Table 1 Summary of unique the sequences (Seq) and reads (Reads) of sncRNAs mapping to genetic mitochondrial features, matching with miRNA and piRNA databases, differentiating those that map exclusively to the nuclear genome (NU), exclusively to the mitochondrial genome (MT), or to both genomes (NUMT). Note that (*) indicates other sncRNAs that, mapping to mitochondrial sequences, do not only correspond to miRNAs or piRNAs.

Samples	Total reads (> 10 CPM)		Mitochondrial Small-RNAs		miRNAs						piRNAs
					NU		Mitochondrial				NU		Mitochondrial
					NU		NUMTs		MT		NU		NUMTs		MT
	Seq	Reads	Seq	Reads	Seq	Reads	Seq	Reads	Seq	Reads	Seq	Reads	Seq	Reads	Seq	Reads
PGC11F	8500	6,888,195	68	35,377	1514	1,838,954	1	730	0	0	5423	4,182,089	43	27,777	12	4479
PGC11M	8727	4,862,017	129	45,192	876	591,746	2	316	0	0	5356	2,782,782	76	30,371	20	7917
PGC12F	9297	5,926,773	52	18,489	454	262,577	0	0	0	0	5614	3,174,696	29	12,202	12	3859
PGC12M	9270	5,178,085	77	29,524	506	294,223	1	147	0	0	5538	2,760,811	45	22,131	14	4054
PGC13F	8901	5,058,940	100	42,942	892	627,937	0	0	0	0	5665	2,929,960	51	27,600	20	8828
PGC13M	8077	5,316,411	135	46,442	680	518,919	1	191	0	0	4769	2,936,741	74	27,668	23	10,728
SC11F	7124	5,700,359	79	32,770	2374	2,867,435	1	569	0	0	4830	4,039,697	48	24,720	13	3911
SC11M	8137	4,405,948	99	29,865	1246	892,796	1	267	0	0	5251	2,719,611	54	18,142	18	7246
SC12F	8033	5,928,611	56	21,317	2064	2,554,390	1	435	0	0	5101	3,717,637	35	16,990	8	1760
SC12M	8051	5,619,407	81	32,213	1922	2,233,411	1	499	0	0	5200	3,529,894	42	22,920	17	5229
SC13F	8093	6,712,405	138	64,297	2055	2,907,810	1	766	0	0	5246	4,456,638	79	46,651	23	8624
SC13M	7344	4,535,372	144	68,467	2117	1,722,383	1	438	0	0	4561	2,838,307	83	49,195	20	10,350
Average	8296	5,511,044	97	38,908	1392	1,442,715	1	363	0	0	5213	3,339,072	55	27,197	17	6415
Prop. of total reads:		100%		0.71%
Proportion related to mito-small-RNAs				100%	*			0.9%		0.0%				69.9%		16.5%

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