O. sativa and C. elegans [1], where they were found to have a 5’-TC and 3’CTRR (where R stands for A or G) motif and a short hairpin at 10–12 nucleotides distance from the 3’ terminus. DINEs, known as HINEs, the most abundant TE in Drosophila, are non-autonomous elements derived from Helentrons [3] (see [7] for a recent review)

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