Drifter, a novel, low copy hAT-like transposon in Fusarium oxysporum is activated during starvation

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Abstract

The facultative pathogenic fungus Fusarium oxysporum is known to harbour many different transposable and/or repetitive elements. We have identified Drifter, a novel DNA transposon of the hAT family in F. oxysporum. It was found adjoining SIX1-H, a truncated homolog of the SIX1 avirulence gene in F. oxysporum f. sp. lycopersici. Absence of a target site duplication as well as the 5′ part of SIX1-H suggests that transposition of Drifter into the ancestor of SIX1-H was followed by loss of a chromosomal segment through recombination between Drifters. F. oxysporum isolates belonging to various formae speciales harbour between 0 and 5 full-length copies of Drifter and/or one or more copies with an internal deletion. Transcription of Drifter is activated during starvation for carbon or nitrogen.

Introduction

Fusarium oxysporum, an asexual, plant-pathogenic fungus, has proven to be a rich source of transposable elements of all major families (Daboussi and Capy, 2003, Daboussi and Langin, 1994). This richness in transposable and/or repetitive elements may be a consequence of the asexual lifestyle of F. oxysporum, which precludes elimination of repetitive elements through meiotic processes like repeat-induced point mutation (RIP) (Daboussi, 1997). At the same time, in the absence of sexual recombination, transposons are probably the main source of the generation of genetic variation. This has a special relevance for F. oxysporum because it is a species complex with a large number of host-specific forms (formae speciales), that can usually be further subdivided into physiological races that are defined by cultivar (R-gene) specific virulence patterns (Armstrong and Armstrong, 1981, Gordon and Martyn, 1997). Many formae speciales are not monophyletic (Baayen et al., 2000, O’Donnell et al., 1998) and races within formae speciales can also have polyphyletic origin (Mes et al., 1994, Mes et al., 1999), indicating that host- and cultivar specificity can arise within different clonal lines. To understand this evolutionary process, it is important to explore the underlying mechanisms of genome dynamics. This exploration should include identification of transposable elements and their association with potential host-form or race specific genes, as well as analysis of transposon activity.

We describe here a novel member of the hAT family of DNA transposons in F. oxysporum. It was found adjoining an incomplete avirulence gene homolog, that it had apparently disrupted. It is present in low copy numbers in several isolates of F. oxysporum and is transcribed during starvation in culture.

Section snippets

Fungal isolates

Isolates of F. oxysporum used in this study are listed in Table 1.

BAC identification, isolation, and subcloning

A BAC clone containing the SIX1-H locus was isolated using SIX1-specific primers as described earlier (Rep et al., 2004). From this BAC clone, a 5.3 kb BamHI fragment containing all sequences homologous to SIX1 was subcloned in pBluescript KS+ (Stratagene) and sequenced (GenBank Accession No. AY751529).

CHEF gel and southern analysis

Genomic DNA of F. oxysporum was isolated according to Raeder and Broda (Raeder and Broda, 1985). The CHEF blots with chromosomes

A copy of Drifter adjoins SIX1-H, a truncated homolog of the SIX1 avirulence gene

The SIX1 gene of F. oxysporum f. sp. lycopersici (Fol) encodes a small, cysteine-rich protein that is secreted during colonization of tomato xylem vessels. It is present in all 45 Fol isolates of a world-wide collection but not in several isolates from other formae speciales (Rep et al., 2005, Rep et al., 2004). We previously reported that at least four Fol isolates (but not the isolates from other formae speciales) also contain SIX-H, a sequence with high similarity to SIX1 based on

Discussion

We have identified Drifter, a new transposon of the hAT family of class II (DNA) transposons in F. oxysporum. The hAT family is distributed over all eukaryotic kingdoms (Kempken and Windhofer, 2001) and widespread among filamentous fungi (Daboussi and Capy, 2003). In fungi, most class II transposons exist in 5–20 copies per genome (Gómez-Gómez et al., 1999, Hua-Van et al., 2000, Kempken and Kuck, 1996, Linder-Basso et al., 2001; Okuda et al., 1998, Panaccione et al., 1996), sometimes in as many

Acknowledgments

We thank Hedwich Teunissen for use of her CHEF blots, and Ringo van Wijk and Michiel Meijer for assistance. The research of Dr. M. Rep has been made possible by a fellowship of the Royal Netherlands Academy of Arts and Sciences.

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