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

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polyN

smaller_than_18nt

5'adapter_contaminants

insert_null

3'adapter_null

clean_reads

Pe

rce

nt

(%)

sr-Tubers20C sr-Tubers4C

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Not mapped

Mapping to genome

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Ⅰ Ⅱ Ⅲ Ⅳ Ⅴ Ⅵ Ⅶ Ⅷ Ⅸ Ⅹ Ⅺ Ⅻ0

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Chromosome

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Unique sRNAs Total sRNAs

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Tubers4C_specific

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sr-Tubers20C sr-Tubers4C

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miRNA

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a

b c

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Fig. S1

<80 80-120 120-160 160-200 200-240 >240

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-miR

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Minimal folding free enerage (-kcal mol-1)

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-miR

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Fig. S2

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ove

l006

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ove

l012

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ove

l021

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ove

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l036

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ove

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ove

l067

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l088

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-miR

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Fig. S3

deg-Tubers20C deg-Tubers4C

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Pe

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Unique sRNAs Total sRNAs

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(%)

Ⅰ Ⅱ Ⅲ Ⅳ Ⅴ Ⅵ Ⅶ Ⅷ Ⅸ Ⅹ Ⅺ Ⅻ0

5

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deg-Tubers20C deg-Tubers4C

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Mapping to genome

Pe

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deg-Tubers20C deg-Tubers4C

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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