Genome-wide analysis of parasitic fitness traits in a non-model tree pathogen

Figures & data

Fig. 1 (Colour online) Symptoms of Dutch elm disease (DED): (A) extensive crown dieback in a mature American elm (Ulmus americana) naturally infected by DED; note the healthy U. americana individual in the background; (B) close-up of external symptoms developing within 2 weeks on a U. americana sapling inoculated with Ophiostoma novo-ulmi under greenhouse conditions; (C) typical internal symptoms characterized by brown streaks in the xylem of a DED-infected U. americana individual. Streaks result from the oxidation of phenolics produced in response to infection (photo courtesy of G. Bussières, Université Laval).

Table 1. Current nomenclature of the Dutch elm disease fungi.

Name reference	Remarks	Reference
Ophiostoma ulmi (Buisman) Nannf.	The species responsible for the first pandemic of DED. Originally identified as Graphium ulmi Schwarz (anamorph) and Ceratostomella ulmi Buisman (teleomorph). Commonly referred to as the non-aggressive strain of Ceratocystis ulmi (Buisman) C. Moreau in the literature of the 1970s–1980s	Schwarz (1922) Buisman (1932) de Hoog and Scheffer (1984)
Ophiostoma novo-ulmi Brasier	The species responsible for the second, ongoing pandemic of DED. More virulent and fit than O. ulmi which it has rapidly replaced in most regions where DED occurs. Commonly referred to as the aggressive strain of C. ulmi in the literature of the 1970s–1980s. Two subspecies, novo-ulmi and americana, are recognized in O. novo-ulmi	Brasier (1991) Brasier and Kirk (2001)
Ophiostoma himal-ulmi Brasier & MD Mehrotra	This species is endemic to the Himalayas where it is found as an endophyte on symptomless elms. It is, however, moderately to highly virulent towards European elm species such as Ulmus procera	Brasier and Mehrotra (1995)

Fig. 2 (Colour online) Summary of the effect of various physical and chemical factors on the yeast-mycelium transition in the Dutch elm disease fungi (photos of yeast-like spores and mycelium courtesy of M. Aoun and K.V. Plourde, Université Laval). Arrows indicate the effect of a given stimulus. Initial cell density can have opposite effects: inoculation with a low yeast cell density stimulates mycelial growth, whereas a high concentration inoculum favours yeast growth.

Table 2. Summary of genome statistics for Dutch elm disease pathogens and two other Ophiostomatales.

	Ophiostoma novo-ulmi H327	Ophiostoma ulmi W9	Ophiostoma piceae UAMH-11346	Grosmannia clavigera kw1407
Lifestyle	Pathogen	Pathogen	Saprobe	Pathogen
Genome size (Mb)	31.8	31.5	32.8	29.8
Number of scaffolds	8	ND*	45	7
%GC Genome	50.1	50.0	52.8	53.4
Protein-coding genes	8 640	8 639	8 884	8 314
%Genome coding for genes	45.3	45.0	46.0	45.8
Gene density	1 per 3.7 kb	1 per 3.6 kb	1 per 3.7 kb	1 per 3.5 kb
Mean gene length (bp)	1 786	1 854	1 401	1 641
Mean number of introns/gene	1.77	1.14	NA	1.86

Statistics were compiled from the original genome publications. For O. novo-ulmi, Forgetta et al. (2013) and Comeau et al. (2015); for O. ulmi, Khoshraftar et al. (2013); for O. piceae, Haridas et al. (2013); and for G. clavigera, DiGuistini et al. (2011).

*The O. ulmi W9 genome assembly consists of 3415 contigs. The high number of scaffolds (n = 45) in the O. piceae genome reflects the state of the assembly rather than the actual number of chromosomes of the strain that was chosen for sequencing.

NA: data not available.

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