Table 2. Categorization and abundance of sRNA reads from CHS, CHR and ZZ.

Data Processing/Strain	Reads all			Reads unique
	CHS	CHR	ZZ	CHS	CHR	ZZ
Raw reads	45297627	47566639	40906561	5066237	5421221	4643140
Clean reads	31952995	33561726	29468332	4076241	4431220	3484682
Mapped to P. xylostella miRNAs reported by Etebari et al. or Liang et al. in 201322	1400099 (4.38%)	1448802 (4.31%)	621992 (2.20%)	1595 (0.04%)	1602 (0.03%)	1350 (0.04%)
Mapped to other RNAs (RFam: rRNA, tRNA, snRNA, snoRNA and others)	7781970 (24.35%)	7883299 (23.49%)	7968865 (27.04%)	314018 (7.70%)	313629 (7.08%)	311243 (8.93%)
Mapped to known P. xylostella genes	1427410 (4.47%)	1199346 (3.57%)	552586 (1.88%)	483528 (11.86%)	434144 (9.80%)	222222 (6.38%)
Mapped to Repbase	542288 (1.70%)	504062 (1.50%)	501382 (1.70%)	23230 (0.57%)	20743 (0.47%)	20311 (0.58%)
Unannotated Sequences	20801228 (65.10%)	22526217 (67.12%)	19823507 (67.27%)	3253872 (79.83%)	3661102 (82.62%)	2929556 (84.07%)