The Distribution of Miniature Impala Elements and SIX Genes in the Fusarium Genus is Suggestive of Horizontal Gene Transfer

Peter van Dam,Martijn Rep

doi:10.1007/s00239-017-9801-0

Abstract

The mimp family of miniature inverted-repeat transposable elements was previously found only in genomes of Fusarium oxysporum and is contextually associated with virulence genes in this species. Through extensive comparative analysis of 83 F. oxysporum and 52 other Fusarium genomes, we uncovered the distribution of different mimp families throughout the genus. We show that (i) mimps are not exclusive to F. oxysporum; (ii) pathogenic isolates generally possess more mimps than non-pathogenic strains and (iii) two isolates of F. hostae and one F. proliferatum isolate display evidence for horizontal transfer of genetic material to or from F. oxysporum. Multiple instances of mimp elements identical to F. oxysporum mimps were encountered in the genomes of these isolates. Moreover, homologs of effector genes (SIX1, 2, 6, 7, 11 and FomAVR2) were discovered here, several with very high (97–100%) pairwise nucleotide sequence identity scores. These three strains were isolated from infected flower bulbs (Hyacinthus and Lilium spp.). Their ancestors may thus have lived in close proximity to pathogenic strains of F. oxysporum f. sp. hyacinthi and f. sp. lilii. The Fo f. sp. lycopersici SIX2 effector gene was found to be widely distributed (15/18 isolates) throughout the F. fujikuroi species complex, exhibiting a predominantly vertical inheritance pattern. These findings shed light on the potential evolutionary mechanism underlying plant-pathogenicity in Fusarium and show that interspecies horizontal gene transfer may have occurred.

Highlights

Transposable elements (TEs) are DNA sequences that can duplicate or move from one site to another within a genome
Class II TEs on the other hand, transpose through a ‘‘cut-and-paste’’ mechanism. This latter class of TEs is flanked by Terminal Inverted Repeats (TIRs) that facilitate the recognition for DNA excision
Based on the described inverted repeats in Bergemann et al (2008), we extracted the sequences of mimps from all currently available Fusarium genome assemblies

Summary

Introduction

Transposable elements (TEs) are DNA sequences that can duplicate or move from one site to another within a genome. Class I transposons ( called retrotransposons) transpose by transcription into an RNA intermediate and reverse transcription into cDNA before insertion into a new site. Class II TEs (or DNA transposons) on the other hand, transpose through a ‘‘cut-and-paste’’ mechanism. This latter class of TEs is flanked by Terminal Inverted Repeats (TIRs) that facilitate the recognition for DNA excision. Miniature inverted-repeat transposable elements (MITEs) are short [\500 base pairs (bp)] non-autonomous class II TEs (Bergemann et al 2008). Their structure resembles defective DNA transposons and they are thought to originate through the deletion of the transposase open reading frame (ORF) between the TIRs (Feschotte and Pritham 2007). Several studies have shown that MITEs can be mobilized by full-length class II TEs (Feschotte et al 2002; Dufresne et al 2007; Bergemann et al 2008)

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