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Supplementary Figure Captions. Fig. S1 Overview of small RNA sequencing data - PowerPoint PPT Presentation
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Fig. S1 Overview of small RNA sequencing dataa Data cleaning of small RNA sequencing; b Mapping statics of small RNA; c Distribution of small RNA on each chromosome; d Summary of common and specific sequences between sr-Tubers4C and sr-Tubers20C; e small RNA annotation
Fig. S4 Overview of degradome sequencing dataa Data cleaning of degradome sequencing; b Length distribution of degradome sequences; c Mapping statics of degradome sequences; d Distribution of degradome sequences on each chromosome; e Summary of common and specific sequences between deg-Tubers4C and deg-Tubers20C; f Degradome sequences annotation
Fig. S2 Overview of known miRNAs expressed in potato tubersa Length distribution of mature miRNA sequences; b miRNA nucleotide bias at each position; c Distribution of pre-miRNAs minimal folding free energy; d Distribution of pre-miRNAs length
Fig. S3 Overview of novel miRNAs identified in potato tubersa Length distribution of mature miRNA sequences; b miRNA nucleotide bias at each position; c Number of miRNAs for each novel miRNA; d Distribution of pre-miRNAs minimal folding free energy; e Distribution of pre-miRNAs length
Supplementary Figure Captions
Fig. S5 Expression patterns of the cold-responsive miRNAs/miRNA*s and their targetsPotato tubers were stored at 4 °C and 20 °C, and sampled at 0 d (T0), 1 d, 2 d, 5 d, and 15 d. The expression patterns of miRNAs/miRNA*s were determined by stem-loop RT-qPCR and the expression patterns of targets were determined by RT-qPCR. The results were illustraited by MeV 4.8 software. The expression level of each miRNA/target at T0 was set as 0 for 10908-06 and ED25, respectively. The name or the accession number and the abbreviated annotation of the miRNAs/targets were shown on the right. The color scale for logarithm signal values is shown on the top
sr-Tubers20C sr-Tubers4C
0
10
20
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100
polyN
smaller_than_18nt
5'adapter_contaminants
insert_null
3'adapter_null
clean_reads
Pe
rce
nt
(%)
sr-Tubers20C sr-Tubers4C
0
10
20
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Not mapped
Mapping to genome
Pe
rce
nt
(%)
Ⅰ Ⅱ Ⅲ Ⅳ Ⅴ Ⅵ Ⅶ Ⅷ Ⅸ Ⅹ Ⅺ Ⅻ0
5
10
15
20
25
30 sr-Tubers20C
sr-Tubers4C
Chromosome
Pe
rce
nt
(%)
Unique sRNAs Total sRNAs
0
10
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Tubers4C_specific
Tubers20C_&_Tubers4C
Tubers20C_specific
Pe
rce
nt
(%)
sr-Tubers20C sr-Tubers4C
0
10
20
30
40
50
60
70
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100 tRNA
snoRNA
snRNA
repeat
rRNA
intron_sense
intron_antisense
exon_sense
exon_antisense
unann
miRNA
Pe
rce
nt
(%)
a
b c
d e
Fig. S1
<80 80-120 120-160 160-200 200-240 >240
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Length (nt)
Nu
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pre
-miR
NA
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20 21 22
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Length (nt)
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
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G
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U
Position (nt)N
um
be
r o
f m
iRN
As
<20 20-40 40-60 60-80 80-100 >100
0
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Minimal folding free enerage (-kcal mol-1)
Nu
mb
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pre
-miR
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c d
Fig. S2
20 21 22 23
0
5
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Length (nt)
Nu
mb
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of
miR
NA
s
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23
0
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G
C
A
U
Position (nt)
Nu
mb
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miR
NA
s
no
vel0
01n
ove
l006
no
vel0
10n
ove
l012
no
vel0
14n
ove
l021
no
vel0
23n
ove
l025
no
vel0
27n
ove
l036
no
vel0
41n
ove
l045
no
vel0
52n
ove
l055
no
vel0
58n
ove
l061
no
vel0
63n
ove
l067
no
vel0
74n
ove
l081
no
vel0
83n
ove
l088
no
vel0
91n
ove
l096
no
vel0
99n
ove
l104
no
vel1
11n
ove
l113
no
vel1
19n
ove
l122
0
1
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Novel miRNA
Nu
mb
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pre
-miR
NA
s
<20 20-40 40-60 60-80 80-100 >100
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Minimal folding free enerage (-kcal mol-1)
Nu
mb
er
of
pre
-miR
NA
s
<80 80-120 120-160 160-200 200-240 >240
0
5
10
15
20
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35
40
Length (nt)
Nu
mb
er
of
pre
-miR
NA
s
a b
c
d e
Fig. S3
deg-Tubers20C deg-Tubers4C
0
10
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80
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100 unann
tRNA
snoRNA
snRNA
rRNA
cDNA_antisense
cDNA_sense
Pe
rce
nt
(%)
Unique sRNAs Total sRNAs
0
10
20
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Tubers4C_specific
Tubers20C_&_Tubers4C
Tubers20C_specific
Pe
rce
nt
(%)
Ⅰ Ⅱ Ⅲ Ⅳ Ⅴ Ⅵ Ⅶ Ⅷ Ⅸ Ⅹ Ⅺ Ⅻ0
5
10
15
20
25
30 deg-Tubers20C
deg-Tubers4C
Chromosome
Pe
rce
nt
(%)
deg-Tubers20C deg-Tubers4C
0
10
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Not mapped
Mapping to genome
Pe
rce
nt
(%)
18 19 20 21 22 23 24 25 26 27 28 29 30
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10
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deg-Tubers4C
Length (nt)
Pe
rce
nt
(%)
deg-Tubers20C deg-Tubers4C
0
10
20
30
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50
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polyN
smaller_than_18nt
5'adapter_contaminants
insert_null
3'adapter_null
clean_reads
Pe
rce
nt
(%)
a b
c d
e f
Fig. S4
T0 1d 2d 5d 15d 1d 2d 5d 15d T0 1d 2d 5d 15d 1d 2d 5d 15d
20°C 4°C 20°C 4°C
10908-06 ED25
stu-miR166PGSC0003DMT400006735, HD-ZIP ⅢPGSC0003DMT400068037, HD-ZIP ⅢPGSC0003DMT400074932, HD-ZIP Ⅲ
stu-miR172PGSC0003DMT400031401, RAP2PGSC0003DMT400065313, AP2PGSC0003DMT400018466, DOLKPGSC0003DMT400042918, DCLPGSC0003DMT400054945, BEL29
stu-miR396PGSC0003DMT400034693, GADPGSC0003DMT400061170, SnRK2.4
stu-miR396a-3pPGSC0003DMT400001086, IRX7PGSC0003DMT400049314, PDR
stu-miR482f-5pPGSC0003DMT400069706, SUO
Fig. S5
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