Supplementary Figure 1. Stem-loop structures of 52 putative miRNA precursors


JcumiRNA002 in

U U U C CU C U C CC Y UAC \ -----------^ \ ---------------------------------
G-U ACG AUA - .-GAGGG| .-GGAAAAGGUAGAAG G GGGC GGGG CG GUGCG GGUG GGUG GGUCGUAU GGGCG GAU UCA G CCCU GC CACGU UCAC CCAU CUAGCGUG UCCGC CUA GGU R AG - AA- GA- A \GG ---^ \ -------------- G GGGA
U- -GGAGA G C UA CGUUUGUGUU .-GA| AA GU UGGG GGUUA AU GAA GG AUGGU UGAGCG GGAGU CGUGCGUGU UG G ACCC CCAAU UA UUU UC UACCG ACUUGC CUUCA GUACGUACA AC A A UU A AAGAG G - -- ---------- \ --^ --AA
-- - .-U - .-AAG --| G UU GCGCCGGGGAG GGUG GUGG GG GUGG GCAG CCGGGC GG \ UGCGGCUCUUC UCGC CGCC CC CGCC UGUU GGCUCG CC G GAAG G \ -G \ --- UA^ G
G GAAC .-UUCUC - .-UUCAACCCA U CU .-AUG UCAACU | G A CCA ACGCA UCGGA GCCG CCC GA CGC UCCAG GCCCAG UGGGA--CUU AGCUC \ GGU UGCGU AGUCU CGGC GGG CU GUG AGGUU UGGGUU ACCCU GAG UUGAG A G GUCA \U----- U \ ---------U -- \ --- C----- \ ^ A C

in Rattus norvegicus (Mir3596a)

  

	Jcu-miRNA007 in Euphorbia genistoides			
	dG=-22.80 10 JcumiRNA013 in Populus trichocarpapa 20 | U U AU dG = -18.6			
	UAAAGGAGCAAUA CCAAUU CU C 10 20				30	40
	AUUUCCUCGUUAU GGUUGG GA A U UG AUCU G ---					.-UG|	AGG	G
	^ CAUUUUA U U	-	-AA GUU GAUA	AUGGUUCC	UUGG	GUU A
	. GUAAGAU G G 40 30		UAA UUGU		UAUUAAGG	GACU	UAA A
		U GU ----	G		GGA					\ --^	GUA	A
	JcumiRNA008 in Medicago truncatu 100 90					80 (20nt side loop)
	Vitis vinifera 20 JcumiRNA014 precusor in Oryza sativa dG = -18.1 10 UCUC-| UU GU UA dG = -44.10	30	CUA	40 UUGAAUU	50	UA
	AGA dG = -30.4 UUUAU GGCU AAC UAGUA 10 20 30 10 20 30 UCU AAGUG UCGG UUG GUCGU A UCG GUUAA CU A CGC-AA AUAA UACUC^ UU GC UG GUGGU GAGCGG GCU CUGA GGUC C AG-UGCUA AUGAU ---| GUAGGUUC 40 40 -------UAUGU \ 50 AUACA U .-GAA| AC UU UCCU \ GG AAAGAU GUGGCCU UGG 90 80 70 60 UAUCG CUUGCC UGG GAUU CCAG CGUUCGGG AGGG U GGCG UCGC--CUCC A UUUUUA CACUGGA ACC -CAA AUGAG C-UUU \ ---^ GU UUGC AGCG GAGG G G CUUU --A---U \ ^ GC . 90 80 (20nt side loop) JcumiRNA003 in Jatropha curcas dG = -31.10 10 20 30 CC-A GUACCU .-UG| G UGCCUG UUU GACUCCACA CAUU C ACGGAU GAG CUGGGGUGU GUGA A 140 130 120 110 (44nt side loop) JcumiRNA009 in Jatropha curcas dG = -21.10 10 20 JcumiRNA015 Initial dG = -34.20 30 A CU---| U C 10 20 30 40 U GGAU | CU G U UAGAGUUACA UUG AUUCGGCUCAAUC UUU A CUUA UCCCAGG GAG UAG AGGUUGUAUAGUU \ AAU UGAGCCGGGUUAG AAA G A ACGUU^ U A AGGGUUC UUC AUC UCCGACAUGUCAA A U 60 50 ^ CU G C UAGAGGGAAC 40 80 70 60 50
	GUA JcumiRNA010 in Arabidopsis thaliana C UCUC--JcumiRNA016 in Mimulus guttatus		\ --^	C
	90 dG = -30.1 dG = -47.40		80							40
		10 10			20 20					30 30	40	40	50	60
	JcumiRNA004 in Oryza sativa U UG U AG--GGUC GUC AUUUU GUUUUU CUAGC CA C-CAC G .-UCC dG = -53.10 10 20 30 UCGG CGG UAAGA CAAGAG GAUUG CGG UCGCA AUGUCA AC CAUUGGA CGAAC-AUUAAUGG .-CGAA| AG UGAUUGCC GUAG A 40 A| G G AGCUUGU G --U CAAA UG CAUUAU GCC AGCGU UGCAGU UG GUAAUCU CAUC C GGA CGACG GAUAUUGG GCGGUUCAAUCAGAA GCUCC A 150 140 130 120 110 (40nt side loop) .-AACUUUUUC| UCGGA U U AGCUU U \ ---------^ A UA U--G \ ---\ ----^ GC
	GCUGC CUAUAACC UGCCGAGUUAGUUUU C^ A G . 180 (91nt side loop) 80 90 80 70 dG = -27.38 JcumiRNA011 in Vitis vinifera JcumiRNA017	CGAGG (24nt side loop) G CUCAUCU AGC 60 50
	JcumiRNA005 in Populus trichocarpapa 10 20	30
	U dG = -28.0 AGGC 10 GUGG UCA | A AUAG GUAGCAUUGG 20 U GUAUU .-AACUGCUAU| 30 GUAGGC U U 40 CCU CGCC AGU CAUUGUAACC CAUUUG U AAGGUCGUUGU GU UGG GA CCCG -----\ ---------^ U GUCAC C G UUUUAGCGGCA CG GCC CU GGGC CAGUG G 100 (43nt side loop)
	^ . JcumiRNA012 in Oryza sativa A ----C AGCUU 70 60 JcumiRNA006 in Strongylocentrotus purpuratus C--50 dG = -58.70	G
	dG=-37.80 10			20				30			40	50	60	70
	U|	10 G CA-	U		20 GAUA UU	-			30 --------------| C UAU A GC UU G U	40 U UUUU	50 CCA GUUUA U	AA CA
	CCUAU GG UGUUUUUGGG GGAAUG GUCUGGUUC AG CCC AGGAU UG GAU UGGGC UGG GCAU GGG GA	GUC GGUAG GGU GAUG	AGGA C UGCAUU U
	GGAUG CC AUAGAGACUC CCUUAC CGGACCAGG UC GGG UUCUA GC CUA ACCCG ACC CGUG CCC CU UAG UCGUU UCA CUAC	UCCU C GCGUAG C
	G^	G ACC 120	C	110	GA--UU	A	100	UCAUCCCCCCUUCU^ A U--90 80 C UU U-G U	-U---	-70 AA---	CG-	GG 60 UU
		130			120			110				100	90	80
	Osa-miR166e is labeled in blue.					

