擬南芥響應高鈣的miRNAs的篩選與鑒定

李 菲,石天龍,龔記熠,張習敏,湯曉辛,乙 引,*

(貴州師范大學生命科學學院a.西南喀斯特山地生物多樣性保護國家林業局重點實驗室；b.貴州省植物生理與發育調控重點實驗室，中國貴州 貴陽 550001)

Calcium-rich crops and vegetables can improve calcium intake in the human body.Scientists have tried to increase calcium levels in food crops through genetic engineering.However,advances in this area are limited because excessive intracellular calcium content has a negative effect on plant growth.Calcium is an essential macronutrient which plays key structural and signal transduction roles for plants[1～2].However,excessive calcium in cells will be precipitated with phosphate,inhibit seed germination,interfere with photosynthesis,reduce plant growth rate,and form withered spots on fruits[3～4].Calcium enters into the plant body from soil solution through the root system in the form of Ca2+,and is transported from the root to shoot by transpiration pull and soil Ca2+concentration[5].Once transported into the cell,calcium becomes relatively immobile[6].Therefore,soil Ca2+concentration and transpiration have a significant effect on calcium content in plants.When soil Ca2+concentration increases,many plants will reduce transpiration to limit Ca2+uptake[7].Therefore,improvement of the plant adaptability to high-calcium soils is a key step in producing highcalcium crops.

The karst area accounts for about 15% of the world’s farmland.Karst landforms are characterized by calcium-rich soils,which is a major limiting factor for crop yields in the area.However,this is a natural advantage for growing high-calcium crops.Understanding how plants absorb,transport,store and tolerate calcium in high-calcium soils will pave the way for generation and production of high-calcium crops in karst areas.Such efforts will ultimately benefit agriculture,ecosystems,and economic development in vast karst regions.

Gene expression can be regulated by miRNAs at the post-transcriptional level[8].Since this was first discovered,miRNAs have now been regarded as an important regulatory factor in plants.These regulatory factors usually target transcription factors and participate in the regulation of various physiological processes[9～10].Therefore,miRNAs can be regarded as the core of gene expression regulation network.Many studies have shown that miRNAs are responsive to biotic and abiotic stress in plants,such as cold[11～12],salt[13],heat[11],oxidative stress[14],and pathogen infection[15].miRNAs are transcribed from non-proteinencoded DNA sequences by RNA polymeraseⅡinto primary miRNAs(pri-miRNAs)with secondary hairpin structures[16].Dicer-like 1 (DCL1) of the RNaseⅢenzyme family plays a key role in pri-miRNA cleavage and mature miRNA formation.The primiRNA is first cleaved into the precursor miRNA(pre-miRNA) in the nucleus,and then the premiRNA is cleaved into miRNAs that function in the cytoplasm[17].Then miRNAs are loaded into the cytoplasmic RNA-induced silencing complex (RISC)and degrade mRNA targets.

So for,little research has been done on the mechanisms of plant responses to high calcium stress.The effects of high calcium stress on plant miRNAs expression have not yet been reported.In this study,high calcium-responsive Arabidopsis miRNAs were identified through high-throughput sequencing technology,and their target genes were analyzed.These experiments were expected to provide a theoretical basis for revealing the mechanisms of plants responding to high calcium stress and the roles of miRNAs in this process.

1 Materials and methods

1.1 Plant growth and high calcium treatment

The Arabidopsis thaliana Col-0 (ordered from Arashare,http：//www.arashare.cn)used in the experiment was cultured in plates containing 1/2 MS medium at 22 ℃.For high calcium treatment,the calcium chloride mother liquor was added to 1/2 MS medium to reach a final concentration of 40 mmol/L.The control treatment was 1/2 MS medium without calcium chloride.The main root length was measured using a vernier ruler.Three replicates of 10 seedlings from each treatment were used for analysis.The seedling roots were collected and immediately frozen in liquid nitrogen.They were then stored at -80 ℃for RNA extraction.

1.2 Total RNA extraction and small RNA iso原lation and sequencing

Total RNA was isolated from high calcium-treated and control A.thaliana roots using Trizol reagent (Shanghai Biotech Co.,Ltd.).Six small RNA libraries were constructed according to the method described by Lagos-Quintana et al[18].The method is summarized as follows：total RNA extracted was separated by 15% polyacrylamide gel electrophore sis(PAGE)to isolate small RNAs(between 18～30 nt).These small RNAs were ligated to 5＇ (5＇-GUUCAGAGUUCUACAGUCCGACGAUC-3＇) and 3＇ (5＇-UCGUAUGCCGUCUUCUGCUUGU -3＇) adapters.They were then reverse transcribed and amplified using polymerase chain reaction (PCR),and then sent to the Beijing Genomics Institute (BGI) for sequencing.

1.3 Bioinformatics analysis of miRNA sequencing data

Quality control was performed on 50 nt sequencing tags.Through quality control,the follow ing reads were removed：1)low quality reads;2)reads contaminated with 5＇ primers; 3) reads without 3＇primers; 4) reads without inserted tags; 5) poly(A)reads; 6) reads less than 18 nt.High-quality small RNA reads were mapped to the TAIR10 Arabidopsis genome using SOAP[19]to analyze their expression and distribution.

1.4 Differential expression analysis of miRNAs

In order to identify differentially expressed mi-RNAs,miRNAs expression was normalized accord ing to a standardized formula (actual miRNA counts/total number of clean reads)×1 000 000 to obtain expression data for transcript per million (TPM).And then,the fold change (FC) and false discovery rate (FDR) were calculated based on the normalized expression results.

1.5 Prediction and annotation of target genes for differentially expressed miRNAs

Using the plant miRNA target prediction online software psRNATarget[20](http：//plantgrn.noble.org/psRNATarget/) with default parameters,target genes for 12 differentially expressed miRNAs were predicted.GO(http：//www.Geneontology.org/)and KEGG(http：//www.Genome.jp/kegg/)were used for functional enrichment analysis of target genes.

1.6 RT-qPCR analysis of high calcium-responsive miRNAs and their predicted target genes

One Step PrimeScript miRNA cDNA Synthesis Kit (Takara,Japan) was used for reverse transcription reaction.RT-qPCR analysis was performed using SYBRH Premix Ex TaqII (Takara,Japan).The reverse primers and Uni-miR qPCR primers were included with the kit.Specific primers for miRNAs and their target genes are shown in Table 1.All sample analyses were performed using 3 biological replicates.△△Ct method was used to calculate the expression levels of miRNAs and their target genes[21].

2 Results

2.1 High-throughput sequencing results of small RNA libraries from Arabidopsis roots

In order to understand the effects of exogenous high calcium stress on the growth of A.thaliana,the growth of A.thaliana seedlings on normal 1/2 MS medium and 1/2 MS medium supplemented with 40 mmol/L CaCl2was compared.The main root length of Arabidopsis seedlings grown on 1/2 MS medium supplemented with 40 mmol/L CaCl2for 48 h was approximate 64% of that of Arabidopsis plantsgrown on normal 1/2 MS medium(Fig.1).The significant negative effect of high calcium stress on Arabidopsis growth prompted us to further explore the molecular mechanisms and the roles of miRNAs in this process.

Table 1 RT-qPCR primers for miRNAs and their target genes

Fig.1 Growth of A.thaliana seedlings under control and 40 mmol/L CaCl2 treatment

In order to identify miRNAs related to plant high calcium tolerance,six small RNA libraries were constructed for control and high calcium treated Arabidopsis root samples.High-throughput sequencing produced raw reads ranged from 38 914 168 to 51 612 516 from these libraries(Table 2).After quality control to remove low quality reads,small RNA libraries from control treatment obtained an average of 15 827 767 clean reads(three biological replicates with a minimum of 14 042 702 and a maximum of 17 756 079 clean reads),and libraries from high calcium treatment obtained an average of 14 856 068 clean reads (Table 2).Using Rfam database,these reads were mapped to the TAIR10 Arabidopsis thaliana reference genome.The total and unique mapped reads of the control and high-calcium treated samples were 8 904 023/3 105 740 and 8 096 307/3 021 139,respectively.These sequences were divided into tRNA,siRNA,miRNA,snoRNA,rRNA,and snRNA categories by further annotation and classification(Fig.2).Plentiful miRNAs existed in all six small RNA libraries,and they were used for further analysis.

2.2 Differential expression analysis of Ara原bidopsis miRNAs under high calcium stress

To identify differentially expressed miRNAs,the expression levels of miRNAs between control and high-calcium treated samples were compared.According to the sequencing results,miRNAs with|log2FC|＞0.585 and FDR＜0.05 between the control and high calcium treatments were selected as the significantly differentially expressed miRNAs.A total of 12 miRNAs were significantly differentially expressed between the control and the high calcium treatment (Fig.3,Table 3),of which 6 were up-regulated and 6 were down-regulated by high calcium treatment.

2.3 Target prediction and annotation of differ原entially expressed miRNAs

In general,plant miRNA targets have perfect or near-perfect complementary sites and can be identified using bioinformatics methods.In this study,the online programs psRNATarget (http：//plantgrn.noble.org/psRNATarget/),Gene Ontology(http：//www.Geneontology.org/),and KEGG(http：//www.Genome.jp/kegg/)were used to predict and annotate target genes.Twelve differentially expressed miRNAs were searched to find their potential target genes.There were 314 target transcripts in total,and the target gene accession numbers(Arabidopsis TAIR10)and the matched sequences to miRNAs are shown in Supplemental Table 1 (supplement data are available on-line).The number of miRNA target genes was ranged from 3 (ath-miR160b) to 38 (ath-miR159c).GO and KEGG enrichment analyses showed that transcription factors and functional proteins were included in these miRNA target genes,and their functions were diverse (including metabolism,cell differentiation,growth,and response to biotic and abiotic stress) (Fig.4).

Table 2 Statistical analysis of sequencing reads for the six small RNA libraries

Fig.2 Small RNA annotation and distribution of mRNAs in Arabidopsis small RNA libraries

Fig.3 miRNA expression profile and cluster analysis of the control and the high calcium treatment

Table 3 Differentially expressed miRNAs between control and high calcium treatment Arabidopsis roots

2.4 RT-qPCR analysis of high calcium-re原sponsive miRNAs and their target genes

Fig.4 GO and KEGG enrichment analyses of target genes for miRNAs in response to high calcium stress

In order to verify the data obtained from highthroughput sequencing,real-time quantitative PCR(RT-qPCR) analysis was performed to validate the expression pattern of 8 miRNAs and their predicted target genes in response to high calcium stress(Fig.5).The results showed that 6 out of the 8 miRNAs had the same relative expression trends as in the analysis with high-throughput sequencing.These includ-ed 4 downregulated miRNAs(ath-miR394b-5p,athmiR159c,ath-miR164a and ath-miR399c-5p) and 2 upregulated ones(ath-miR160b and ath-miR2938)in response to high calcium stress.The expression trends for other 2 miRNAs (i.e.,miR319a and miR-5015) were different from those obtained by highthroughput sequencing.The transcription factor MYB120(AT5G55020),serine/threonine-protein kinaselike protein gene ACR4 (AT3G59420),and histonelysine N-methyltransferase gene ATX3 (AT3G61-740),which were predicted to be the target genes for ath-miR159c,ath-miR399c-5p,and ath-miR-164a,respectively,were up-regulated under high calcium stress,while auxin response factor 16(ARF-16,AT4G30080) and jasmonic acid-amido synthetase gene JAR1 (AT2G46370),which were the potential target genes for ath-miR160b and ath-miR-2938,respectively,were down-regulated.

Fig.5 RT-qPCR verification of the deep sequencing-selected miRNAs and their potential target genes in response to high calcium stress

3 Discussion

High soil calcium levels have a negative effect on plant growth and development,often leading to low crop yields,and are one of the main limiting factors for economic and social development in karst areas.Understanding how plants tolerate high calcium soils will pave the way for high-calcium crops grown in karst areas.This will significantly benefit the sustainable development of agriculture and economy in the vast karst regions.

miRNAs are a class of small non-coding RNAs that play an important role in post-transcriptional gene regulation by cutting the target mRNAs or inhibiting translation.High-throughput sequencing has been used to identify miRNAs at the genome-wide level in multiple plant species,including A.thaliana[22],Oryza sativa[23],Solanum lycopersicum[24],Populus euphratica[25],Triticum aestivum[26],and so on.However,the responses of miRNAs to high calcium stress in Arabidopsis and their possible regulatory genes have not been reported.

In this study,high-throughput sequencing was used to analyze the effect of high calcium treatment on the expression level of miRNAs in Arabidopsis roots in order to find high calcium-responsive miR-NAs.The results obtained from the differential expression and functional analysis of miRNAs and their target genes indicate that miRNAs may play a key role in the plant response to high calcium stress.Target molecules for differentially expressed miRNAs were obtained from our predictions and annotations,including transcription factors and key functional proteins such as auxin response factor 16,jasmonic acid-amido synthetase JAR1,serine/threonine-protein kinase-like protein ACR4,histonelysine N-methyltransferase ATX3.

RT-qPCR results showed that the relative expression trends of six miRNAs (ath-miR394b-5p,ath-miR159c,ath-miR164a,ath-miR399c-5p,athmiR160b,ath-miR2938)were the same as those analyzed by high-throughput sequencing.And their accumulation was negatively correlated with the target gene expression pattern.The current results indicate that differentially expressed miRNAs should be involved in the physiological processes of plants responding to high calcium stress.Further research is still needed to clarify the molecular mechanisms of the high calcium responsive miRNAs and their target genes.

Supplement data

Supplemental Table 1 is available online.

