pubmed.ncbi.nlm.nih.gov

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach - PubMed

Multi-locus tree and species tree approaches toward resolving a complex clade of downy mildews (Straminipila, Oomycota), including pathogens of beet and spinach

Young-Joon Choi et al. Mol Phylogenet Evol. 2015 May.

Abstract

Accurate species determination of plant pathogens is a prerequisite for their control and quarantine, and further for assessing their potential threat to crops. The family Peronosporaceae (Straminipila; Oomycota) consists of obligate biotrophic pathogens that cause downy mildew disease on angiosperms, including a large number of cultivated plants. In the largest downy mildew genus Peronospora, a phylogenetically complex clade includes the economically important downy mildew pathogens of spinach and beet, as well as the type species of the genus Peronospora. To resolve this complex clade at the species level and to infer evolutionary relationships among them, we used multi-locus phylogenetic analysis and species tree estimation. Both approaches discriminated all nine currently accepted species and revealed four previously unrecognized lineages, which are specific to a host genus or species. This is in line with a narrow species concept, i.e. that a downy mildew species is associated with only a particular host plant genus or species. Instead of applying the dubious name Peronospora farinosa, which has been proposed for formal rejection, our results provide strong evidence that Peronospora schachtii is an independent species from lineages on Atriplex and apparently occurs exclusively on Beta vulgaris. The members of the clade investigated, the Peronospora rumicis clade, associate with three different host plant families, Amaranthaceae, Caryophyllaceae, and Polygonaceae, suggesting that they may have speciated following at least two recent inter-family host shifts, rather than contemporary cospeciation with the host plants.

Keywords: Cospeciation; Host shift; Multi-locus phylogeny; Oomycetes; Peronospora farinosa; Species tree.

Copyright © 2015 Elsevier Inc. All rights reserved.

PubMed Disclaimer

Figures

Fig. 1
Fig. 1

Phylogenetic tree inferred from Maximum Likelihood analysis of a concatenated alignment (4378 nucleotides with 123 parsimony informative sites) of five mitochondrial (cox2, coxS, cox1, nad1, rps10) and two nuclear loci (ITS and hsp90). Support values (ML BS/ME BS/ MP BS/MCMC PP) higher than 60% are given above or below the branches. The scale bar equals the number of nucleotide substitutions per site. Specimens originating from different host families are marked with black (Amaranthaceae), pink (Polygonaceae), and green (Caryophyllaceae) bars. ML: Maximum Likelihood, ME: Minimum Evolution, MP: Maximum Parsimony, MCMC: Bayesian inference, BS: Bootstrap support, PP: Posterior Probabilities. (For interpretation of thereferences to color in this figure legend, the reader is referred to the web version of this article.)

Fig. 2
Fig. 2

Species tree estimation from five mitochondrial (cox2, coxS, cox1, nad1, rps10) and two nuclear loci (ITS and hsp90) using *BEAST. (a) Maximum clade credibility tree visualized by FigTree. Bars correspond to the 95% highest posterior density range, and posterior probabilities higher than 0.60 are shown above branches. (b) Cloudogram of all trees of the MCMC visualized by DensiTree (Bouckaert, 2010). Each possible topology is shown in green with branch lengths averaged among all trees showing that particular topology. Four alternative interpretations are shown in black for the consensus tree, blue for the most frequently occurring topology, red for second, and yellow for third most frequently occurring topology. Higher levels of uncertainty are represented by lower densities of the lines. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Similar articles

Cited by

References

    1. Ainsworth GC. Ainsworth & Bisby’s Dictionary of the Fungi. CAB International; Wallingford: 2008.
    1. Antonovics J, Hood M, Partain J. The ecology and genetics of a host shift: Microbotryum as a model system. Am Nat. 2002;160:S40–S53. - PubMed
    1. Bachofer M. Molekularbiologische Populationsstudien an Plasmopara halstedii, dem Falschen Mehltau der Sonnenblume. University of Hohenheim; Stuttgart: 2004.
    1. Belbahri L, Calmin G, Pawlowski J, Lefort F. Phylogenetic analysis and real time PCR detection of a presumably undescribed Peronospora species on sweet basil and sage. Mycol Res. 2005;109:1276–1287. - PubMed
    1. Berlese AN, De Toni JB. In: Peronosporaceae. Saccardo PA, editor. Sylloge Fungorum; Padua: 1888. pp. 233–264.

Publication types

MeSH terms

Substances

LinkOut - more resources