Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.)

Table 1 Statistics of small RNA sequence reads

	All reads (%)					Distinct reads (%)
Library	Leaf	-3 DPA	0 DPA	+3 DPA	Total	Leaf	-3 DPA	0 DPA	+3 DPA	Total
Matching CGI9 (EST assembly)	51.60	31.83	9.48	10.58	25.92	13.91	12.12	4.52	3.97	5.54
Matching G. raimondii (genomic trace reads)	61.25	42.67	24.99	24.57	38.42	26.83	23.47	19.26	17.56	18.66
Matching miRNAs	0.80	1.82	0.82	1.19	1.06	0.09	0.13	0.05	0.06	0.05
Other cellular RNAs	57.88	39.10	8.21	9.39	27.96	17.87	14.92	3.55	3.03	5.95
rRNA	53.83	29.56	6.37	7.03	24.47	16.25	11.42	2.82	2.20	4.88
tRNA	3.09	7.97	1.48	2.00	2.82	0.90	2.54	0.45	0.58	0.68
snoRNA	0.02	0.31	0.01	0.02	0.05	0.03	0.14	0.01	0.02	0.02
snRNA	0.02	0.04	0.01	0.01	0.01	0.03	0.06	0.02	0.01	0.02
Mitochondria	0.02	0.17	0.04	0.04	0.04	0.05	0.27	0.05	0.04	0.06
Chloroplast	0.91	1.05	0.29	0.30	0.57	0.62	0.49	0.20	0.18	0.29
Total raw reads	1,359,250	372,521	639,801	1,732,919	4,104,491	526,304	191,591	505,504	1,180,742	2,169,534

ISSN: 1474-760X