Supplemental Table 1

a t h-m i R 1 5 9 c A T 5 G 2 7 3 9 5.1 2.5 2 1.9 4 7 1 2 1 2 6 3 2 8 3 U U U G G A U U G A A G G G A G C U C C U : :::.::.:::..::.:::: A U G A G U U C U C U U U G A U U C A A A C l e a v a g e a t h-m i R 1 5 9 c A T 2 G 3 4 0 1 0.1 2.5 1 4.6 1 7 1 2 1 4 3 8 4 5 8 U U U G G A U U G A A G G G A G C U C C U :::: :::::::: ::::: U A G A G C C C C C U U C A A A C C A A A C l e a v a g e a t h-m i R 1 5 9 c A T 3 G 6 1 7 4 0.2 2.5 1 2.8 8 1 2 1 3 3 7 1 3 3 9 1 U U U G G A U U G A A G G G A G C U C C U ::::::.::: :.::.::: U A G A G C U C U C U U A A G U C U A A A T r a n s l a t i o n a t h-m i R 1 5 9 c A T 3 G 6 1 7 4 0.1 2.5 1 2.8 8 1 2 1 3 4 7 9 3 4 9 9 U U U G G A U U G A A G G G A G C U C C U ::::::.::: :.::.::: U A G A G C U C U C U U A A G U C U A A A T r a n s l a t i o n a t h-m i R 1 5 9 c A T 1 G 3 5 8 7 0.1 3 1 7.9 2 8 1 2 1 2 9 2 1 2 9 4 1 U U U G G A U U G A A G G G A G C U C C U :::: ::::.:::: :::::: A G G A U C U C C U U U C A U U C C A A A C l e a v a g e a t h-m i R 1 5 9 c A T 4 G 3 1 2 4 0.2 3 1 2.0 4 4 1 2 1 3 8 8 4 0 8 U U U G G A U U G A A G G G A G C U C C U : ::.::::::::::..::.U G C A G U U C C C U U C A A U U U A A G C l e a v a g e a t h-m i R 1 5 9 c A T 4 G 3 1 2 4 0.1 3 1 2.0 4 4 1 2 1 6 5 6 6 7 6 U U U G G A U U G A A G G G A G C U C C U : ::.::::::::::..::.U G C A G U U C C C U U C A A U U U A A G C l e a v a g e a t h-m i R 1 5 9 c A T 2 G 2 6 9 6 0.1 3 2 1.3 1 5 1 2 1 8 6 4 8 8 4 U U U G G A U U G A A G G G A G C U C C U :::.:::::::: ::::: U C G A G U U C C C U U C A U U C C A A U C l e a v a g e a t h-m i R 1 5 9 c A T 2 G 1 5 9 4 0.1 3 1 6.6 6 8 1 2 1 1 2 4 6 1 2 6 6 U U U G G A U U G A A G G G A G C U C C U .:::::: :::: .::::::.G G G A G C U G C C U U A G A U C C A A G T r a n s l a t i o n a t h-m i R 1 5 9 c A T 1 G 4 2 1 1 0.1 3 1 8.3 8 6 1 2 1 1 3 3 8 1 3 5 8 U U U G G A U U G A A G G G A G C U C C U .:::::: :::: .::::::.G G G A G C U G C C U U A G A U C C A A G T r a n s l a t i o n a t h-m i R 1 5 9 c A T 2 G 0 6 5 8 0.1 3 1 9.9 5 8 1 2 1 2 6 3 2 8 3 U U U G G A U U G A A G G G A G C U C C U :::.:.:.:::::::.:: G C G A G U U U C U U U C A A U C U A A C C l e a v a g e a t h-m i R 1 5 9 c A T 2 G 2 2 8 1 0.1 3 1 6.5 2 3 1 2 1 3 1 5 3 3 5 U U U G G A U U G A A G G G A G C U C C U :::.:.:.::..::.:::: U C G A G U U U C U U U U G A U U C A A A C l e a v a g e a t h-m i R 1 5 9 c A T 2 G 0 6 9 8 0.1 3 1 5.9 3 6 1 2 1 1 5 1 9 1 5 3 9 U U U G G A U U G A A G G G A G C U C C U :::::::.:::.::.:: : U C G A G C U C C U U U C G A U U C A C A C l e a v a g e a t h-m i R 1 5 9 c A T 3 G 0 8 8 5 0.1 3 2 0.1 5 6 1 2 1 3 7 3 0 3 7 5 0 U U U G G A U U G A A G G G A G C U C C U :.:.:..::::::::::..C U G G G U U U U C U U C A A U C C A G G C l e a v a g e a t h-m i R 1 5 9 c A T 5 G 5 9 3 7 0.1 3 1 5.4 8 6 1 2 1 4 8 3 5 0 3 U U U G G A U U G A A G G G A G C U C C U : ::::::.:::::::.:: C G A A G C U C C U C U C A A U C C G A A T r a n s l a t i o n a t h-m i R 1 5 9 c A T 5 G 5 9 3 7 0.2 3 1 5.4 8 6 1 2 1 6 9 4 7 1 4 U U U G G A U U G A A G G G A G C U C C U : ::::::.:::::::.:: C G A A G C U C C U C U C A A U C C G A A T r a n s l a t i o n| S y m b o l s: | M i t o c h o n d r i a l i n n e r m e m b r a n e t r a n s l o c a s e c o m p l e x,s u b u n i t T i m 4 4-r e l a t e d p r o t e i n |c h r 5:9 6 7 1 4 9 6-9 6 7 4 2 5 6 R E V E R S E L E N G T H=1 4 6 2| S y m b o l s: | u n k n o w n p r o t e i n; B E S T A r a b i d o p s i s t h a l i a n a p r o t e i n m a t c h i s: u n k n o w n p r o t e i n(T A I R:A T 1 G 2 9 0 1 0.1); H a s 3 2 B l a s t h i t s t o 3 1 p r o t e i n s i n 9 s p e c i e s:A r c h a e - 0; B a c t e r i a - 0; M e t a z o a -0; F u n g i - 5; P l a n t s - 2 5; V i r u s e s- 0; O t h e r E u k a r y o t e s - 2 (s o u r c e:N C B I B L i n k).| c h r 2:1 4 3 6 8 8 5 6-1 4 3 7 0 4 3 8 F O R W A R D L E N G T H=1 2 2 1| S y m b o l s: S D G 1 4,A T X 3 | S E T d o m a i n p r o t e i n 1 4 | c h r 3:2 2 8 5 0 8 3 7-2 2 8 5 6 9 7 2 R E V E R S E L E N G T H=3 6 6 9| S y m b o l s: S D G 1 4,A T X 3 | S E T d o m a i n p r o t e i n 1 4 | c h r 3:2 2 8 5 0 8 3 7-2 2 8 5 6 9 7 2 R E V E R S E L E N G T H=3 7 7 7| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 1:1 3 3 3 5 2 5 7-1 3 3 3 9 5 8 7 F O R W A R D L E N G T H=4 3 3 1| S y m b o l s: | p r o t e i n k i n a s e C-l i k e z i n c f i n g e r p r o t e i n |c h r 4:1 5 1 7 6 4 5 5-1 5 1 7 8 5 0 8 R E V E R S E L E N G T H=1 4 4 0| S y m b o l s: | p r o t e i n k i n a s e C-l i k e z i n c f i n g e r p r o t e i n |c h r 4:1 5 1 7 6 4 5 5-1 5 1 7 8 7 6 8 R E V E R S E L E N G T H=1 7 0 8| S y m b o l s: A t M Y B 8 1,M Y B 8 1 | m y b d o m a i n p r o t e i n 8 1 | c h r 2:1 1 5 0 6 0 6 5-1 1 5 0 7 4 2 6 R E V E R S E L E N G T H=1 2 8 5| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 2:6 9 4 2 9 1 4-6 9 4 4 7 9 4 F O R W A R D L E N G T H=1 8 8 1| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 1:1 5 7 2 5 2 9 8-1 5 7 2 7 4 3 4 F O R W A R D L E N G T H=2 1 3 7| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 2:2 6 2 5 0 4 3-2 6 2 8 0 3 3 F O R W A R D L E N G T H=2 9 9 1| S y m b o l s: A C S 4,A C C 4,A T A C S 4 | 1-a m i n o c y c l o p r o p a n e-1-c a r b o x y l a t e s y n t h a s e 4 | c h r 2:9 7 1 7 7 9 1-9 7 1 9 4 7 2 R E V E R S E L E N G T H=1 4 2 5| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 2:2 8 8 3 4 2 5-2 8 8 6 1 6 6 F O R W A R D L E N G T H=2 7 4 2| S y m b o l s: R A P T O R 1 B,A T R A P T O R 1 B,R A P T O R 1 | H E A T r e p e a t ;W D d o m a i n,G-b e t a r e p e a t p r o t e i n p r o t e i n |c h r 3:2 6 8 6 5 8 3-2 6 9 5 3 0 0 R E V E R S E L E N G T H=4 8 1 9| S y m b o l s: A C T 4 | a c t i n 4 |c h r 5:2 3 9 4 9 7 3 9-2 3 9 5 1 8 3 7 F O R W A R D L E N G T H=1 5 4 4| S y m b o l s: A C T 4 | a c t i n 4 |c h r 5:2 3 9 4 9 7 3 9-2 3 9 5 1 8 3 7 F O R W A R D L E N G T H=1 7 5 5 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

a t h-m i R 1 5 9 c A T 3 G 4 3 6 8 4.1 3 1 7.8 1 1 1 2 1 1 6 5 1 8 5 U U U G G A U U G A A G G G A G C U C C U .:::::: ::.::::::: A A U G G C U C C C A U C G A U C C A A A T r a n s l a t i o n a t h-m i R 1 5 9 c A T 2 G 4 6 8 9 0.1 3 1 1.9 9 8 1 2 1 1 4 0 1 6 0 U U U G G A U U G A A G G G A G C U C C U ::::::.:::: ::.::: C A G A G C U C U C U U C U A U U C A A U C l e a v a g e a t h-m i R 1 5 9 c A T 1 G 2 9 0 1 0.1 3 1 4.5 1 3 1 2 1 4 0 4 4 2 4 U U U G G A U U G A A G G G A G C U C C U :::: .::::::: ::::: U A G A G C C U C C U U C A A G C C A A A C l e a v a g e a t h-m i R 1 5 9 c A T 1 G 2 1 8 1 0.1 3 1 4.3 2 7 1 2 1 1 7 0 9 1 7 2 9 U U U G G A U U G A A G G G A G C U C C U :::.:.:.: :::::::.: U U G A G U U U C U U G C A A U C C A G A T r a n s l a t i o n a t h-m i R 1 5 9 c A T 3 G 4 3 4 4 4.1 3 1 6.7 1 2 1 2 1 4 7 8 4 9 8 U U U G G A U U G A A G G G A G C U C C U ::::::.:::: : ::::: U U G A G C U C U C U U C C A G C C A A A C l e a v a g e a t h-m i R 1 6 0 b A T 1 G 7 7 8 5 0.1 0.5 2 1.8 1 5 1 2 1 1 4 0 9 1 4 2 9 U G C C U G G C U C C C U G U A U G C C A ::::::.:::::::::::::: U G G C A U G C A G G G A G C C A G G C A C l e a v a g e a t h-m i R 1 6 0 b A T 2 G 2 8 3 5 0.1 1 1 8.1 3 9 1 2 1 1 3 2 9 1 3 4 9 U G C C U G G C U C C C U G U A U G C C A :: ::::::::::::::::: A G G A A U A C A G G G A G C C A G G C A C l e a v a g e a t h-m i R 1 6 0 b A T 4 G 3 0 0 8 0.1 1.5 2 0.3 0 9 1 2 1 1 5 0 8 1 5 2 8 U G C C U G G C U C C C U G U A U G C C A ::.:::::::::::::::: G G G U U U A C A G G G A G C C A G G C A C l e a v a g e a t h-m i R 1 6 4 a A T 5 G 0 7 6 8 0.2 0.5 1 2.0 0 4 1 2 1 6 5 1 6 7 1 U G G A G A A G C A G G G C A C G U G C A : .:::::::::::::::::: U U U A C G U G C C C U G C U U C U C C A C l e a v a g e a t h-m i R 1 6 4 a A T 5 G 0 7 6 8 0.1 0.5 1 2.0 0 4 1 2 1 8 4 3 8 6 3 U G G A G A A G C A G G G C A C G U G C A : .:::::::::::::::::: U U U A C G U G C C C U G C U U C U C C A C l e a v a g e a t h-m i R 1 6 4 a A T 5 G 6 1 4 3 0.1 0.5 1 1.2 8 9 1 2 1 8 4 0 8 6 0 U G G A G A A G C A G G G C A C G U G C A : .:::::::::::::::::: U C U A C G U G C C C U G C U U C U C C A C l e a v a g e a t h-m i R 1 6 4 a A T 3 G 1 5 1 7 0.1 1 1 8.0 4 1 2 1 6 6 4 6 8 4 U G G A G A A G C A G G G C A C G U G C A :::::::.::::.::::::: A G C A C G U G U C C U G U U U C U C C A C l e a v a g e a t h-m i R 1 6 4 a A T 5 G 5 3 9 5 0.1 1 9.5 2 7 1 2 1 8 0 1 8 2 1 U G G A G A A G C A G G G C A C G U G C A :::::::.::::.::::::: A G C A C G U G U C C U G U U U C U C C A C l e a v a g e a t h-m i R 1 6 4 a A T 1 G 5 6 0 1 0.1 1 8.7 0 1 1 2 1 7 7 7 7 9 7 U G G A G A A G C A G G G C A C G U G C A :::::: ::::::::::::: A G C A C G U A C C C U G C U U C U C C A C l e a v a g e| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 3:1 5 5 8 5 5 3 2-1 5 5 8 7 1 0 5 R E V E R S E L E N G T H=1 0 2 4| S y m b o l s: | P r o t e i n o f u n k n o w n f u n c t i o n (D U F 1 2 9 5) | c h r 2:1 9 2 6 6 7 3 3-1 9 2 6 8 1 7 0 R E V E R S E L E N G T H=1 1 5 1| S y m b o l s: | u n k n o w n p r o t e i n; B E S T A r a b i d o p s i s t h a l i a n a p r o t e i n m a t c h i s: u n k n o w n p r o t e i n(T A I R:A T 2 G 3 4 0 1 0.1); H a s 1 8 B l a s t h i t s t o 1 7 p r o t e i n s i n 3 s p e c i e s:A r c h a e - 0; B a c t e r i a - 0; M e t a z o a -0; F u n g i - 0; P l a n t s - 1 8; V i r u s e s- 0; O t h e r E u k a r y o t e s - 0 (s o u r c e:N C B I B L i n k).| c h r 1:1 0 1 1 7 7 1 5-1 0 1 1 9 0 8 5 F O R W A R D L E N G T H=1 0 1 5| S y m b o l s: | P l a n t p r o t e i n o f u n k n o w n f u n c t i o n (D U F 8 6 9) |c h r 1:7 6 5 6 3 9 9-7 6 5 8 6 3 4 R E V E R S E L E N G T H=2 0 6 6| S y m b o l s: | t r a n s p o s a b l e e l e m e n t g e n e | c h r 3:1 5 3 7 7 5 6 8-1 5 3 8 1 6 0 8 F O R W A R D L E N G T H=4 0 4 1| S y m b o l s: A R F 1 7 | a u x i n r e s p o n s e f a c t o r 1 7 | c h r 1:2 9 2 7 2 3 1 3-2 9 2 7 5 4 1 9 F O R W A R D L E N G T H=2 0 7 6| S y m b o l s: A R F 1 0 | a u x i n r e s p o n s e f a c t o r 1 0 | c h r 2:1 2 1 1 4 3 3 1-1 2 1 1 6 8 4 8 F O R W A R D L E N G T H=2 2 6 5| S y m b o l s: A R F 1 6 | a u x i n r e s p o n s e f a c t o r 1 6 | c h r 4:1 4 7 0 3 2 0 1-1 4 7 0 6 3 3 6 R E V E R S E L E N G T H=2 3 6 0| S y m b o l s: A N A C 0 8 0,N A C 0 8 0 | N A C d o m a i n c o n t a i n i n g p r o t e i n 8 0 |c h r 5:2 4 3 5 9 8 3-2 4 3 7 4 9 9 F O R W A R D L E N G T H=1 1 9 2| S y m b o l s: A N A C 0 8 0,A N A C 0 7 9,A T N A C 4,N A C 0 8 0 | N A C d o m a i n c o n t a i n i n g p r o t e i n 8 0 |c h r 5:2 4 3 5 8 7 5-2 4 3 7 4 8 0 F O R W A R D L E N G T H=1 3 6 5| S y m b o l s: A N A C 1 0 0,A T N A C 5,N A C 1 0 0| N A C d o m a i n c o n t a i n i n g p r o t e i n 1 0 0| c h r 5:2 4 7 0 1 1 2 2-2 4 7 0 2 7 6 1 R E V E R S E L E N G T H=1 4 2 5| S y m b o l s: C U C 1,A N A C 0 5 4,A T N A C 1 |N A C (N o A p i c a l M e r i s t e m) d o m a i n t r a n s c r i p t i o n a l r e g u l a t o r s u p e r f a m i l y p r o t e i n | c h r 3:5 1 0 9 8 8 3-5 1 1 1 4 4 7 F O R W A R D L E N G T H=9 7 4| S y m b o l s: C U C 2,A N A C 0 9 8,A T C U C 2 |N A C (N o A p i c a l M e r i s t e m) d o m a i n t r a n s c r i p t i o n a l r e g u l a t o r s u p e r f a m i l y p r o t e i n |c h r 5:2 1 9 0 1 9 6 6-2 1 9 0 3 8 2 3 R E V E R S E L E N G T H=1 1 5 6| S y m b o l s: N A C 1,a n a c 0 2 1 | N A C d o m a i n c o n t a i n i n g p r o t e i n 1 |c h r 1:2 0 9 4 6 5 7 1-2 0 9 4 8 0 4 0 R E V E R S E L E N G T H=1 3 6 8 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR164a AT1G56010.2 1 8.701 1 21 802 822 UGGAGAAGCAGGGCACGUGCA :::::: ::::::::::::: AGCACGUACCCUGCUUCUCCA Cleavage ath-miR164a AT3G12977.1 1.5 5.024 1 21 717 737 UGGAGAAGCAGGGCACGUGCA :::.:: ::::::::::::: AGCAUGUACCCUGCUUCUCCA Cleavage ath-miR164a AT5G39610.1 1.5 13.246 1 21 770 790 UGGAGAAGCAGGGCACGUGCA :::::: :::::::::::.CUCACGUGACCUGCUUCUCCG Cleavage ath-miR164a AT1G10530.1 2 22.889 1 21 365 385 UGGAGAAGCAGGGCACGUGCA : ::::::.:: ::::::::.UACACGUGUCCAGCUUCUCCG Translation ath-miR164a AT4G39400.1 2.5 15.487 1 21 517 537 UGGAGAAGCAGGGCACGUGCA : :: ::::.::::::::..: UUCAAGUGCUCUGCUUCUUUA Cleavage ath-miR164a AT3G33142.1 2.5 19.525 1 21 1096 1115 UGGAGAAGCAGGGCACGUGCA :::: :.:::::::::::: ACCACG-GUCCUGCUUCUCCA Cleavage ath-miR164a AT2G37960.1 3 6.789 1 21 1635 1655 UGGAGAAGCAGGGCACGUGCA :.:: ::.:: ::::::::: CGUACUUGUCCAGCUUCUCCA Translation ath-miR164a AT4G27520.1 3 6.825 1 21 753 773 UGGAGAAGCAGGGCACGUGCA : ::::: :::::.::: ::: UCCACGUCCCCUGUUUCCCCA Cleavage ath-miR164a AT4G35380.1 3 17.111 1 21 5000 5020 UGGAGAAGCAGGGCACGUGCA ::::::.:: ::::::.: AACACGUGUCCAGCUUCUUCC Translation ath-miR164a AT5G13010.1 3 21.994 1 21 1100 1120 UGGAGAAGCAGGGCACGUGCA .:.:: ..::::::::::: ACUAUGUCUUCUGCUUCUCCA Cleavage ath-miR164a AT3G54320.1 3 9.241 1 21 147 167 UGGAGAAGCAGGGCACGUGCA : ::: ::..:: :::::::: UCCACUUGUUCUUCUUCUCCA Translation| Symbols: NAC1,ANAC022 | NAC domain containing protein 1 |chr1:20946571-20949281 REVERSE LENGTH=1393| Symbols: | NAC (No Apical Meristem) domain transcriptional regulator superfamily protein |chr3:4143726-4145967 FORWARD LENGTH=1053| Symbols: ATNAC2,ORE1,ANAC092,ATNAC6,NAC2,NAC6 | NAC domain containing protein 6 |chr5:15858400-15859788 REVERSE LENGTH=1187| Symbols: | unknown protein;FUNCTIONS IN: molecular_function unknown; INVOLVED IN: N-terminal protein myristoylation; BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT1G60010.1); Has 143 Blast hits to 143 proteins in 14 species:Archae - 0; Bacteria - 0; Metazoa -0; Fungi - 0; Plants - 143; Viruses- 0; Other Eukaryotes - 0 (source:NCBI BLink).| chr1:3471456-3472672 REVERSE LENGTH=996| Symbols: BRI1,CBB2,DWF2,BIN1,ATBRI1 | Leucine-rich receptor-like protein kinase family protein |chr4:18324661-18328826 FORWARD LENGTH=4166| Symbols: | transposable element gene | chr3:13950958-13954678 FORWARD LENGTH=3721| Symbols: | unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT3G54060.2); Has 418 Blast hits to 247 proteins in 92 species:Archae - 0; Bacteria - 163; Metazoa- 49; Fungi - 80; Plants - 28;Viruses - 0; Other Eukaryotes - 98(source: NCBI BLink).|chr2:15886548-15889220 REVERSE LENGTH=1793| Symbols: ENODL2,AtENODL2 | early nodulin-like protein 2 |chr4:13750440-13751905 REVERSE LENGTH=1364| Symbols: | SEC7-like guanine nucleotide exchange family protein| chr4:16819883-16826061 FORWARD LENGTH=5222| Symbols: EMB3011 | RNA helicase family protein | chr5:4122410-4128861 FORWARD LENGTH=4306| Symbols: WRI1,WRI,ASML1,ATWRI1| Integrase-type DNA-binding superfamily protein |chr3:20114684-20118627 FORWARD LENGTH=1470 1 1 1 1 1 1 1 1 1 1 1

