Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2017 Sep 18;18(1):735.
doi: 10.1186/s12864-017-4116-5.

Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Balázs Brankovics  1   2 , Peter van Dam  3 , Martijn Rep  3 , G Sybren de Hoog  4   5 , Theo A J van der Lee  6 , Cees Waalwijk  6 , Anne D van Diepeningen  4   6
Affiliations

Mitochondrial genomes reveal recombination in the presumed asexual Fusarium oxysporum species complex

Balázs Brankovics et al. BMC Genomics. .

Abstract

Background: The Fusarium oxysporum species complex (FOSC) contains several phylogenetic lineages. Phylogenetic studies identified two to three major clades within the FOSC. The mitochondrial sequences are highly informative phylogenetic markers, but have been mostly neglected due to technical difficulties.

Results: A total of 61 complete mitogenomes of FOSC strains were de novo assembled and annotated. Length variations and intron patterns support the separation of three phylogenetic species. The variable region of the mitogenome that is typical for the genus Fusarium shows two new variants in the FOSC. The variant typical for Fusarium is found in members of all three clades, while variant 2 is found in clades 2 and 3 and variant 3 only in clade 2. The extended set of loci analyzed using a new implementation of the genealogical concordance species recognition method support the identification of three phylogenetic species within the FOSC. Comparative analysis of the mitogenomes in the FOSC revealed ongoing mitochondrial recombination within, but not between phylogenetic species.

Conclusions: The recombination indicates the presence of a parasexual cycle in F. oxysporum. The obstacles hindering the usage of the mitogenomes are resolved by using next generation sequencing and selective genome assemblers, such as GRAbB. Complete mitogenome sequences offer a stable basis and reference point for phylogenetic and population genetic studies.

Keywords: Comparative genomics; Mitochondrial genome; Mitochondrial recombination; Phylogenomics.

PubMed Disclaimer

Conflict of interest statement

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Publisher’s Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Mitochondrial genome of Fusarium oxysporum f. sp. cubense race 4 (strain B2; LT571433). Green blocks: tRNA coding genes, blue arrows: genes, yellow arrows: protein coding sequences, red arrows: rDNA coding sequence, purple arrows: intron encoded homing endonuclease genes, gray segment: large variable (LV) region with orf2229 (LV-uORF)
Fig. 2
Fig. 2
Genealogical concordance phylogenetic species recognition based on the 10 loci data set. The 10 loci used in the analysis were: act, tub2, cal, tef1a, tef3, rpl10a, rpb2, top1, rDNA repeat and the conserved part of the mitogenome. Only clades that were highly supported (BPP ≥0.95) in at least two single locus phylogenies were included in the analysis. The three clades within the FOSC were recognized as phylogenetic species and shown in the tree. The support values indicate how many single locus phylogenies supported the given clade with BPP ≥0.95 out of the 10 loci
Fig. 3
Fig. 3
Mitochondrial genome of Fusarium oxysporum f. sp. cumini strain F11. Green blocks: tRNA coding genes, blue arrows: genes, yellow arrows: protein coding sequences, red arrows: rDNA coding sequence, purple arrows: intron encoded homing endonuclease genes, gray segment: large variable (LV) region with orf2285 (LV-uORF)
Fig. 4
Fig. 4
The three variants of the large variable region. a Variant 1 represented by F. oxysporum strain Fon015, b variant 2 represented by F. oxysporum strain FOSC3-a and c variant 3 represented by F. oxysporum strain NRRL37622. Green blocks: tRNA coding genes, blue arrows: ORFs, yellow arrows: ORFs that are not present in all representatives of the given variant
Fig. 5
Fig. 5
Tanglegram of the trees based on a the large variable region variant 2, b the conserved part of the mitogenome and c the variant 1 of the LV region, respectively. Clades with high Bayesian posterior probability (BPP) support are displayed with thicker branches. The support values are BPP values. The three phylogenetic clades identified within the FOSC are highlighted in different shades of gray. The strains that contain variant 3 are highlighted by blue boxes
See this image and copyright information in PMC

References

    1. Baayen RP, O’Donnell K, Bonants PJM, Cigelnik E, Kroon LPNM, Roebroeck EJA, Waalwijk C. Gene genealogies and AFLP analyses in the Fusarium oxysporum complex identify monophyletic and nonmonophyletic formae speciales causing wilt and rot disease. Phytopathology. 2000;90(8):891–900. doi: 10.1094/PHYTO.2000.90.8.891. - DOI - PubMed
    1. Michielse CB, Rep M. Pathogen profile update: Fusarium oxysporum. Mol Plant Pathol. 2009;10(3):311–24. doi: 10.1111/j.1364-3703.2009.00538.x. - DOI - PMC - PubMed
    1. O’Donnell K, Sutton DA, Wiederhold N, Robert VARG, Crous PW, Geiser DM. Veterinary Fusarioses within the United States. J Clin Microbiol (Epub ahead of print). 2016. doi:10.1128/JCM.01607-16. - DOI - PMC - PubMed
    1. van Diepeningen AD, Al-Hatmi AMS, Brankovics B, de Hoog GS. Taxonomy and Clinical Spectra of Fusarium Species: Where Do We Stand in 2014? Curr Clin Microbiol Rep. 2014;1(1-2):10–18. doi: 10.1007/s40588-014-0003-x. - DOI
    1. Fuchs JG, Moënne-Loccoz Y, Défago G. Nonpathogenic Fusarium oxysporum strain Fo47 induces resistance to Fusarium wilt in tomato, Plant Dis. 1997;81(5):492–6. doi: 10.1094/PDIS.1997.81.5.492. - DOI - PubMed

LinkOut - more resources