in Oryza sativa (Osa microRNA MIR457)

  

	JcumiRNA019 in Oryza sativa				
	Initial dG = -48.70						
		10			20		30	
	G			U		.-AAA .-AGA|		UU
	CUU GCCAUUUG GUUGCGUU	GC		AACAUUU \
	GAG UGGUAAAC CGAUGUAG	CG		UUGUAAG G
	A			U		\GGG-\ ---^		UU
	190			180			(121nt side loop)	40
	JcumiRNA020 in Oryza sativa				
	dG = -49.80								
		10			20	30			40	50
	C	UUU		GC			.-U		.-UCA| UG UUG
	CU CUU	UUGGAU UGAAGGUGAUUUU	UGUUGUUU	UC CC	U
	GA GAA	AACUUA ACUUCCAUUGAAG	ACAACAAA	AG GG	C
	C	CGC		AA			\ -		\ ---^ GU UCA
	.	230			220		180 (112nt side loop)60
	JcumiRNA021 in Vitis vinifera				
	dG = -38.08							
		10		20		30	40		50	60	70	80	90	100
	---	-	UU	U	U	C AC	G	UU-.-UUCGUUUUUUU|	.-UUUUUCAUCGUUUUUUUUKUAUUCUCUUUUUCUC
	UU									
	GAG GC UG GUU GGUG AAU GGG GCUAU CU CUGA CUUU		UC	UUUUAUA
	GUC \									
	CUC UG AC CAA CCGC UUG CCC UGAUG YA GGCU GAGA		AG	AGAAUGU
	CAG C									
	dG = -40.15							
		10			20		30		40
	CC	ACAA	GC		A	.	-A GC-|	AC	CCA	UA
	AGACC	GCA AGC GCAG	GA	AUCUGG CGU	AUC C
	UCUGG	CGU UCG CGUC	CU	UAGACC GCA	UAG U
	CU	----	A-		-	\ ACCU-AAU^	AU	ACC	CA
			170			(19nt side loop) 60	50
	JcumiRNA018 in Oryza sativa (Osa microRNA 169c gene)
	dG = -68.75							
			10			20		30			40	50	60	70
	-AA	A-A A		UA				CA	.-AACUCCAA| CGC	A
	CA CGCU GA GA GAGAGC GGUGUAGCCAAGGA GACUUGCCGGCU	GG	UUCAGC \
	GU GUGA CU CU CUCUUG CUACGUCGGUUCCU CUGAACGGCCGA	CC	GAGUCG A
	G AC	CA C C		CC				A-	\ --------^ UUA	A
		140			130	120			110	100	(11nt side loop)
Supplementary Figure 1. Stem-loop structures of 52 putative miRNA precursors