Table 1.

Differences between the genome reorganization processes among ciliates

	Paramecium tetraurelia	Tetrahymena thermophila	Oxytricha trifallax
MIC chromosomes	?	5 [37]	?
MAC chromosomes	188 [39, 40]	225 [38]	15,600 [43]
Nanochromosomes	No	No	Yes [43]
Unscrambling	No	Noa	Yes [178]
IES percentage	30% [48]	30% [179]	90% [31]
IES location	Genic and intergenic regions [48]	Intergenic Regions [90]	Genic and intergenic regions [180]
Small RNA source	MDS and IES [25, 81]	Biased towards IES [111]	MDS [83]
Small RNA target	IES [81]	IES [80]	MDS [82, 83]
DNA methylation	6 mA (P. aurelia) [132]	6 mA [131]	5mC, 6 mA [127, 135]

^aOne locus showing unscrambling [181]