ath-miR164a AT3G54320.2 3 9.241 1 21 147 167 UGGAGAAGCAGGGCACGUGCA : ::: ::..:: :::::::: UCCACUUGUUCUUCUUCUCCA Translation ath-miR164a AT3G54320.3 3 9.241 1 21 147 167 UGGAGAAGCAGGGCACGUGCA : ::: ::..:: :::::::: UCCACUUGUUCUUCUUCUCCA Translation ath-miR164a AT5G01600.1 3 15.04 1 21 525 544 UGGAGAAGCAGGGCACGUGCA :::: ::.::::::::::.CUCACG-GCUCUGCUUCUCCG Cleavage ath-miR164a AT1G77770.2 3 20.102 1 21 830 850 UGGAGAAGCAGGGCACGUGCA : :: : ::::::::::::: UCCAGCUCCCCUGCUUCUCCA Cleavage ath-miR164a AT1G77770.1 3 23.086 1 21 824 844 UGGAGAAGCAGGGCACGUGCA : :: : ::::::::::::: UCCAGCUCCCCUGCUUCUCCA Cleavage ath-miR164b-5p AT5G07680.2 0.5 12.004 1 21 651 671 UGGAGAAGCAGGGCACGUGCA : .:::::::::::::::::: UUUACGUGCCCUGCUUCUCCA Cleavage ath-miR164b-5p AT5G07680.1 0.5 12.004 1 21 843 863 UGGAGAAGCAGGGCACGUGCA : .:::::::::::::::::: UUUACGUGCCCUGCUUCUCCA Cleavage ath-miR164b-5p AT5G61430.1 0.5 11.289 1 21 840 860 UGGAGAAGCAGGGCACGUGCA : .:::::::::::::::::: UCUACGUGCCCUGCUUCUCCA Cleavage ath-miR164b-5p AT3G15170.1 1 18.04 1 21 664 684 UGGAGAAGCAGGGCACGUGCA :::::::.::::.::::::: AGCACGUGUCCUGUUUCUCCA Cleavage ath-miR164b-5p AT5G53950.1 1 9.527 1 21 801 821 UGGAGAAGCAGGGCACGUGCA :::::::.::::.::::::: AGCACGUGUCCUGUUUCUCCA Cleavage ath-miR164b-5p AT1G56010.1 1 8.701 1 21 777 797 UGGAGAAGCAGGGCACGUGCA :::::: ::::::::::::: AGCACGUACCCUGCUUCUCCA Cleavage ath-miR164b-5p AT1G56010.2 1 8.701 1 21 802 822 UGGAGAAGCAGGGCACGUGCA :::::: ::::::::::::: AGCACGUACCCUGCUUCUCCA Cleavage ath-miR164b-5p AT3G12977.1 1.5 5.024 1 21 717 737 UGGAGAAGCAGGGCACGUGCA :::.:: ::::::::::::: AGCAUGUACCCUGCUUCUCCA Cleavage ath-miR164b-5p AT5G39610.1 1.5 13.246 1 21 770 790 UGGAGAAGCAGGGCACGUGCA :::::: :::::::::::.CUCACGUGACCUGCUUCUCCG Cleavage| Symbols: WRI1,WRI,ASML1 |Integrase-type DNA-binding superfamily protein |chr3:20114684-20118639 FORWARD LENGTH=1580| Symbols: WRI1,WRI,ASML1 |Integrase-type DNA-binding superfamily protein |chr3:20114684-20118639 FORWARD LENGTH=1584| Symbols: ATFER1,FER1 | ferretin 1 | chr5:227953-230051 REVERSE LENGTH=1421| Symbols: | Protein of unknown function (DUF1644) | chr1:29246205-29248028 REVERSE LENGTH=1189| Symbols: | Protein of unknown function (DUF1644) | chr1:29246074-29248022 REVERSE LENGTH=1216| Symbols: ANAC080,NAC080 | NAC domain containing protein 80 |chr5:2435983-2437499 FORWARD LENGTH=1192| Symbols: ANAC080,ANAC079,ATNAC4,NAC080 | NAC domain containing protein 80 |chr5:2435875-2437480 FORWARD LENGTH=1365| Symbols: ANAC100,ATNAC5,NAC100| NAC domain containing protein 100| chr5:24701122-24702761 REVERSE LENGTH=1425| Symbols: CUC1,ANAC054,ATNAC1 |NAC (No Apical Meristem) domain transcriptional regulator superfamily protein | chr3:5109883-5111447 FORWARD LENGTH=974| Symbols: CUC2,ANAC098,ATCUC2 |NAC (No Apical Meristem) domain transcriptional regulator superfamily protein |chr5:21901966-21903823 REVERSE LENGTH=1156| Symbols: NAC1,anac021 | NAC domain containing protein 1 |chr1:20946571-20948040 REVERSE LENGTH=1368| Symbols: NAC1,ANAC022 | NAC domain containing protein 1 |chr1:20946571-20949281 REVERSE LENGTH=1393| Symbols: | NAC (No Apical Meristem) domain transcriptional regulator superfamily protein |chr3:4143726-4145967 FORWARD LENGTH=1053| Symbols: ATNAC2,ORE1,ANAC092,ATNAC6,NAC2,NAC6 | NAC domain containing protein 6 |chr5:15858400-15859788 REVERSE LENGTH=1187 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR164b-5p AT1G77770.2 3 20.102 1 21 830 850 UGGAGAAGCAGGGCACGUGCA : :: : ::::::::::::: UCCAGCUCCCCUGCUUCUCCA Cleavage ath-miR164b-5p AT1G77770.1 3 23.086 1 21 824 844 UGGAGAAGCAGGGCACGUGCA : :: : ::::::::::::: UCCAGCUCCCCUGCUUCUCCA Cleavage ath-miR167a-5p AT5G41300.1 2 19.68 1 21 829 849 UGAAGCUGCCAGCAUGAUCUA :::::: ::::::::::..AUGAUCAUUCUGGCAGCUUUG Cleavage ath-miR167a-5p AT5G58590.1 2.5 12.755 1 21 817 837 UGAAGCUGCCAGCAUGAUCUA :: :::: :::.::::::: CUGAACAUGAUGGUAGCUUCA Cleavage ath-miR167a-5p AT3G61310.1 3 23.878 1 21 1206 1227 UGAAGCUGCCAGC-AUGAUCUA ::.:::: :.::::::::::: CAGGUCAUUGUUGGCAGCUUCA Cleavage ath-miR167a-5p AT3G06868.1 3 21.201 1 21 428 448 UGAAGCUGCCAGCAUGAUCUA ::: :::::: :::::::: AAGAACAUGCUCGCAGCUUCU Translation ath-miR167a-5p AT5G19950.2 3 19.223 1 21 1198 1219 UGAAGCUGCCA-GCAUGAUCUA ::::: ::: ::::::::::: AAGAUCUUGCAUGGCAGCUUCA Translation ath-miR167a-5p AT5G19950.3 3 16.555 1 21 1198 1219 UGAAGCUGCCA-GCAUGAUCUA ::::: ::: ::::::::::: AAGAUCUUGCAUGGCAGCUUCA Translation ath-miR167a-5p AT5G19950.1 3 19.223 1 21 1198 1219 UGAAGCUGCCA-GCAUGAUCUA ::::: ::: ::::::::::: AAGAUCUUGCAUGGCAGCUUCA Translation ath-miR167a-5p AT1G08570.4 3 22.646 1 21 561 581 UGAAGCUGCCAGCAUGAUCUA .:.::.::.: :::::::.: AGGGUCGUGUUUGCAGCUUUA Translation ath-miR167a-5p AT1G08570.2 3 22.646 1 21 616 636 UGAAGCUGCCAGCAUGAUCUA .:.::.::.: :::::::.: AGGGUCGUGUUUGCAGCUUUA Translation ath-miR167a-5p AT1G08570.3 3 22.646 1 21 633 653 UGAAGCUGCCAGCAUGAUCUA .:.::.::.: :::::::.: AGGGUCGUGUUUGCAGCUUUA Translation ath-miR167a-5p AT1G08570.1 3 22.646 1 21 709 729 UGAAGCUGCCAGCAUGAUCUA .:.::.::.: :::::::.: AGGGUCGUGUUUGCAGCUUUA Translation ath-miR167a-5p AT1G02800.1 3 19.889 1 21 1044 1064 UGAAGCUGCCAGCAUGAUCUA ::: ::::::: .::.:::: AAGAGCAUGCUGAUAGUUUCA Translation ath-miR167a-5p AT5G35840.1 3 23.152 1 21 2709 2729 UGAAGCUGCCAGCAUGAUCUA :::.:: :::.::::::: ACCAUCGUGAUGGUAGCUUCA Cleavage ath-miR167a-5p AT5G23060.1 3 17.042 1 21 1216 1236 UGAAGCUGCCAGCAUGAUCUA .:::.:: : :::::::::.CGGAUUAUCCCGGCAGCUUCG Translation| Symbols: | Protein of unknown function (DUF1644) | chr1:29246205-29248028 REVERSE LENGTH=1189| Symbols: | Protein of unknown function (DUF1644) | chr1:29246074-29248022 REVERSE LENGTH=1216| Symbols: | Receptor-like protein kinase-related family protein |chr5:16515004-16516102 FORWARD LENGTH=864| Symbols: RANBP1 | RAN binding protein 1 | chr5:23680079-23681798 REVERSE LENGTH=984| Symbols: | AT hook motif DNA-binding family protein |chr3:22690596-22692834 REVERSE LENGTH=1657| Symbols: | unknown protein;FUNCTIONS IN: molecular_function unknown; INVOLVED IN:biological_process unknown; LOCATED IN: cellular_component unknown;BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT5G49100.1); Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12; Bacteria -1396; Metazoa - 17338; Fungi -3422; Plants - 5037; Viruses - 0;Other Eukaryotes - 2996 (source:NCBI BLink).| chr3:2167730-2169222 FORWARD LENGTH=1493| Symbols: | Domain of unknown function (DUF1767) | chr5:6740777-6743773 REVERSE LENGTH=1670| Symbols: | Domain of unknown function (DUF1767) | chr5:6740777-6743773 REVERSE LENGTH=1783| Symbols: | Domain of unknown function (DUF1767) | chr5:6740777-6743773 REVERSE LENGTH=1789| Symbols: ACHT4 | atypical CYS HIS rich thioredoxin 4 | chr1:2712930-2714733 FORWARD LENGTH=1268| Symbols: ACHT4 | atypical CYS HIS rich thioredoxin 4 | chr1:2712892-2714734 FORWARD LENGTH=1324| Symbols: ACHT4 | atypical CYS HIS rich thioredoxin 4 | chr1:2712883-2714733 FORWARD LENGTH=1340| Symbols: ACHT4 | atypical CYS HIS rich thioredoxin 4 | chr1:2712892-2714734 FORWARD LENGTH=1417| Symbols: ATCEL2,CEL2 | cellulase 2 | chr1:613216-616191 REVERSE LENGTH=1764| Symbols: PHYC | phytochrome C |chr5:14007826-14011764 FORWARD LENGTH=3704| Symbols: CaS | calcium sensing receptor | chr5:7736590-7738535 REVERSE LENGTH=1457 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR167a-5p AT3G60870.1 3 19.991 1 21 565 585 UGAAGCUGCCAGCAUGAUCUA :.::.: ::::::::::: GUGGUCGUUAUGGCAGCUUCA Cleavage ath-miR167a-5p AT2G35350.1 3 21.659 1 21 267 287 UGAAGCUGCCAGCAUGAUCUA .:::::: : ::::::::: CGGAUCAUCCGAGCAGCUUCA Translation ath-miR2937 AT1G77160.1 2 23.006 1 21 155 175 AUAAGAGCUGUUGAAGGAGUC :::.:::::: .:::::::: CACUUCUUCAAAGGCUCUUAU Translation ath-miR2937 AT3G47640.1 2 6.778 1 21 668 688 AUAAGAGCUGUUGAAGGAGUC ::::: ::::::.::::.: UCCUCCUGCAACAGUUCUUGU Cleavage ath-miR2937 AT3G47640.3 2 6.778 1 21 680 700 AUAAGAGCUGUUGAAGGAGUC ::::: ::::::.::::.: UCCUCCUGCAACAGUUCUUGU Cleavage ath-miR2937 AT3G47640.2 2 6.778 1 21 682 702 AUAAGAGCUGUUGAAGGAGUC ::::: ::::::.::::.: UCCUCCUGCAACAGUUCUUGU Cleavage ath-miR2937 AT3G02450.1 2.5 14.591 1 21 1100 1120 AUAAGAGCUGUUGAAGGAGUC ::.:::::..::: ::::::: GAUUCCUUUGACACCUCUUAU Cleavage ath-miR2937 AT3G12890.1 2.5 9.701 1 21 157 177 AUAAGAGCUGUUGAAGGAGUC :.::::::::::: ::::: : GGCUCCUUCAACACCUCUUCU Cleavage ath-miR2937 AT2G23800.1 2.5 17.447 1 21 1113 1133 AUAAGAGCUGUUGAAGGAGUC .::::::.:..:::::::: UGCUCCUUUAGUAGCUCUUAC Cleavage ath-miR2937 AT3G56100.1 2.5 11.417 1 21 922 942 AUAAGAGCUGUUGAAGGAGUC :::.::::::..::::::: AACUUCUUCAAUGUCUCUUAU Cleavage ath-miR2937 AT1G75750.2 2.5 13.748 1 21 148 168 AUAAGAGCUGUUGAAGGAGUC :.:: .::::: ::::::::: GGCUAUUUCAAAAGCUCUUAU Translation ath-miR2937 AT1G75750.1 2.5 13.847 1 21 86 106 AUAAGAGCUGUUGAAGGAGUC :.:: .::::: ::::::::: GGCUAUUUCAAAAGCUCUUAU Translation ath-miR2937 AT3G30712.1 2.5 18.045 1 21 126 146 AUAAGAGCUGUUGAAGGAGUC ::::.:::: ::::::::: UACUCUCUCAAAAGCUCUUAU Translation ath-miR2937 AT1G22610.1 2.5 16.164 1 21 976 996 AUAAGAGCUGUUGAAGGAGUC ::::::.:.:::::: ::: UCCUCCUUUAGCAGCUCGUAU Cleavage ath-miR2937 AT1G52520.1 2.5 15.824 1 21 1056 1076 AUAAGAGCUGUUGAAGGAGUC ::.: ::.::::.:::::: AUCUUCAUCGACAGUUCUUAU Cleavage ath-miR2937 AT1G22020.1 2.5 13.009 1 21 172 192 AUAAGAGCUGUUGAAGGAGUC .::::::::: : :::::.: AGCUCCUUCAAAAACUCUUGU Translation| Symbols: AHL18 | AT-hook motif nuclear-localized protein 18 |chr3:22493204-22494001 FORWARD LENGTH=798| Symbols: PLL1 | poltergeist like 1 | chr2:14881039-14884116 REVERSE LENGTH=2673| Symbols: | Protein of unknown function (DUF506) | chr1:28995146-28996594 REVERSE LENGTH=1105| Symbols: PYE | basic helix-loophelix (bHLH) DNA-binding superfamily protein |chr3:17567597-17569315 FORWARD LENGTH=1074| Symbols: PYE | basic helix-loophelix (bHLH) DNA-binding superfamily protein |chr3:17567126-17569385 FORWARD LENGTH=1156| Symbols: PYE | basic helix-loophelix (bHLH) DNA-binding superfamily protein |chr3:17567126-17569385 FORWARD LENGTH=1158| Symbols: | cell division protein ftsH,putative | chr3:502707-505230 REVERSE LENGTH=2238| Symbols: ASML2 | activator of spomin::LUC2 | chr3:4099199-4100473 FORWARD LENGTH=976| Symbols: GGPS2,GGPS5 |geranylgeranyl pyrophosphate synthase 2 | chr2:10131489-10132779 REVERSE LENGTH=1291| Symbols: MRLK,IMK3 |meristematic receptor-like kinase |chr3:20816931-20819517 REVERSE LENGTH=2303| Symbols: GASA1 | GAST1 protein homolog 1 | chr1:28441645-28442429 REVERSE LENGTH=607| Symbols: GASA1 | GAST1 protein homolog 1 | chr1:28441526-28442367 REVERSE LENGTH=667| Symbols: | transposable element gene | chr3:12295250-12295639 FORWARD LENGTH=390| Symbols: | C2 calcium/lipidbinding plant phosphoribosyltransferase family protein | chr1:7994291-7997588 FORWARD LENGTH=3298| Symbols: FRS6 | FAR1-related sequence 6 | chr1:19565769-19568384 FORWARD LENGTH=2412| Symbols: SHM6 | serine hydroxymethyltransferase 6 |chr1:7754321-7757383 FORWARD LENGTH=2374 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR2937 AT2G32010.2 2.5 4.782 1 21 ath-miR2937 AT2G32010.1 2.5 4.782 1 21 ath-miR2937 AT1G52210.1 3 16.108 1 21 ath-miR2937 AT5G11370.1 3 13.633 1 21 208 228 AUAAGAGCUGUUGAAGGAGUC ::::::::: : :::::.: UCCUCCUUCAAGAACUCUUGU Translation 208 228 AUAAGAGCUGUUGAAGGAGUC ::::::::: : :::::.: UCCUCCUUCAAGAACUCUUGU Translation 2144 2164 AUAAGAGCUGUUGAAGGAGUC :::::::::.:..:.::::: GACUCCUUCGAUGGUUCUUAA Cleavage 302 322 AUAAGAGCUGUUGAAGGAGUC ::..:::::::.:::.:::: GAUCUCUUCAACGGCUUUUAU Cleavage ath-miR2937 AT3G57965.1 3 17.713 1 21 575 595 AUAAGAGCUGUUGAAGGAGUC :.::.::::::::.::::.AAUUCUUUCAACAGUUCUUGC Cleavage ath-miR2937 AT1G77145.1 3 22.591 1 21 140 160 AUAAGAGCUGUUGAAGGAGUC :: :.:: ::::.:::::::: GAGUUCUACAACGGCUCUUAU Cleavage ath-miR2937 AT5G62970.1 3 16.142 1 21 575 595 AUAAGAGCUGUUGAAGGAGUC :..:::::::.:::.:::: AAUCUCUUCAACGGCUUUUAU Cleavage ath-miR2937 AT3G13672.2 3 12.836 1 21 961 981 AUAAGAGCUGUUGAAGGAGUC :::::::::::.:.::: UCGUCCUUCAACAGUUUUUAC Cleavage ath-miR2937 AT3G13672.1 3 12.836 1 21 963 983 AUAAGAGCUGUUGAAGGAGUC :::::::::::.:.::: UCGUCCUUCAACAGUUUUUAC Cleavage ath-miR2937 AT5G63195.1 3 13.823 1 21 752 772 AUAAGAGCUGUUGAAGGAGUC : .:::::::::::::.: .: GUUUCCUUCAACAGCUUUAGU Cleavage ath-miR2937 AT5G03800.1 3 18.465 1 21 437 457 AUAAGAGCUGUUGAAGGAGUC :..:.::: ::::::::::: GGUUUCUUACACAGCUCUUAU Cleavage ath-miR2937 AT1G18910.1 3 16.498 1 21 899 919 AUAAGAGCUGUUGAAGGAGUC ::.:::..::.::::::: AUCUUCUUUGACGGCUCUUAC Cleavage ath-miR2937 AT4G14090.1 3 7.81 1 21 488 508 AUAAGAGCUGUUGAAGGAGUC ::: :::::::: :::::: UACUACUUCAACACCUCUUAC Cleavage ath-miR2937 AT3G03300.3 3 4.986 1 21 86 106 AUAAGAGCUGUUGAAGGAGUC ::.:::::::::.:.:: : AUCUUCUUCAACAGUUUUUUU Cleavage ath-miR2937 AT5G37381.1 3 21.125 1 21 1293 1313 AUAAGAGCUGUUGAAGGAGUC .::..:.:.:::::::::: AGCUUUCUUAGCAGCUCUUAU Cleavage ath-miR2937 AT3G05660.1 3 6.278 1 21 831 851 AUAAGAGCUGUUGAAGGAGUC :.:::::: :.: ::::::: CAUUCCUUCUAUAACUCUUAU Cleavage ath-miR2937 AT5G37017.1 3 8.862 1 21 604 624 AUAAGAGCUGUUGAAGGAGUC :.::::.:: :::::::: UUAUUCUUCGACUGCUCUUAU Translation ath-miR2937 AT4G03100.1 3 13.937 1 21 914 934 AUAAGAGCUGUUGAAGGAGUC ::: :.:::.:::::::: AGAUCCAUUAACGGCUCUUAU Cleavage| Symbols: CVL1 | CVP2 like 1 |chr2:13624792-13629121 FORWARD LENGTH=2686| Symbols: CVL1 | CVP2 like 1 |chr2:13624792-13629146 FORWARD LENGTH=2745| Symbols: | transposable element gene | chr1:19446190-19450533 FORWARD LENGTH=4344| Symbols: | FBD / Leucine Rich Repeat domains containing protein |chr5:3627849-3629717 FORWARD LENGTH=936| Symbols: | Potential natural antisense gene,locus overlaps with AT3G57970 | chr3:21464702-21466627 REVERSE LENGTH=1429| Symbols: | Protein of unknown function (DUF506) | chr1:28989927-28991346 REVERSE LENGTH=1090| Symbols: | Protein with RNI-like/FBD-like domains |chr5:25272033-25273537 FORWARD LENGTH=1350| Symbols: | TRAF-like superfamily protein | chr3:4472563-4474364 REVERSE LENGTH=1662| Symbols: | TRAF-like superfamily protein | chr3:4472562-4474378 REVERSE LENGTH=1665| Symbols: | other RNA |chr5:25346729-25348386 REVERSE LENGTH=1520| Symbols: EMB175,emb1899,EMB166| Pentatricopeptide repeat (PPR)superfamily protein | chr5:1010780-1013586 REVERSE LENGTH=2807| Symbols: | zinc ion binding;zinc ion binding | chr1:6532559-6538145 REVERSE LENGTH=4064| Symbols: | UDPGlycosyltransferase superfamily protein | chr4:8122188-8123835 REVERSE LENGTH=1648| Symbols: DCL2 | dicer-like 2 |chr3:767926-775248 REVERSE LENGTH=4580| Symbols: | transposable element gene | chr5:14822784-14825642 FORWARD LENGTH=2859| Symbols: AtRLP33,RLP33 |receptor like protein 33 |chr3:1648843-1652001 REVERSE LENGTH=3043| Symbols: | Pseudogene of AT5G16486 | chr5:14628221-14628847 REVERSE LENGTH=627| Symbols: | Rho GTPase activating protein with PAK-box/P21-Rhobinding domain | chr4:1374281-1376231 FORWARD LENGTH=1691 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR2937 AT5G13990.1 3 7.348 1 21 2280 2300 AUAAGAGCUGUUGAAGGAGUC : ::.::::::: :.:.::.: GUCUUCUUCAACUGUUUUUGU Translation ath-miR2937 AT1G04310.1 3 9.17 1 21 104 124 AUAAGAGCUGUUGAAGGAGUC ::.:::: ::::::.::: UUCUUCUUCUACAGCUUUUAC Cleavage ath-miR2937 AT3G28923.1 3 21.015 1 21 275 295 AUAAGAGCUGUUGAAGGAGUC ::..::::: .:::.:::: CCCUUUUUCAAAGGCUUUUAU Translation ath-miR2937 AT1G55050.1 3 13.516 1 21 105 126 AUAAGAGCUGU-UGAAGGAGUC :::.:::: ::::.:::::: AUCUCUUUCAGACAGUUCUUAU Translation ath-miR2937 AT4G32590.2 3 17.278 1 21 168 188 AUAAGAGCUGUUGAAGGAGUC ::::: .:::::::::: : AUCUCCUGUAACAGCUCUUCU Cleavage ath-miR2937 AT4G32590.4 3 17.278 1 21 187 207 AUAAGAGCUGUUGAAGGAGUC ::::: .:::::::::: : AUCUCCUGUAACAGCUCUUCU Cleavage ath-miR2937 AT3G49010.5 3 9.149 1 21 592 612 AUAAGAGCUGUUGAAGGAGUC .::.:::: :::.:.:::: UUUUCUUUCAUCAGUUUUUAU Translation ath-miR2937 AT4G32590.3 3 17.278 1 21 187 207 AUAAGAGCUGUUGAAGGAGUC ::::: .:::::::::: : AUCUCCUGUAACAGCUCUUCU Cleavage ath-miR2937 AT4G32590.1 3 17.278 1 21 187 207 AUAAGAGCUGUUGAAGGAGUC ::::: .:::::::::: : AUCUCCUGUAACAGCUCUUCU Cleavage ath-miR2937 AT1G45145.1 3 14.386 1 21 724 744 AUAAGAGCUGUUGAAGGAGUC : :.::::::::::: ::: AUCACUUUCAACAGCUCAUAU Cleavage ath-miR2937 AT4G01915.3 3 13.397 1 21 21 41 AUAAGAGCUGUUGAAGGAGUC ::::::::::.:::: :: UCCUCCUUCAACGACUCUCAU Cleavage| Symbols: ATEXO70C2,EXO70C2 |exocyst subunit exo70 family protein C2 | chr5:4514568-4516892 REVERSE LENGTH=2325| Symbols: ERS2 | ethylene response sensor 2 | chr1:1154764-1157711 REVERSE LENGTH=2470| Symbols: | Pseudogene of AT5G01080; beta-galactosidase |chr3:10954202-10954708 FORWARD LENGTH=507| Symbols: | unknown protein;FUNCTIONS IN: molecular_function unknown; INVOLVED IN:biological_process unknown; LOCATED IN: cellular_component unknown;EXPRESSED IN: cultured cell; BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT1G09040.1); Has 2440 Blast hits to 1999 proteins in 271 species: Archae - 0; Bacteria -138; Metazoa - 960; Fungi - 166;Plants - 162; Viruses - 14; Other Eukaryotes - 1000 (source: NCBI BLink).| chr1:20541887-20545762 FORWARD LENGTH=3022| Symbols: | 2Fe-2S ferredoxin-like superfamily protein |chr4:15721343-15722822 FORWARD LENGTH=646| Symbols: | 2Fe-2S ferredoxin-like superfamily protein |chr4:15721324-15722869 FORWARD LENGTH=712| Symbols: ATBBC1,BBC1,RSU2 |breast basic conserved 1 |chr3:18166769-18168690 REVERSE LENGTH=720| Symbols: | 2Fe-2S ferredoxin-like superfamily protein |chr4:15721324-15722869 FORWARD LENGTH=724| Symbols: | 2Fe-2S ferredoxin-like superfamily protein |chr4:15721324-15722908 FORWARD LENGTH=747| Symbols: ATTRX5,ATH5,LIV1,TRX5| thioredoxin H-type 5 |chr1:17074942-17076330 REVERSE LENGTH=753| Symbols: | unknown protein; Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798;Bacteria - 22429; Metazoa - 974;Fungi - 991; Plants - 531; Viruses- 0; Other Eukaryotes - 9610(source: NCBI BLink).|chr4:827237-828607 FORWARD LENGTH=768 1 1 1 1 1 1 1 1 1 1 1

