Table 3.

Detection and identification of viroids by NGS.

Viroid	Target	Reference
Potato spindle tuber viroid	sRNAs	Diermann et al., 2010; Di Serio et al., 2010; Wang et al., 2011; Li et al., 2012; Adkar-Purushothama et al., 2015
Citrus exocortis viroid	Total RNA	Poojari et al., 2013
Apple dimple fruit viroid	sRNAs	Chiumenti et al., 2014
Peach latent mosaic viroid	sRNAs	Di Serio et al., 2009; Bolduc et al., 2010; Glouzon et al., 2014
Hop stunt viroid	sRNAs	Navarro et al., 2009; Martinez et al., 2010; Alabi et al., 2012; Giampetruzzi et al., 2012; Seguin et al., 2014; Pirovano et al., 2015
	Total RNA	Poojari et al., 2013
Citrus bark cracking viroid	Total RNA, sRNAs	Jakse et al., 2015
Grapevine yellow speckle viroid 1	sRNAs	Navarro et al., 2009; Martinez et al., 2010; Giampetruzzi et al., 2012; Seguin et al., 2014
	Total RNA	Poojari et al., 2013; Jo et al., 2015
Grapevine yellow speckle viroid 2	sRNAs	Alabi et al., 2012
Grapevine latent viroid	Total RNA	Zhang et al., 2014
Persimmon viroid 2	dsRNA	Ito et al., 2013
Pathogenic circular RNAs	sRNA	Wu et al., 2012