Cotton Genomics and Genetics 2016, Vol.7, No.2, 1-23
7
Continuing Table 3
Contig ID
Small RNA sequence identified in this study
Length
MFE
*
GC(%)
#
Contig_15835
GAAGAGAUCACUUCUAUCUGU
21
-48.3
38
Contig_1094
GACACGAACACGUGUUGCUGCUCAACCACC
30
-100.8
57
Contig_8575
GUCACACACGGUCUAGACACACGCC
25
-68.6
60
Contig_19062
UCACAGGGAUCAAAAUUGGGA
21
-92.9
43
Contig_15122
UGGAAGGUUUGGAGGAGAUUGA
22
-63.7
46
Contig_9778
GUAAGGGAGAACCUAGAUUCAUUACCCAGC
30
-77.2
47
Contig_16528
GUAAGGGAGAUCUAGAUUCAUAA
23
-67.9
35
Contig_18252
UAUAACAAGGAAUGGAUGAUU
21
-69.0
29
Contig_18054
UAUGACCUACAAGCUUACCGGAG
23
-82.5
48
Contig_16564
GAACCCUUUGUUGGAGAGUCC
21
-67.4
52
Contig_15875
UUGCAGUCGCAGAACUCCGUACCUU
25
-84.2
52
Contig_13633
UGUGUGUUUCGCGCGUGGACGACGUAA
27
-77.7
56
Contig_17693
UUAUAGGUCUUUCAUUUAAAGU
22
-79.4
23
Contig_11693
UAUGACCUACAAGCUUACCGGAGA
24
-83.9
46
Contig_21397
UUGCAGUCGCAGAACUCCGUACCU
24
-84.2
54
Contig_18244
CAUUCCAGUGAUUUCCAGAGGC
22
-67.8
50
Contig_21146
AGUUCCUUCAAAUUCUUCAAC
21
-78.0
33
Contig_18155
AUUAAAGUAGUGUCCUGCAAACU
23
-47.8
35
Contig_15570
UGUGUUUCGCGCGUGGACGACG
22
-76.4
64
Contig_15717
GGCUGUGGUUGAUUCGGCAAGA
22
-78.5
55
Contig_20599
UGAAACAAACAUAUUUACAUUGUCGAUACA
30
-84.0
27
Contig_21324
UCACAUUUACUUGGCAAGUGAU
22
-75.4
36
Contig_20427
UGGCAAGUGAUUGUGCGCCACG
22
-72.3
59
Contig_21332
AACAUGGCGAAUAAUAUGAUGGAAAU
26
-93.7
31
Contig_18969
UCACAGGGAUCAAAAUUGGGA
21
-92.9
43
Contig_7495
UCCAGAAGAUACAUUAGCACCAUGGGAUAU
30
-117.0
40
Contig_5490
GGAAGUGGGGUGCGAGGAAAGAUCA
25
-68.1
56
Contig_17372
AUCAACCGUGUUACUCUGUCUAAUC
25
-63.6
40
Contig_15837
UUUCUAAAGCUCUAGAUAACGUUA
24
-71.9
29
Contig_16924
AGCUCGUUAUCGAGAAUUCAAUAUGUUGUGUC
32
-65.2
38
Contig_12125
UGAGGGUCCAAGACUGACCUCC
22
-94.4
59
Contig_20315
UCAGCGCGACCUGCCGACGUG
21
-114.3
71
Contig_4359
UGGACUUGGAUACGUUGAAGAAGUGG
26
-127.7
46
Contig_14297
GUAAGGGAGAUCCUAGAUUCA
21
-47.6
43
Contig_16284
UGGAUGGAAAACUCGCUCCUGG
22
-66.8
55
Note: * MFE: minimum folding energy identified through mFold;
#
GC content (%) found in Corresponding precursor sequence
identified from G. raimondii genome
Comparison of differentially expressed miRNAs between the small RNA libraries derived from KC3 under water
stress and Suvin under water stress revealed 36 novel miRNAs. All the miRNAs (except nine miRNAs) were
down regulated in drought susceptible Suvin under water stress. Among them, contig_18155 had shown highest
down regulation (33.688 fold) and contig_4359 had highest up regulation (11.054 fold) in Suvin-WS (Table 4).
Contig_16568 accumulated abundantly with more than 17 RPKM. Contig_16528, Contig_1094, Contig_15570
and Contig_5490 were also detected in relatively high levels with more than 10 RPKM in these two libraries.
Interestingly, the majority of the novel miRNAs was detected in more than 3.5 RPKM (Table 4).