ath-miR2937 AT4G29350.1 3 13.484 1 21 689 709 AUAAGAGCUGUUGAAGGAGUC ::::: ..:..:::::::: CUCUCCUAUGAUGGCUCUUAU Cleavage ath-miR2937 AT3G49010.4 3 9.149 1 21 747 767 AUAAGAGCUGUUGAAGGAGUC .::.:::: :::.:.:::: UUUUCUUUCAUCAGUUUUUAU Translation ath-miR2937 AT3G49010.2 3 9.149 1 21 753 773 AUAAGAGCUGUUGAAGGAGUC .::.:::: :::.:.:::: UUUUCUUUCAUCAGUUUUUAU Translation ath-miR2937 AT3G49010.1 3 9.149 1 21 763 783 AUAAGAGCUGUUGAAGGAGUC .::.:::: :::.:.:::: UUUUCUUUCAUCAGUUUUUAU Translation ath-miR2937 AT3G49010.3 3 9.149 1 21 778 798 AUAAGAGCUGUUGAAGGAGUC .::.:::: :::.:.:::: UUUUCUUUCAUCAGUUUUUAU Translation ath-miR2937 AT4G01935.1 3 9.543 1 21 66 86 AUAAGAGCUGUUGAAGGAGUC ::::::::::.:::: :: UUCUCCUUCAACGACUCUCAU Cleavage ath-miR2937 AT4G01915.1 3 13.397 1 21 21 41 AUAAGAGCUGUUGAAGGAGUC ::::::::::.:::: :: UCCUCCUUCAACGACUCUCAU Cleavage ath-miR2937 AT2G04810.1 3 17.759 1 21 265 285 AUAAGAGCUGUUGAAGGAGUC ::::: :::::::: ::.: UUCUCCUACAACAGCUAUUGU Cleavage ath-miR2937 AT4G01915.2 3 13.397 1 21 21 41 AUAAGAGCUGUUGAAGGAGUC ::::::::::.:::: :: UCCUCCUUCAACGACUCUCAU Cleavage ath-miR2937 AT1G78880.1 3 4.847 1 21 2002 2022 AUAAGAGCUGUUGAAGGAGUC :::.::.::.: .:::::: CUCUCUUUUAAUAUUUCUUAU Cleavage ath-miR2937 AT1G78882.1 3 4.847 1 21 2002 2022 AUAAGAGCUGUUGAAGGAGUC :::.::.::.: .:::::: CUCUCUUUUAAUAUUUCUUAU Cleavage| Symbols: PFN2,PRO2,PRF2 |profilin 2 | chr4:14450008-14451394 FORWARD LENGTH=798| Symbols: ATBBC1,BBC1,RSU2 |breast basic conserved 1 |chr3:18166769-18168692 REVERSE LENGTH=875| Symbols: ATBBC1,BBC1,RSU2 |breast basic conserved 1 |chr3:18166769-18168692 REVERSE LENGTH=881| Symbols: ATBBC1,BBC1,RSU2 |breast basic conserved 1 |chr3:18166769-18168580 REVERSE LENGTH=891| Symbols: ATBBC1,BBC1,RSU2 |breast basic conserved 1 |chr3:18166769-18168645 REVERSE LENGTH=906| Symbols: | unknown protein;FUNCTIONS IN: molecular_function unknown; INVOLVED IN:biological_process unknown; LOCATED IN: chloroplast; Has 37 Blast hits to 37 proteins in 17 species:Archae - 0; Bacteria - 0; Metazoa -0; Fungi - 0; Plants - 30; Viruses- 0; Other Eukaryotes - 7 (source:NCBI BLink).| chr4:841057-842364 FORWARD LENGTH=952| Symbols: | unknown protein; Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798;Bacteria - 22429; Metazoa - 974;Fungi - 991; Plants - 531; Viruses- 0; Other Eukaryotes - 9610(source: NCBI BLink).|chr4:827237-828607 FORWARD LENGTH=1126| Symbols: | Protein of unknown function (DUF295) | chr2:1688773-1689966 FORWARD LENGTH=1194| Symbols: | unknown protein; Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798;Bacteria - 22429; Metazoa - 974;Fungi - 991; Plants - 531; Viruses- 0; Other Eukaryotes - 9610(source: NCBI BLink).|chr4:827237-828607 FORWARD LENGTH=1209| Symbols: | Ubiquitin-specific protease family C19-related protein| chr1:29652633-29655949 REVERSE LENGTH=2246| Symbols: CPuORF56 | conserved peptide upstream open reading frame 56 | chr1:29652633-29655949 REVERSE LENGTH=2246 1 1 1 1 1 1 1 1 1 1 1

