Non-canonical Helitrons in Fusarium oxysporum

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.

Multiple Evolutionary Trajectories Have Led to the Emergence of Races in Fusarium oxysporum f. sp. lycopersici

“…However, except for the conserved residues in the rep and hel domains, there is virtually no homology with the HelA and HelB proteins. A BLAST search of the ORF3 sequence against the genome sequence of FOL strain 4287 (FOL4287) identified four copies (sequence identity over 99%) belonging to FoHeli3 (Table S3), one of the Helitron families that have been identified in F. oxysporum (48). Moreover, analysis of the flanking sequences of ORF3 confirmed that it possesses terminal structural features specific for FoHeli3.…”

“…S3 in the supplemental material) of the AVR1 locus from which HelB could have been excised and comparing the sequence with the HelB flanking sequences did not reveal any potential excision footprint. Helitron transposons are found throughout the genome of FOL4287 but are most abundant on chromosome 14 (7 copies, of which 6 share Ͼ97% sequence identity) (42,48). No Helitron transposons are found near AVR2, but one Helitron copy is located ϳ20 kb upstream and another 3,455 bp downstream of AVR3 (42,48).…”

Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

“…Non-canonical Helitrons appear to be a key feature of Fo pathogenicity chromosomes 29 . In our analysis only Foc PS regions, were enriched for Helitron helicase-like domains (IPR025476) (Supp.…”

Pangenomic analysis reveals pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

“…These results support recent identification of helitrons in F. oxysporum ff. spp 29 , and indicate that a Helitron-based mechanism of genomic rearrangement is characteristic of PS regions, rather than core regions, or non-pathogen associated LS regions of the Foc genome.…”

“…Non-canonical Helitrons appear to be a key feature of Fo pathogenicity chromosomes 29 genes were identified as helitron/helicase-like transposable elements (IPR025476, PF14214) in the Foc genome, with one on an unplaced contig (contig 33) and the rest located on PS regions. Furthermore, these transposable elements showed evidence of expression in planta , with six of the 35 genes having a mean fpkm > 5.…”