Table I.

Arabidopsis miRNA families

	miRNA Family	Locus	Sequence^a	ASRP Library^b		Plant Species^c	Target Family
	miRNA Family	Locus	Sequence^a	Col-0	rdr2/dcl3	Plant Species^c	Target Family
1	miR156	a-f	`UGACAGAAGAGAGUGAGCAC`	+	+	At, Bn, Gm, Ha, Hv, Lj, Mt, Nt, Os, Pta, Ptr, Sb, Si, So, St, Vv, Zm	SBP^d ^e
	miR156	g	`CGACAGAAGAGAGUGAGCACA`	−	−	At
	miR156	h	`UUGACAGAAGAAAGAGAGCAC`	−	−	At
	miR157	a-d	`UUGACAGAAGAUAGAGAGCAC`	−	+	At, Ptr
2	miR158	a	`UCCCAAAUGUAGACAAAGCA`	+	−	At
		b	`CCCCAAAUGUAGACAAAGCA`	−	−	At
3	miR159	a	`UUUGGAUUGAAGGGAGCUCUA`	+	+	At, Gm, Hv, Lj, Mt, Os, Pg, Ptr, So, Sb, Ta*, Vv, Zm	MYB^d ^f ^g
	miR159	b	`UUUGGAUUGAAGGGAGCUCUU`	−	+	At
	miR159	c	`UUUGGAUUGAAGGGAGCUCCU`	−	−	At
	miR319	a-b	`UUGGACUGAAGGGAGCUCCCU`	+	+	At, Bo, Gm, Lt, Os, Ptr, Ta	TCP^g
	miR319	c	`UUGGACUGAAGGGAGCUCCUU`	−	−	At, Os
4	miR160	a-c	`UGCCUGGCUCCCUGUAUGCCA`	+	+	At, Gm, Os, Ptr, Tt, Zm	ARF^d ^e
5	miR161.1	a	`UUGAAAGUGACUACAUCGGGG`	+	+	At	PPR^d ^h
	miR161.2	a	`UCAAUGCAUUGAAAGUGACUA`	+	+	At
6	miR162	a-b	`UCGAUAAACCUCUGCAUCCAG`	+	+	At, Gm, Ll, Mt, Os, Ptr, Vv	DCL1ⁱ
7	miR163	a	`UUGAAGAGGACUUGGAACUUCGAU`	+	−	At	SAMT^h
8	miR164	a-b	`UGGAGAAGCAGGGCACGUGCA`	−	+	At, Pb, Ta	NAC^d ^e ^j ^k
	miR164	c	`UGGAGAAGCAGGGCACGUGCG`	+	+	At
9	miR165	a-b	`UCGGACCAGGCUUCAUCCCCC`	−	+	At, Hc, Ptr	HD-ZIPIII^l ^m
	miR166	a-g	`UCGGACCAGGCUUCAUUCCCC`	+	+	At, Gm, Hv, In*, Mt, Os, Ptr, Sb, Zm
10	miR167	a-b	`UGAAGCUGCCAGCAUGAUCUA`	+	+	At, Gm, Os, Pc*, Ptr, Zm	ARF^d ^e
	miR167	c	`UUAAGCUGCCAGCAUGAUCUU`	−	−	At
	miR167	d	`UGAAGCUGCCAGCAUGAUCUGG`	+	+	At, Gm, In, Ptr, So
11	miR168	a-b	`UCGCUUGGUGCAGGUCGGGAA`	+	+	At, Bp, Gm, Ht, Hv, Le, Os, Ptr, Sb, So, St, Vv, Zm	AGO1^d ⁿ
12	miR169	a	`CAGCCAAGGAUGACUUGCCGA`	+	+	At, Gm, Os, Ptr	HAP2^o
	miR169	b-c	`CAGCCAAGGAUGACUUGCCGG`	+	+	At, Gm, Os, Ptr, Zm
	miR169	d-g	`UGAGCCAAGGAUGACUUGCCG`	+	+	At, Ptr
	miR169	h-n	`UAGCCAAGGAUGACUUGCCUG`	+	+	At, Ls, Os, Pb, Ptr, Sb, So, Ta
13	miR170	a	`UGAUUGAGCCGUGUCAAUAUC`	−	+	At	SCR^d ^p
	miR171	a	`UGAUUGAGCCGCGCCAAUAUC`	+	+	At, Os, Ptr, Ta, Zm
	miR171.2	b-c	`UUGAGCCGUGCCAAUAUCACG`	+	−	At, Os, Ptr, Ta, Zm
	miR171.1	c	`UGAUUGAGCCGUGCCAAUAUC`	−	+	At, Gm, Hc, Hv, Os, Ptr, Ta, Zm
14	miR172	a-b	`AGAAUCUUGAUGAUGCUGCAU`	−	+	At, Gm, Le, Os, Ptr, St	AP2^e ^q ^r