ath-miR2937 AT3G61300.1 3 16.518 1 21 255 275 AUAAGAGCUGUUGAAGGAGUC ::.:::::::: :::: :: UUCUUCUUCAACAUCUCUGAU Cleavage ath-miR2937 AT5G26910.3 3 16.391 1 21 1220 1240 AUAAGAGCUGUUGAAGGAGUC :::::::: :::.:: ::: UUCUCCUUCAUCAGUUCCUAU Translation ath-miR2937 AT5G26910.2 3 16.391 1 21 1289 1309 AUAAGAGCUGUUGAAGGAGUC :::::::: :::.:: ::: UUCUCCUUCAUCAGUUCCUAU Translation ath-miR2937 AT5G26910.1 3 16.391 1 21 1289 1309 AUAAGAGCUGUUGAAGGAGUC :::::::: :::.:: ::: UUCUCCUUCAUCAGUUCCUAU Translation ath-miR2937 AT4G21570.1 3 14.722 1 21 223 243 AUAAGAGCUGUUGAAGGAGUC .::.:::: .::::::::: CGCUUCUUCCCUAGCUCUUAU Translation ath-miR2937 AT1G75880.1 3 15.944 1 21 745 765 AUAAGAGCUGUUGAAGGAGUC .::.:::.:: :::::::: CGCUUCUUUCACCGCUCUUAU Translation ath-miR2937 AT1G75880.2 3 15.944 1 21 748 768 AUAAGAGCUGUUGAAGGAGUC .::.:::.:: :::::::: CGCUUCUUUCACCGCUCUUAU Translation ath-miR2937 AT3G14640.1 3 18.102 1 21 138 158 AUAAGAGCUGUUGAAGGAGUC ::::::: ::: ::::::: AACUCCUUACACACCUCUUAU Cleavage ath-miR2938 AT4G08870.1 1.5 15.525 1 21 768 788 GAUCUUUUGAGAGGGUUCCAG :::::.:::::::::::: UGCGAACCUUCUCAAAAGAUC Cleavage ath-miR2938 AT4G08900.1 2 23.969 1 21 880 900 GAUCUUUUGAGAGGGUUCCAG :::::.::::.::::::: UGCGAACCUUCUCGAAAGAUC Cleavage ath-miR2938 AT2G31081.1 2 14.826 1 21 179 199 GAUCUUUUGAGAGGGUUCCAG ::.: :.:::::::::::: GAGGGAACUUCUCAAAAGAUC Cleavage| Symbols: | C2 calcium/lipidbinding plant phosphoribosyltransferase family protein | chr3:22687570-22690619 FORWARD LENGTH=3050| Symbols: | unknown protein;FUNCTIONS IN: molecular_function unknown; INVOLVED IN:biological_process unknown; LOCATED IN: mitochondrion; EXPRESSED IN: 22 plant structures; EXPRESSED DURING:13 growth stages; BEST Arabidopsis thaliana protein match is: unknown protein (TAIR:AT3G58650.1).|chr5:9465941-9470337 REVERSE LENGTH=3323| Symbols: | unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT3G58650.1); Has 990 Blast hits to 447 proteins in 125 species: Archae - 0; Bacteria -525; Metazoa - 80; Fungi - 59;Plants - 91; Viruses - 0; Other Eukaryotes - 235 (source: NCBI BLink).| chr5:9465929-9470403 REVERSE LENGTH=3394| Symbols: | unknown protein; BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT3G58650.1); Has 1322 Blast hits to 684 proteins in 162 species: Archae - 4; Bacteria -497; Metazoa - 157; Fungi - 101;Plants - 155; Viruses - 0; Other Eukaryotes - 408 (source: NCBI BLink).| chr5:9465929-9470403 REVERSE LENGTH=3404| Symbols: | Protein of unknown function (DUF300) | chr4:11470883-11472981 REVERSE LENGTH=1380| Symbols: | SGNH hydrolase-type esterase superfamily protein |chr1:28490449-28492464 FORWARD LENGTH=1409| Symbols: | SGNH hydrolase-type esterase superfamily protein |chr1:28490443-28492464 FORWARD LENGTH=1412| Symbols: CYP72A10 | cytochrome P450,family 72,subfamily A,polypeptide 10 | chr3:4919856-4921787 FORWARD LENGTH=1545| Symbols: | Arginase/deacetylase superfamily protein | chr4:5646439-5648727 REVERSE LENGTH=1284| Symbols: | arginase |chr4:5703347-5705346 FORWARD LENGTH=1347| Symbols: CLE4 | CLAVATA3/ESRRELATED 4 | chr2:13238047-13238600 FORWARD LENGTH=554 1 1 1 1 1 1 1 1 1 1 1

