Table 1.

Comparison of the transcriptomic effects of different beneficial and pathogenic fungi on their hosts

Beneficial/pathogen	Host	Fungus	Association type	Trend	DEGa	Analysis	Reference
Beneficial	Perennial ryegrass	Epichloë festucae	Endophyte	Down	38%	RNAseq	This study
Beneficial	Rice	Glomus intraradices	Mycorrhiza	Up	0.5%	Microarray	Güimil et al. (2005)
Beneficial	Tomato	Funneliformis mosseae	Mycorrhiza	Up	3%	RNAseq	Zouari et al. (2014)
Beneficial	California poplar	Laccaria bicolor	Mycorrhiza	Variable	0.8%	Microarray	Plett et al. (2015)
Beneficial	Grapevine	Trichoderma harzianum	Endophyte	Up	1%	Microarray	Perazzolli et al. (2012)
Beneficial	Arabidopsis thaliana	Trichoderma harzianum	Endophyte	Up	<1%	Microarray	Morán‐Diez et al. (2012)
Pathogen	Lettuce	Botrytis cinerea	Necrotroph	Up	20%	RNAseq	De Cremer et al. (2013)
Pathogen	Maize	Ustilago maydis	Biotroph	Up	22%	Microarray	Doehlemann et al. (2008)
Pathogen	Rice	Magnaporthe oryzae	Hemibiotroph	Up	13%	RNAseq	Kawahara et al. (2012)

^aDEG, the proportion of host differentially expressed genes.