	miR172	c-d	`AGAAUCUUGAUGAUGCUGCAG`	+	−	At, Cs
	miR172	e	`GGAAUCUUGAUGAUGCUGCAU`	−	+	At, Os, Ptr
15	miR173	a	`UUCGCUUGCAGAGAGAAAUCAC`	−	+	At	TAS1, TAS2^s
16	miR390	a-b	`AAGCUCAGGAGGGAUAGCGCC`	+	+	At, Os, Ptr, St, Zm	TAS3^s
	miR391	a	`UUCGCAGGAGAGAUAGCGCCA`	−	+	At
17	miR393	a-b	`UCCAAAGGGAUCGCAUUGAUC`	−	−	At, Os, Ptr	TIR1/F-box^o
							bHLH^o
18	miR394	a-b	`UUUGGCAUUCUGUCCACCUCC`	−	−	At, Gm, Os, Ptr, Rp	F-box^o
19	miR395	a, d-e	`CUGAAGUGUUUGGGGGAACUC`	−	−	At, Gm, Os, Ptr, Ta	ATPS^o, AST^s
	miR395	b-c, f	`CUGAAGUGUUUGGGGGGACUC`	−	−	At
20	miR396	a	`UUCCACAGCUUUCUUGAACUG`	−	+	At, Bv, Gm, Mc, Os, Ptr, So, St, Zm	GRF^o
	miR396	b	`UUCCACAGCUUUCUUGAACUU`	−	−	At, Bn, Gm, Mc, Os, Ptr, St
21	miR397	a	`UCAUUGAGUGCAGCGUUGAUG`	−	+	At, Hv, Os, Ptr	Laccase^o
	miR397	b	`UCAUUGAGUGCAUCGUUGAUG`	−	−	At
22	miR398	a	`UGUGUUCUCAGGUCACCCCUU`	−	−	At, Cs, Gm, Lj, Mt, Os, Ptr	CSD^o
	miR398	b-c	`UGUGUUCUCAGGUCACCCCUG`	−	+	At, Gm, Ha, Ls, Mt, Nb, Os, Zm*	CytC oxidase^o
23	miR399	a	`UGCCAAAGGAGAUUUGCCCUG`	−	−	At	E2-UBC^s
	miR399	b, c	`UGCCAAAGGAGAGUUGCCCUG`	−	+	At, Mt, Os, Ptr, Sb
	miR399	d	`UGCCAAAGGAGAUUUGCCCCG`	−	−	At, Os
	miR399	e	`UGCCAAAGGAGAUUUGCCUC`G	−	−	At
	miR399	f	`UGCCAAAGGAGAUUUGCCCGG`	−	−	At, Os
24	miR403	a	`aUUAGAUUCACGCACAAACUCG`	+	−	At, Ptr	AGO2^s
25	miR447	a-b	`UUGGGGACGAGAUGUUUUGUUG`	−	+	At	2PGK^s
	miR447	c	`UUGGGGACGACAUCUUUUGUUG`	−	−

↵a miRNAs are grouped by related families, with differences among families marked in bold.
↵b Col-0 libraries included Col-0 and jaw-d sequences.
↵c Presence of miRNA in genomic sequence is indicated in regular text, EST sequences are in bold, and sequences with 1 to 2 base changes from the Arabidopsis sequence are indicated by an asterisk. See Supplemental Table IV for plant species abbreviations.
↵d Vazquez et al. (2004).
↵e Kasschau et al. (2003).
↵f Achard et al. (2004).
↵g Palatnik et al. (2003).
↵h Allen et al. (2004).
↵i Xie et al. (2003).
↵j Mallory et al. (2004a).
↵k Laufs et al. (2004).
↵l Tang et al. (2003).
↵m Emery et al. (2003).
↵n Vaucheret et al. (2004).
↵o Jones-Rhoades and Bartel (2004).
↵p Llave et al. (2002b).
↵q Aukerman and Sakai (2003).
↵r Chen (2004).
↵s Allen et al. (2005).