ath-miR2938 AT5G01110.1 2.5 15.839 1 21 1570 1590 GAUCUUUUGAGAGGGUUCCAG ::::.:.::.::::::::: AUGGAGCUCUUUCAAAAGAUG Cleavage ath-miR2938 AT5G64816.1 2.5 16.901 1 21 254 274 GAUCUUUUGAGAGGGUUCCAG .::::.:..:::: ::::::: UUGGAGCUUUCUCUAAAGAUC Cleavage ath-miR2938 AT5G64816.2 2.5 16.901 1 21 306 326 GAUCUUUUGAGAGGGUUCCAG .::::.:..:::: ::::::: UUGGAGCUUUCUCUAAAGAUC Cleavage ath-miR2938 AT1G73820.1 2.5 17.34 1 21 516 536 GAUCUUUUGAGAGGGUUCCAG .::::::.:: ::::.::::.UUGGAACUCUGUCAAGAGAUU Translation ath-miR2938 AT5G52810.1 2.5 18.851 1 21 714 734 GAUCUUUUGAGAGGGUUCCAG ::: ::::::::: ::.:::: CUGAAACCCUCUCCAAGGAUC Cleavage ath-miR2938 AT4G08262.1 2.5 14.193 1 21 1228 1248 GAUCUUUUGAGAGGGUUCCAG ::: ::.:: ::::::::::: CUGCAAUCCCCUCAAAAGAUC Cleavage ath-miR2938 AT1G50500.1 2.5 17.175 1 21 377 397 GAUCUUUUGAGAGGGUUCCAG :::::.:::::: :::::.GAGGAACUCUCUCAUAAGAUU Cleavage ath-miR2938 AT1G50500.2 2.5 17.175 1 21 392 412 GAUCUUUUGAGAGGGUUCCAG :::::.:::::: :::::.GAGGAACUCUCUCAUAAGAUU Cleavage ath-miR2938 AT4G17585.1 3 18.286 1 21 70 90 GAUCUUUUGAGAGGGUUCCAG :: :::::.::: :.:::::: CUAGAACCUUCUGAGAAGAUC Translation ath-miR2938 AT4G17970.1 3 19.57 1 21 144 164 GAUCUUUUGAGAGGGUUCCAG :: :::::.::: :::::::.CUCGAACCUUCUGAAAAGAUU Translation ath-miR2938 AT5G17125.1 3 18.307 1 21 1 21 GAUCUUUUGAGAGGGUUCCAG ::::.:.::::::::::: AUGGAGACUUCUCAAAAGAUG Cleavage ath-miR2938 AT4G38340.1 3 11.133 1 21 4 24 GAUCUUUUGAGAGGGUUCCAG :::.:::.:.: :::::::.GUGGGACCUUUUAAAAAGAUU Translation ath-miR2938 AT1G50970.1 3 15.276 1 21 199 219 GAUCUUUUGAGAGGGUUCCAG :::::.:::::: ::::: GAGGAACUCUCUCAUAAGAUA Cleavage ath-miR2938 AT1G77140.1 3 23.844 1 21 920 940 GAUCUUUUGAGAGGGUUCCAG .::::: .::.::::::::: UUGGAAGUCUUCCAAAAGAUC Translation| Symbols: | Tetratricopeptide repeat (TPR)-like superfamily protein | chr5:41768-44375 REVERSE LENGTH=2608| Symbols: | unknown protein; Has 30201 Blast hits to 17322 proteins in 780 species: Archae - 12;Bacteria - 1396; Metazoa - 17338;Fungi - 3422; Plants - 5037;Viruses - 0; Other Eukaryotes -2996 (source: NCBI BLink).|chr5:25913028-25914003 FORWARD LENGTH=583| Symbols: | unknown protein; Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798;Bacteria - 22429; Metazoa - 974;Fungi - 991; Plants - 531; Viruses- 0; Other Eukaryotes - 9610(source: NCBI BLink).|chr5:25913000-25914027 FORWARD LENGTH=659| Symbols: | Ssu72-like family protein | chr1:27755512-27757211 REVERSE LENGTH=863| Symbols: | NAD(P)-binding Rossmann-fold superfamily protein |chr5:21399331-21400603 FORWARD LENGTH=1273| Symbols: | transposable element gene | chr4:5204783-5210272 FORWARD LENGTH=5490| Symbols: HIT1,ATVPS53,VPS53 |Membrane trafficking VPS53 family protein | chr1:18707987-18715977 REVERSE LENGTH=2895| Symbols: HIT1 | Membrane trafficking VPS53 family protein |chr1:18707990-18715935 REVERSE LENGTH=2907| Symbols: | Aluminium activated malate transporter family protein |chr4:9792523-9793259 REVERSE LENGTH=459| Symbols: ALMT12,ATALMT12 |aluminum-activated,malate transporter 12 | chr4:9975408-9977722 FORWARD LENGTH=1757| Symbols: | transposable element gene | chr5:5630538-5634764 FORWARD LENGTH=4227| Symbols: | Plant regulator RWP-RK family protein | chr4:17954710-17957828 FORWARD LENGTH=2304| Symbols: | Membrane trafficking VPS53 family protein |chr1:18896323-18900268 FORWARD LENGTH=1710| Symbols: VPS45,ATVPS45 |vacuolar protein sorting 45 |chr1:28984025-28987983 FORWARD LENGTH=2150 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR2938 AT1G72850.1 3 21.636 1 21 310 330 GAUCUUUUGAGAGGGUUCCAG ::::::::.::::.:: :.GCGGAACCCUUUCAAGAGCUU Cleavage ath-miR2938 AT4G13750.1 3 20.123 1 21 5635 5655 GAUCUUUUGAGAGGGUUCCAG : ::::...:.::::.::::.CGGGAAUUUUUUCAAGAGAUU Cleavage ath-miR2938 AT1G72270.1 3 15.418 1 21 6260 6280 GAUCUUUUGAGAGGGUUCCAG : ::::.:.:.:..::::::.CAGGAAUCUUUUUGAAAGAUU Cleavage ath-miR2938 AT2G46370.3 3 11.729 1 21 536 556 GAUCUUUUGAGAGGGUUCCAG : ::::..::::.:.::::: CCGGAAUUCUCUUCAGAGAUC Cleavage ath-miR2938 AT2G46370.2 3 11.729 1 21 710 730 GAUCUUUUGAGAGGGUUCCAG : ::::..::::.:.::::: CCGGAAUUCUCUUCAGAGAUC Cleavage ath-miR2938 AT2G46370.1 3 11.729 1 21 785 805 GAUCUUUUGAGAGGGUUCCAG : ::::..::::.:.::::: CCGGAAUUCUCUUCAGAGAUC Cleavage ath-miR2938 AT2G46370.4 3 11.729 1 21 1148 1168 GAUCUUUUGAGAGGGUUCCAG : ::::..::::.:.::::: CCGGAAUUCUCUUCAGAGAUC Cleavage ath-miR2938 AT3G30300.1 3 17.018 1 21 1944 1963 GAUCUUUUGAGAGGGUUCCAG :::::.:.:: ::::::::: AUGGAAUCUUC-CAAAAGAUC Translation ath-miR2938 AT1G50840.1 3 14.776 1 21 654 674 GAUCUUUUGAGAGGGUUCCAG ::: :::::::.:::::.UAUGAAACCUCUCAGAAGAUU Cleavage ath-miR2938 AT4G06487.1 3 18.818 1 21 3593 3613 GAUCUUUUGAGAGGGUUCCAG ::: :.::::::::.::: UAGGAUCUCUCUCAAAGGAUG Cleavage ath-miR2938 AT1G53910.2 3 20.018 1 21 1194 1214 GAUCUUUUGAGAGGGUUCCAG :::..:.::: ::.::::: GAGGAGUCUUCUGAAGAGAUC Translation ath-miR2938 AT1G53910.3 3 18.3 1 21 1188 1208 GAUCUUUUGAGAGGGUUCCAG :::..:.::: ::.::::: GAGGAGUCUUCUGAAGAGAUC Translation ath-miR2938 AT1G53910.1 3 18.3 1 21 1194 1214 GAUCUUUUGAGAGGGUUCCAG :::..:.::: ::.::::: GAGGAGUCUUCUGAAGAGAUC Translation ath-miR2938 AT1G07380.1 3 17.123 1 21 1425 1445 GAUCUUUUGAGAGGGUUCCAG ::::::::.:: ..::::.GGGGAACCCUUUCUGGAGAUU Cleavage| Symbols: | Disease resistance protein (TIR-NBS class) |chr1:27413971-27415335 FORWARD LENGTH=1269| Symbols: NOV | Histidine kinase-,DNA gyrase B-,and HSP90-like ATPase family protein |chr4:7975191-7987620 FORWARD LENGTH=8252| Symbols: | CONTAINS InterPro DOMAIN/s: Ribosome 60S biogenesis N-terminal (InterPro:IPR021714);BEST Arabidopsis thaliana protein match is: unknown protein(TAIR:AT4G27010.1); Has 772 Blast hits to 657 proteins in 120 species: Archae - 0; Bacteria - 0;Metazoa - 344; Fungi - 94; Plants -322; Viruses - 0; Other Eukaryotes- 12 (source: NCBI BLink).|chr1:27199733-27211161 REVERSE LENGTH=8577| Symbols: JAR1,FIN219 | Auxinresponsive GH3 family protein |chr2:19033790-19036659 FORWARD LENGTH=1931| Symbols: JAR1,FIN219 | Auxinresponsive GH3 family protein |chr2:19033782-19036659 FORWARD LENGTH=2105| Symbols: JAR1,FIN219 | Auxinresponsive GH3 family protein |chr2:19033790-19036659 FORWARD LENGTH=2180| Symbols: JAR1 | Auxin-responsive GH3 family protein | chr2:19033741-19036445 FORWARD LENGTH=2329| Symbols: | O-fucosyltransferase family protein | chr3:11921198-11924574 REVERSE LENGTH=2486| Symbols: POLGAMMA2 | polymerase gamma 2 | chr1:18839107-18844559 FORWARD LENGTH=3569| Symbols: | transposable element gene | chr4:3099364-3105303 FORWARD LENGTH=5940| Symbols: RAP2.12 | related to AP2 12 | chr1:20135112-20136941 FORWARD LENGTH=1453| Symbols: RAP2.12 | related to AP2 12 | chr1:20135112-20136970 FORWARD LENGTH=1590| Symbols: RAP2.12 | related to AP2 12 | chr1:20135112-20136970 FORWARD LENGTH=1596| Symbols: | Neutral/alkaline nonlysosomal ceramidase |chr1:2264829-2268306 REVERSE LENGTH=2340 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR2938 AT5G09320.1 3 16.464 1 21 307 327 GAUCUUUUGAGAGGGUUCCAG : :::.::.:::.:::::.GAGAAACUCUUUCAGAAGAUU Cleavage ath-miR2938 AT3G20440.3 3 20.325 1 21 2500 2520 GAUCUUUUGAGAGGGUUCCAG :: :.:::.::::.::.:: AGGGUAUCCUUUCAAGAGGUC Cleavage ath-miR2938 AT3G20440.1 3 19.985 1 21 2348 2368 GAUCUUUUGAGAGGGUUCCAG :: :.:::.::::.::.:: AGGGUAUCCUUUCAAGAGGUC Cleavage ath-miR2938 AT3G20440.2 3 19.985 1 21 2438 2458 GAUCUUUUGAGAGGGUUCCAG :: :.:::.::::.::.:: AGGGUAUCCUUUCAAGAGGUC Cleavage ath-miR2938 AT5G24740.1 3 18.161 1 21 9247 9267 GAUCUUUUGAGAGGGUUCCAG ::::.: :.:::..::::: UGGGAAUCAUUUCAGGAGAUC Cleavage ath-miR319a AT2G26950.1 1.5 18.403 1 21 826 846 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: UUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319a AT5G06100.1 1.5 21.666 1 21 1160 1180 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: CUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319a AT5G06100.3 1.5 21.666 1 21 1248 1268 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: CUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319a AT5G06100.2 1.5 21.666 1 21 1160 1180 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: CUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319a AT2G31070.1 2.5 10.122 1 21 1380 1400 UUGGACUGAAGGGAGCUCCCU : ::.:.::::::::::::.AAGGGGUACCCUUCAGUCCAG Cleavage ath-miR319a AT3G66658.1 2.5 22.764 1 21 1087 1107 UUGGACUGAAGGGAGCUCCCU : ::.:: :.::::::::::.AAGGGGCACUCUUCAGUCCAG Cleavage ath-miR319a AT3G66658.2 2.5 22.764 1 21 1101 1121 UUGGACUGAAGGGAGCUCCCU : ::.:: :.::::::::::.AAGGGGCACUCUUCAGUCCAG Cleavage ath-miR319a AT2G29570.1 2.5 15.1 1 21 109 129 UUGGACUGAAGGGAGCUCCCU ::::::.: ::.:::.::: UUGGAGCUUCGUUUAGUUCAA Translation ath-miR319a AT3G15030.3 2.5 13.479 1 21 1300 1320 UUGGACUGAAGGGAGCUCCCU ::.:.::::::::::::.GAGGGGUCCCCUUCAGUCCAG Cleavage ath-miR319a AT3G15030.2 2.5 13.479 1 21 1476 1496 UUGGACUGAAGGGAGCUCCCU ::.:.::::::::::::.GAGGGGUCCCCUUCAGUCCAG Cleavage ath-miR319a AT3G15030.1 2.5 13.479 1 21 1476 1496 UUGGACUGAAGGGAGCUCCCU ::.:.::::::::::::.GAGGGGUCCCCUUCAGUCCAG Cleavage ath-miR319a AT3G33076.1 2.5 18.349 1 21 3305 3325 UUGGACUGAAGGGAGCUCCCU ::: ::::::::: ::::: UAGGAUCUCCCUUCAUUCCAA Cleavage ath-miR319a AT4G22415.1 2.5 23.226 1 21 3332 3352 UUGGACUGAAGGGAGCUCCCU ::: ::::::::: ::::: CAGGAUCUCCCUUCAUUCCAA Cleavage| Symbols: VPS9B | Vacuolar sorting protein 9 (VPS9) domain |chr5:2888655-2892016 REVERSE LENGTH=2491| Symbols: EMB2729 | Alpha amylase family protein | chr3:7123423-7130477 REVERSE LENGTH=2987| Symbols: EMB2729,BE1 | Alpha amylase family protein |chr3:7123197-7130436 REVERSE LENGTH=3088| Symbols: EMB2729,BE1 | Alpha amylase family protein |chr3:7123197-7130436 REVERSE LENGTH=3178| Symbols: | Protein of unknown function (DUF1162) | chr5:8469951-8489703 REVERSE LENGTH=10517| Symbols: AtMYB104,MYB104 | myb domain protein 104 | chr2:11500721-11502136 REVERSE LENGTH=1212| Symbols: MYB33,ATMYB33 | myb domain protein 33 | chr5:1837914-1839997 FORWARD LENGTH=1579| Symbols: MYB33,ATMYB33 | myb domain protein 33 | chr5:1837907-1840417 FORWARD LENGTH=1905| Symbols: MYB33,ATMYB33 | myb domain protein 33 | chr5:1837914-1840727 FORWARD LENGTH=2127| Symbols: TCP10 | TCP domain protein 10 | chr2:13220478-13222609 REVERSE LENGTH=2017| Symbols: ALDH22A1 | aldehyde dehydrogenase 22A1 | chr3:2095105-2099137 REVERSE LENGTH=2155| Symbols: ALDH22A1 | aldehyde dehydrogenase 22A1 | chr3:2095105-2099151 REVERSE LENGTH=2165| Symbols: PCNA2,ATPCNA2 |proliferating cell nuclear antigen 2 | chr2:12649906-12651703 REVERSE LENGTH=1133| Symbols: TCP4 | TCP family transcription factor 4 |chr3:5061681-5064115 FORWARD LENGTH=2033| Symbols: TCP4 | TCP family transcription factor 4 |chr3:5061681-5064038 FORWARD LENGTH=2121| Symbols: TCP4,MEE35 | TCP family transcription factor 4 |chr3:5061681-5064115 FORWARD LENGTH=2209| Symbols: | transposable element gene | chr3:13739731-13744449 REVERSE LENGTH=4719| Symbols: | transposable element gene | chr4:11820325-11825184 REVERSE LENGTH=4860 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR319b AT2G26950.1 1.5 18.403 1 21 826 846 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: UUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319b AT5G06100.1 1.5 21.666 1 21 1160 1180 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: CUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319b AT5G06100.3 1.5 21.666 1 21 1248 1268 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: CUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319b AT5G06100.2 1.5 21.666 1 21 1160 1180 UUGGACUGAAGGGAGCUCCCU ::::::::::::: ::::: CUGGAGCUCCCUUCAUUCCAA Cleavage ath-miR319b AT2G31070.1 2.5 10.122 1 21 1380 1400 UUGGACUGAAGGGAGCUCCCU : ::.:.::::::::::::.AAGGGGUACCCUUCAGUCCAG Cleavage ath-miR319b AT3G66658.1 2.5 22.764 1 21 1087 1107 UUGGACUGAAGGGAGCUCCCU : ::.:: :.::::::::::.AAGGGGCACUCUUCAGUCCAG Cleavage ath-miR319b AT3G66658.2 2.5 22.764 1 21 1101 1121 UUGGACUGAAGGGAGCUCCCU : ::.:: :.::::::::::.AAGGGGCACUCUUCAGUCCAG Cleavage ath-miR319b AT2G29570.1 2.5 15.1 1 21 109 129 UUGGACUGAAGGGAGCUCCCU ::::::.: ::.:::.::: UUGGAGCUUCGUUUAGUUCAA Translation ath-miR319b AT3G15030.3 2.5 13.479 1 21 1300 1320 UUGGACUGAAGGGAGCUCCCU ::.:.::::::::::::.GAGGGGUCCCCUUCAGUCCAG Cleavage ath-miR319b AT3G15030.2 2.5 13.479 1 21 1476 1496 UUGGACUGAAGGGAGCUCCCU ::.:.::::::::::::.GAGGGGUCCCCUUCAGUCCAG Cleavage ath-miR319b AT3G15030.1 2.5 13.479 1 21 1476 1496 UUGGACUGAAGGGAGCUCCCU ::.:.::::::::::::.GAGGGGUCCCCUUCAGUCCAG Cleavage ath-miR319b AT3G33076.1 2.5 18.349 1 21 3305 3325 UUGGACUGAAGGGAGCUCCCU ::: ::::::::: ::::: UAGGAUCUCCCUUCAUUCCAA Cleavage ath-miR319b AT4G22415.1 2.5 23.226 1 21 3332 3352 UUGGACUGAAGGGAGCUCCCU ::: ::::::::: ::::: CAGGAUCUCCCUUCAUUCCAA Cleavage ath-miR319b AT5G28335.1 2.5 18.357 1 21 3571 3591 UUGGACUGAAGGGAGCUCCCU ::: ::::::::: ::::: UAGGAUCUCCCUUCAUUCCAA Cleavage ath-miR319b AT3G33084.1 2.5 18.349 1 21 3613 3633 UUGGACUGAAGGGAGCUCCCU ::: ::::::::: ::::: UAGGAUCUCCCUUCAUUCCAA Cleavage ath-miR319b AT1G30210.2 2.5 20.637 1 21 1012 1032 UUGGACUGAAGGGAGCUCCCU ::.: ::::::::::::: UAGGGGGACCCUUCAGUCCAA Cleavage ath-miR319b AT4G18390.2 2.5 15.631 1 21 1126 1146 UUGGACUGAAGGGAGCUCCCU ::.: ::::::::::::: CAGGGGGACCCUUCAGUCCAA Cleavage ath-miR319b AT1G30210.1 2.5 20.637 1 21 1131 1151 UUGGACUGAAGGGAGCUCCCU ::.: ::::::::::::: UAGGGGGACCCUUCAGUCCAA Cleavage| Symbols: AtMYB104,MYB104 | myb domain protein 104 | chr2:11500721-11502136 REVERSE LENGTH=1212| Symbols: MYB33,ATMYB33 | myb domain protein 33 | chr5:1837914-1839997 FORWARD LENGTH=1579| Symbols: MYB33,ATMYB33 | myb domain protein 33 | chr5:1837907-1840417 FORWARD LENGTH=1905| Symbols: MYB33,ATMYB33 | myb domain protein 33 | chr5:1837914-1840727 FORWARD LENGTH=2127| Symbols: TCP10 | TCP domain protein 10 | chr2:13220478-13222609 REVERSE LENGTH=2017| Symbols: ALDH22A1 | aldehyde dehydrogenase 22A1 | chr3:2095105-2099137 REVERSE LENGTH=2155| Symbols: ALDH22A1 | aldehyde dehydrogenase 22A1 | chr3:2095105-2099151 REVERSE LENGTH=2165| Symbols: PCNA2,ATPCNA2 |proliferating cell nuclear antigen 2 | chr2:12649906-12651703 REVERSE LENGTH=1133| Symbols: TCP4 | TCP family transcription factor 4 |chr3:5061681-5064115 FORWARD LENGTH=2033| Symbols: TCP4 | TCP family transcription factor 4 |chr3:5061681-5064038 FORWARD LENGTH=2121| Symbols: TCP4,MEE35 | TCP family transcription factor 4 |chr3:5061681-5064115 FORWARD LENGTH=2209| Symbols: | transposable element gene | chr3:13739731-13744449 REVERSE LENGTH=4719| Symbols: | transposable element gene | chr4:11820325-11825184 REVERSE LENGTH=4860| Symbols: | transposable element gene | chr5:10308601-10313586 REVERSE LENGTH=4986| Symbols: | transposable element gene | chr3:13675144-13680170 FORWARD LENGTH=5027| Symbols: TCP24 | TEOSINTE BRANCHED 1,cycloidea,and PCF family 24 | chr1:10627185-10630610 REVERSE LENGTH=1553| Symbols: TCP2 | TEOSINTE BRANCHED 1,cycloidea and PCF transcription factor 2 | chr4:10162979-10165546 REVERSE LENGTH=1569| Symbols: TCP24,ATTCP24 |TEOSINTE BRANCHED 1,cycloidea,and PCF family 24 | chr1:10627185-10630538 REVERSE LENGTH=1672 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR319b AT4G18390.1 2.5 15.631 1 21 1376 1396 UUGGACUGAAGGGAGCUCCCU ::.: ::::::::::::: CAGGGGGACCCUUCAGUCCAA Cleavage ath-miR319b AT1G48090.1 2.5 12.037 1 21 6898 6918 UUGGACUGAAGGGAGCUCCCU ::: .::::::::::::: UUGGAAUCCCCUUCAGUCCAA Cleavage ath-miR319b AT5G67090.1 3 19.478 1 21 1154 1174 UUGGACUGAAGGGAGCUCCCU .: :::.:::::::.::.::.GGAGAGUUCCCUUCGGUUCAG Cleavage ath-miR319b AT2G26960.1 3 19.901 1 21 863 883 UUGGACUGAAGGGAGCUCCCU :::.:::::::: ::::: UUCGAGUUCCCUUCAUUCCAA Cleavage ath-miR319b AT5G35413.1 3 20.29 1 21 2718 2738 UUGGACUGAAGGGAGCUCCCU : ::::.:::::::.::....AUGGAGUUCCCUUCGGUUUGG Cleavage ath-miR319b AT1G53230.1 3 14.601 1 21 1184 1204 UUGGACUGAAGGGAGCUCCCU ::.:.:::::::::::: GAGGGGUCCCCUUCAGUCCAU Cleavage ath-miR319b AT3G61740.2 3 13.975 1 21 3370 3390 UUGGACUGAAGGGAGCUCCCU ::::::.::: ::::.:: CUAGAGCUCUCUUAAGUCUAA Cleavage ath-miR319b AT3G61740.1 3 13.975 1 21 3478 3498 UUGGACUGAAGGGAGCUCCCU ::::::.::: ::::.:: CUAGAGCUCUCUUAAGUCUAA Cleavage ath-miR319b AT1G35870.1 3 18.621 1 21 2920 2940 UUGGACUGAAGGGAGCUCCCU : ::: ::::.:::: ::::: AAGGAUCUCCUUUCAUUCCAA Cleavage ath-miR319b AT3G60460.1 3 20.145 1 21 96 116 UUGGACUGAAGGGAGCUCCCU :::::::: :::.::::: UUGGAGCUCCAUUCGAUCCAA Translation ath-miR319b AT5G27550.1 3 19.886 1 21 2214 2234 UUGGACUGAAGGGAGCUCCCU ::::.::::: :::.::: GUGGAGUCCCCUUAAGUUCAA Cleavage ath-miR319b AT5G29053.1 3 22.3 1 21 145 165 UUGGACUGAAGGGAGCUCCCU :::: ::.:: ::::.::: GUGGAGAUCUCUCCAGUUCAA Translation ath-miR394b-5p AT1G27340.1 1 14.87 1 20 1373 1392 UUGGCAUUCUGUCCACCUCC :::::: ::::::::::::: GGAGGUUGACAGAAUGCCAA Cleavage ath-miR394b-5p AT4G20430.2 2.5 17.878 1 20 1779 1798 UUGGCAUUCUGUCCACCUCC : ::::::::: :::::.:: GCAGGUGGACAAAAUGCUAA Translation ath-miR394b-5p AT4G20430.1 2.5 17.878 1 20 1859 1878 UUGGCAUUCUGUCCACCUCC : ::::::::: :::::.:: GCAGGUGGACAAAAUGCUAA Translation ath-miR394b-5p AT3G58570.1 2.5 24.905 1 20 1135 1154 UUGGCAUUCUGUCCACCUCC :::: :::::::::::...UGAGGCGGACAGAAUGCUGG Cleavage| Symbols: TCP2 | TEOSINTE BRANCHED 1,cycloidea and PCF transcription factor 2 | chr4:10162953-10165562 REVERSE LENGTH=1845| Symbols: | calcium-dependent lipid-binding family protein |chr1:17732010-17758444 REVERSE LENGTH=12995| Symbols: | Subtilisin-like serine endopeptidase family protein |chr5:26774018-26776391 REVERSE LENGTH=2374| Symbols: AtMYB81,MYB81 | myb domain protein 81 | chr2:11506065-11507426 REVERSE LENGTH=1285| Symbols: | transposable element gene | chr5:13639182-13643273 REVERSE LENGTH=4092| Symbols: TCP3 | TEOSINTE BRANCHED 1,cycloidea and PCF transcription factor 3 | chr1:19849788-19851725 REVERSE LENGTH=1844| Symbols: SDG14,ATX3 | SET domain protein 14 | chr3:22850837-22856972 REVERSE LENGTH=3669| Symbols: SDG14,ATX3 | SET domain protein 14 | chr3:22850837-22856972 REVERSE LENGTH=3777| Symbols: | transposable element gene | chr1:13335257-13339587 FORWARD LENGTH=4331| Symbols: DUO1 | myb-like HTH transcriptional regulator family protein | chr3:22342429-22343491 REVERSE LENGTH=894| Symbols: | P-loop containing nucleoside triphosphate hydrolases superfamily protein | chr5:9727454-9731341 REVERSE LENGTH=2496| Symbols: | transposable element gene | chr5:11112540-11116875 REVERSE LENGTH=4336| Symbols: | Galactose oxidase/kelch repeat superfamily protein | chr1:9495520-9498085 FORWARD LENGTH=1853| Symbols: | Subtilase family protein | chr4:11017629-11021272 REVERSE LENGTH=2693| Symbols: | Subtilase family protein | chr4:11017656-11021280 REVERSE LENGTH=2746| Symbols: | P-loop containing nucleoside triphosphate hydrolases superfamily protein |chr3:21656504-21660532 FORWARD LENGTH=2341 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR394b-5p AT5G20580.1 3 18.808 1 20 1184 1203 UUGGCAUUCUGUCCACCUCC ::::::::: ::::: .::: GGAGGUGGAGAGAAUAUCAA Translation ath-miR394b-5p AT5G20580.2 3 18.808 1 20 1184 1203 UUGGCAUUCUGUCCACCUCC ::::::::: ::::: .::: GGAGGUGGAGAGAAUAUCAA Translation ath-miR394b-5p AT1G01320.1 3 24.088 1 20 661 680 UUGGCAUUCUGUCCACCUCC ::::::::: ::::: :.:: GGAGGUGGAAAGAAUUCUAA Translation ath-miR394b-5p AT1G01320.2 3 24.088 1 20 668 687 UUGGCAUUCUGUCCACCUCC ::::::::: ::::: :.:: GGAGGUGGAAAGAAUUCUAA Translation ath-miR394b-5p AT3G48460.1 3 15.922 1 20 802 821 UUGGCAUUCUGUCCACCUCC ::: ::: .::::.:::::: GGAUGUGUGCAGAGUGCCAA Cleavage ath-miR394b-5p AT5G36170.2 3 16.726 1 20 1034 1053 UUGGCAUUCUGUCCACCUCC ::: ::::::::::..:: AAAGGAGGACAGAAUGUUAA Cleavage ath-miR394b-5p AT5G36170.1 3 16.726 1 20 1037 1056 UUGGCAUUCUGUCCACCUCC ::: ::::::::::..:: AAAGGAGGACAGAAUGUUAA Cleavage ath-miR394b-5p AT5G36170.3 3 16.717 1 20 1037 1056 UUGGCAUUCUGUCCACCUCC ::: ::::::::::..:: AAAGGAGGACAGAAUGUUAA Cleavage ath-miR394b-5p AT5G56630.1 3 18.278 1 20 879 898 UUGGCAUUCUGUCCACCUCC :::::::::: .:: :::: AGAGGUGGACAUGAUACCAA Translation ath-miR394b-5p AT5G56950.1 3 13.777 1 20 848 867 UUGGCAUUCUGUCCACCUCC ::::: : :::::::::: AAAGGUGCAAAGAAUGCCAA Translation ath-miR394b-5p AT5G26749.2 3 18.683 1 20 659 678 UUGGCAUUCUGUCCACCUCC ::::: :.::::::.::: CGAGGUUGGAAGAAUGUCAA Translation ath-miR399c-5p AT2G33770.1 1 19.497 1 21 829 849 UGCCAAAGGAGAGUUGCCCUG :::::: :::::::::::: UUGGGCAAAUCUCCUUUGGCA Cleavage| Symbols: | BEST Arabidopsis thaliana protein match is: FRIGIDA interacting protein 1(TAIR:AT2G06005.1); Has 167 Blast hits to 167 proteins in 73 species:Archae - 0; Bacteria - 25; Metazoa- 58; Fungi - 25; Plants - 43;Viruses - 0; Other Eukaryotes - 16(source: NCBI BLink).|chr5:6958628-6962804 REVERSE LENGTH=1421| Symbols: | BEST Arabidopsis thaliana protein match is: FRIGIDA interacting protein 1(TAIR:AT2G06005.1); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria -22429; Metazoa - 974; Fungi - 991;Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink).| chr5:6958597-6962804 REVERSE LENGTH=1452| Symbols: | Tetratricopeptide repeat (TPR)-like superfamily protein | chr1:121124-130570 REVERSE LENGTH=6015| Symbols: | Tetratricopeptide repeat (TPR)-like superfamily protein | chr1:121067-130577 REVERSE LENGTH=6049| Symbols: | GDSL-like Lipase/Acylhydrolase superfamily protein | chr3:17949445-17951195 FORWARD LENGTH=1310| Symbols: HCF109,ATPRFB | high chlorophyll fluorescent 109 |chr5:14235876-14238026 REVERSE LENGTH=1627| Symbols: HCF109,ATPRFB | high chlorophyll fluorescent 109 |chr5:14235876-14238026 REVERSE LENGTH=1630| Symbols: HCF109,ATPRFB | high chlorophyll fluorescent 109 |chr5:14235876-14238026 REVERSE LENGTH=1649| Symbols: PFK7 |phosphofructokinase 7 |chr5:22923922-22926963 FORWARD LENGTH=2082| Symbols: NFA03,NFA3,NAP1;3 |nucleosome assembly protein 1;3 |chr5:23032449-23035661 FORWARD LENGTH=1656| Symbols: | C2H2 and C2HC zinc fingers superfamily protein |chr5:9398015-9399267 REVERSE LENGTH=799| Symbols: UBC24,ATUBC24,PHO2 |phosphate 2 | chr2:14277558-14283040 REVERSE LENGTH=4103 1 1 1 1 1 1 1 1 1 1 1 5

