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MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

Sarah M Schmidt1, Petra M Houterman1, Ines Schreiver14, Lisong Ma1, Stefan Amyotte2, Biju Chellappan1, Sjef Boeren3, Frank L W Takken1 and Martijn Rep1*

Author Affiliations

1 Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, the Netherlands

2 Department of Plant Pathology, University of Kentucky, 201F Plant Science Building, 1405 Veterans Drive, 40546-0312, Lexington, KY, USA

3 Laboratory for Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA, Wageningen, the Netherlands

4 Current address: Fachgebiet Medizinische Biotechnologie, Institut für Biotechnologie, Technische Universität Berlin, Gustav-Meyer-Allee 25, Berlin, Germany

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BMC Genomics 2013, 14:119  doi:10.1186/1471-2164-14-119

Published: 22 February 2013

Additional files

Additional file 1:

Detailed annotation of the Fol4287 pathogenicity chromosome.

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Additional file 2:

A putative secondary metabolite gene cluster of Fol is expressed during tomato infection. Roots of ten days old susceptible (without resistance genes) tomato seedlings were inoculated with conidiospores of Fol004. Roots were harvested 8 dpi (days post inoculation). From the collected roots RNA was extracted and (RT-) PCR was performed to detect transcripts of the indicated genes. Numbers represent FOXG numbers of the Fol4287 reference genome. Marker sizes are indicated on the right. C: cDNA, G: genomic DNA.

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Additional file 3:

Significance of the association between the TCGGCA element and upstream regions of effector genes.

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Additional file 4:

Complex repeat structure in SIX8, SIX8b and SIX14 upstream regions. The most upstream sequence shared between the SIX8 and SIX8b loci (dark grey, blue and green highlighted) is more similar between SIX8 and SIX8b loci than the coding sequences and the immediate upstream sequences (light grey). The SIX8b upstream region is the most complex. Compared to that of SIX8, there are: (a) a mimp4 insertion, (b) a Han insertion, (c) an inversion and duplication (indicated with < signs), (d) a mimp1 insertion, (e) a partial mimp3 and (f) an extra sequence that includes an mFot5. A total of 9 mimp-related inverted repeats are present, of which two are interrupted by a TE. Part of the SIX14 upstream region is almost identical to a part of the SIX8b upstream region (green/blue highlighted including the mimp4) – except that the Han insertion is missing in the SIX14 locus. In both cases, a mimp1 is present immediately downstream of this region but, though similar in sequence, these mimp1 insertions appear to be independent. Blue capital letters: effector ORF (introns in lower case); Green capital letters: mimp; Dark red capital letters: mFot5; Orange capital letters: Han; Gray highlight: shared between SIX8 and SIX8b loci only; Light gray highlight: similarity between SIX8 and SIX8b upstream (leader/promoter) sequences; Blue highlight: mimp-like inverted repeat sequence, present one or more times in SIX8, SIX8b and SIX14 loci (numbers of likely orthologous sequences correspond between the three loci – note that mimp-IR1 does not conform to the consensus sequence for mimp inverted repeats); Green and dark green highlight: sequences present one or more times in SIX8, SIX8b and SIX14 loci; Yellow highlight: TGCCGA motif; Bold: target site duplications associated with TE insertions.

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Additional file 5:

Newly identified TEs of Fol.

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Additional file 6:

Primers used in this study.

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