Table 2.

Mean number (per million reads) of paired reads where one read maps to a LTR-RE family and the other to a gene sequence. For each family, the lineage and the superfamily are reported. Statistical significance of differences between cultivars and wild accessions was assessed by PERMANOVA (*** p < 0.001; * p < 0.05).

Superfamily	Lineage	Family	Mean nr. of Gene-RE Mapping Paired Reads per Million Reads
			Cultivars	Wild accessions	PERMANOVA
Gypsy	Chromovirus	CL5	2.95	4.05
Gypsy	Chromovirus	CL18	1.61	1.64
Gypsy	Chromovirus	CL25	4.37	6.53	*
Gypsy	Chromovirus	CL32	1.07	0.80
Gypsy	Chromovirus	CL35	0.80	0.90
Gypsy	Chromovirus	CL47	0.84	1.57	***
Gypsy	Chromovirus	CL57	0.73	1.04	*
Gypsy	Chromovirus	CL64	0.47	0.65
Gypsy	Chromovirus	CL88	0.47	0.81	*
Gypsy	Chromovirus	CL94	0.25	0.32
Gypsy	Chromovirus	CL96	0.76	0.82
Gypsy	Chromovirus	CL102	0.14	0.18
Gypsy	Chromovirus	CL138	0.17	0.14
Gypsy	Chromovirus	CL193	0.03	0.05
Gypsy	Chromovirus	CL232	0.03	0.01
Gypsy	Athila	CL29	1.16	1.34
Gypsy	Athila	CL43	1.31	1.90	*
Gypsy	Athila	CL87	0.42	0.64	*
Mean Gypsy			0.98	1.38
Copia	AleII	CL48	1.08	1.08
Copia	Maximus/SIRE	CL115	0.12	0.21
Copia	Angela	CL100	0.27	0.29
Copia	TAR/Tork	CL255	0.18	0.17
Mean Copia			0.41	0.44