ath-miR399c-5p AT2G33770.1 1.5 11.851 1 21 607 627 UGCCAAAGGAGAGUUGCCCUG .::::::: :::.:::::::: UAGGGCAAAUCUUCUUUGGCA Cleavage ath-miR399c-5p AT2G33770.1 2 23.072 1 21 740 760 UGCCAAAGGAGAGUUGCCCUG .:::::: :::::::::::: UAGGGCAUAUCUCCUUUGGCA Cleavage ath-miR399c-5p AT2G33770.1 2 14.244 1 21 943 963 UGCCAAAGGAGAGUUGCCCUG .:: :::: :::::::::::: UAGAGCAAAUCUCCUUUGGCA Cleavage ath-miR399c-5p AT2G33770.1 2 9.899 1 21 886 906 UGCCAAAGGAGAGUUGCCCUG : :::: :::::::::::: UCGAGCAAAUCUCCUUUGGCA Cleavage ath-miR399c-5p AT3G06500.1 2.5 20.995 1 21 1880 1900 UGCCAAAGGAGAGUUGCCCUG : :: :::::::::: ::::: CUGGCCAACUCUCCUCUGGCA Cleavage ath-miR399c-5p AT1G56560.1 2.5 23.028 1 21 1594 1614 UGCCAAAGGAGAGUUGCCCUG : :: :::: ::.:::::::: CUGGCCAACACUUCUUUGGCA Cleavage ath-miR399c-5p AT3G59420.1 3 19.342 1 21 2488 2508 UGCCAAAGGAGAGUUGCCCUG ::..::::::::::::: GAUAGCGGCUCUCCUUUGGCA Cleavage ath-miR399c-5p AT5G27630.1 3 14.082 1 21 2045 2065 UGCCAAAGGAGAGUUGCCCUG :::.::::::..:::: :: UCGGGUAACUCUUUUUUGUCA Cleavage ath-miR399c-5p AT5G35210.1 3 21.714 1 21 1705 1725 UGCCAAAGGAGAGUUGCCCUG ::::.:::::.::: ::.: AUGGGCGACUCUUCUUGGGUA Cleavage ath-miR399c-5p AT5G35210.2 3 21.714 1 21 1705 1725 UGCCAAAGGAGAGUUGCCCUG ::::.:::::.::: ::.: AUGGGCGACUCUUCUUGGGUA Cleavage ath-miR399c-5p AT1G21270.1 3 18.604 1 21 254 274 UGCCAAAGGAGAGUUGCCCUG :: : :.::::.:::::::: AAGAGAAGCUCUUCUUUGGCA Cleavage ath-miR399c-5p AT2G26900.1 3 15.79 1 21 1484 1504 UGCCAAAGGAGAGUUGCCCUG :: ::: :::..::::::: AUGGACAAAUCUUUUUUGGCA Cleavage ath-miR399c-5p AT2G22300.2 3 22.244 1 21 2298 2317 UGCCAAAGGAGAGUUGCCCUG :::::.:: :.:::::::: UUGGGCAGCU-UUCUUUGGCA Translation ath-miR399c-5p AT2G22300.1 3 22.244 1 21 2311 2330 UGCCAAAGGAGAGUUGCCCUG :::::.:: :.:::::::: UUGGGCAGCU-UUCUUUGGCA Translation ath-miR5015 AT5G18633.1 2 17.297 1 21 3868 3888 UUGGUGUUAUGUGUAGUCUUC :.:: :::.:::::.:::::: GGAGUCUAUACAUAGCACCAA Cleavage ath-miR5015 AT1G71040.1 2 10.435 1 21 641 661 UUGGUGUUAUGUGUAGUCUUC :::::::::::: ::..::: AAAGACUACACAUUACGUCAA Cleavage ath-miR5015 AT5G36740.1 2.5 19.229 1 21 2400 2420 UUGGUGUUAUGUGUAGUCUUC :::::.:.::.::::..:::: GAAGAUUGCAUAUAAUGCCAA Cleavage| Symbols: UBC24,ATUBC24,PHO2 |phosphate 2 | chr2:14277558-14283040 REVERSE LENGTH=4103| Symbols: UBC24,ATUBC24,PHO2 |phosphate 2 | chr2:14277558-14283040 REVERSE LENGTH=4103| Symbols: UBC24,ATUBC24,PHO2 |phosphate 2 | chr2:14277558-14283040 REVERSE LENGTH=4103| Symbols: UBC24,ATUBC24,PHO2 |phosphate 2 | chr2:14277558-14283040 REVERSE LENGTH=4103| Symbols: | Plant neutral invertase family protein |chr3:2012079-2015705 FORWARD LENGTH=2459| Symbols: | Plant neutral invertase family protein |chr1:21192499-21195112 FORWARD LENGTH=2109| Symbols: ACR4,CR4 | crinkly4 |chr3:21959647-21963041 REVERSE LENGTH=3395| Symbols: ACBP5 | acyl-CoA binding protein 5 | chr5:9776023-9781002 FORWARD LENGTH=2247| Symbols: |metalloendopeptidases;zinc ion binding;DNA binding |chr5:13474196-13482591 REVERSE LENGTH=5687| Symbols: |metalloendopeptidases;zinc ion binding;DNA binding |chr5:13474196-13482591 REVERSE LENGTH=6028| Symbols: WAK2 | wall-associated kinase 2 | chr1:7444931-7447549 FORWARD LENGTH=2469| Symbols: | Sodium Bile acid symporter family | chr2:11474952-11477944 REVERSE LENGTH=1508| Symbols: CAMTA3,SR1 | signal responsive 1 | chr2:9471325-9476630 FORWARD LENGTH=3455| Symbols: CAMTA3,SR1 | signal responsive 1 | chr2:9471388-9476646 FORWARD LENGTH=3484| Symbols: | transposable element gene | chr5:6205813-6210644 FORWARD LENGTH=4832| Symbols: LPR2 | Cupredoxin superfamily protein |chr1:26796966-26800322 REVERSE LENGTH=2079| Symbols: | Acyl-CoA N-acyltransferase with RING/FYVE/PHD-type zinc finger protein |chr5:14460790-14465727 FORWARD LENGTH=3540 5 5 5 5 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR5015 AT5G36670.1 2.5 19.229 1 21 2400 2420 UUGGUGUUAUGUGUAGUCUUC :::::.:.::.::::..:::: GAAGAUUGCAUAUAAUGCCAA Cleavage ath-miR5015 AT1G33200.1 2.5 6.817 1 21 2875 2895 UUGGUGUUAUGUGUAGUCUUC ::::.::::::::.::::: UAAGAUUACACAUAGAACCAA Cleavage ath-miR5015 AT4G10460.1 2.5 16.614 1 21 1462 1482 UUGGUGUUAUGUGUAGUCUUC :.:::::::::::::..: UGUGGCUACACAUAACACUGA Cleavage ath-miR5015 AT2G35130.1 2.5 18.604 1 21 1187 1207 UUGGUGUUAUGUGUAGUCUUC .:::::: .::::.::::.: AGAGACUAGGCAUAGCACCGA Cleavage ath-miR5015 AT2G35130.2 2.5 18.604 1 21 1410 1430 UUGGUGUUAUGUGUAGUCUUC .:::::: .::::.::::.: AGAGACUAGGCAUAGCACCGA Cleavage ath-miR5015 AT3G29230.1 3 11.722 1 21 145 166 UUGGUGUUAUGUGUAG-UCUUC ::::: :::::::::.::::.: GAAGAUCUACACAUAGCACCGA Cleavage ath-miR5015 AT5G25780.1 3 16.756 1 21 1590 1610 UUGGUGUUAUGUGUAGUCUUC :::::::.:::: :::::...GAAGACUGCACAAAACACUGG Translation ath-miR5015 AT2G07100.1 3 12.795 1 21 636 656 UUGGUGUUAUGUGUAGUCUUC :::::::: :.::.:.:.::: GAAGACUAGAUAUGAUAUCAA Cleavage ath-miR5015 AT3G22790.1 3 17.38 1 21 3750 3770 UUGGUGUUAUGUGUAGUCUUC :::.::::::::::..: :: UAAGGCUACACAUAAUGCAAA Cleavage ath-miR5015 AT5G34623.1 3 12.531 1 21 4416 4436 UUGGUGUUAUGUGUAGUCUUC :::::: : .:::::::.::: GAAGACAAGGCAUAACAUCAA Cleavage ath-miR5015 AT1G47770.1 3 13.043 1 21 315 335 UUGGUGUUAUGUGUAGUCUUC .::::::.:.::.::::.: AGAGACUAUAUAUGACACUAC Cleavage ath-miR5015 AT4G21010.1 3 13.577 1 21 378 398 UUGGUGUUAUGUGUAGUCUUC :::.::::.:: ::.:.::: UAAGGCUACGCACAAUAUCAA Translation ath-miR5015 AT3G02270.1 3 24.787 1 21 1351 1371 UUGGUGUUAUGUGUAGUCUUC : ::..::::.::..:.:::: GCAGGUUACAUAUGGCGCCAA Cleavage ath-miR5015 AT5G25205.1 3 16.546 1 21 4096 4116 UUGGUGUUAUGUGUAGUCUUC :.:: :::.::: :.:::::: GGAGUCUAUACACAGCACCAA Translation ath-miR5015 AT4G31730.1 3 5.724 1 21 91 111 UUGGUGUUAUGUGUAGUCUUC .:::.:::::: :::: ::: AGAGAUUACACACAACAACAA Translation ath-miR5015 AT2G28315.1 3 11.632 1 21 546 566 UUGGUGUUAUGUGUAGUCUUC .:::::.::.:.:::.::: AGAGACUGAACGUGACAUCAA Cleavage ath-miR5015 AT1G51870.1 3 17.843 1 21 792 812 UUGGUGUUAUGUGUAGUCUUC : .:::::.: ::::::::: GUGGACUAUAGAUAACACCAC Translation| Symbols: | RING/FYVE/PHD zinc finger superfamily protein |chr5:14401491-14406427 FORWARD LENGTH=3582| Symbols: | transposable element gene | chr1:12041779-12044690 FORWARD LENGTH=2912| Symbols: | transposable element gene | chr4:6468166-6472263 FORWARD LENGTH=4098| Symbols: | Tetratricopeptide repeat (TPR)-like superfamily protein | chr2:14807449-14810164 REVERSE LENGTH=1916| Symbols: | Tetratricopeptide repeat (TPR)-like superfamily protein | chr2:14807449-14810229 REVERSE LENGTH=2139| Symbols: | Tetratricopeptide repeat (TPR)-like superfamily protein | chr3:11188803-11190605 FORWARD LENGTH=1803| Symbols: EIF3B-2,EIF3B,ATEIF3B-2 | eukaryotic translation initiation factor 3B-2 |chr5:8973267-8976869 REVERSE LENGTH=2409| Symbols: | transposable element gene | chr2:2942233-2945080 REVERSE LENGTH=2848| Symbols: | Kinase interacting(KIP1-like) family protein |chr3:8052318-8058764 REVERSE LENGTH=5537| Symbols: | transposable element gene | chr5:12928508-12933349 REVERSE LENGTH=4842| Symbols: | Beta-galactosidase related protein | chr1:17590266-17591261 FORWARD LENGTH=618| Symbols: | Transcription initiation factor TFIIE,beta subunit | chr4:11226286-11227363 REVERSE LENGTH=859| Symbols: | Trimeric LpxA-like enzyme | chr3:448977-451007 REVERSE LENGTH=2031| Symbols: | transposable element gene | chr5:8718571-8723552 REVERSE LENGTH=4982| Symbols: GDU1 | glutamine dumper 1 | chr4:15361091-15361850 FORWARD LENGTH=760| Symbols: | Nucleotide/sugar transporter family protein |chr2:12088877-12090701 FORWARD LENGTH=1179| Symbols: | protein kinase family protein | chr1:19262879-19267001 REVERSE LENGTH=2514 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

ath-miR5015 AT3G43210.1 3 14.623 1 21 2317 2337 UUGGUGUUAUGUGUAGUCUUC .::: ::.::.:::.:.::: AGAGAAUAUACGUAAUAUCAA Cleavage ath-miR5015 AT3G53130.1 3 7.502 1 21 1960 1980 UUGGUGUUAUGUGUAGUCUUC .::: ::::.:::::..:: AUGGACCACACGUAACAUUAA Cleavage ath-miR5015 AT5G34770.1 3 10.638 1 21 3550 3570 UUGGUGUUAUGUGUAGUCUUC :::::::::: :: :.::: CCAGACUACACAGAAGAUCAA Translation ath-miR5015 AT5G60730.1 3 9.187 1 21 1365 1385 UUGGUGUUAUGUGUAGUCUUC .:::.:: ::: ::.::::: UGAGAUUAAACAAAAUACCAA Translation ath-miR5015 3 8.019 1 21 1599 1619 UUGGUGUUAUGUGUAGUCUUC .: ::: .:::::::.:::: AGAUACUUUACAUAACGCCAA Cleavage| Symbols: TES,ATNACK2,NACK2 |ATP binding microtubule motor family protein | chr3:15190934-15196168 FORWARD LENGTH=3193| Symbols: LUT1,CYP97C1 |Cytochrome P450 superfamily protein| chr3:19692771-19697542 FORWARD LENGTH=3341| Symbols: | transposable element gene | chr5:12955720-12960171 FORWARD LENGTH=4452| Symbols: | Anion-transporting ATPase | chr5:24422735-24425492 FORWARD LENGTH=1419| Symbols: | Protein kinase superfamily protein with octicosapeptide/Phox/Bem1p domain |chr3:17280430-17284857 REVERSE LENGTH=3516 1 1 1 1 1