Identification of novel soybean microRNAs involved in abiotic and biotic stresses

Kulcheski, Franceli R; de Oliveira, Luiz FV; Molina, Lorrayne G; Almerão, Maurício P; Rodrigues, Fabiana A; Marcolino, Juliana; Barbosa, Joice F; Stolf-Moreira, Renata; Nepomuceno, Alexandre L; Marcelino-Guimarães, Francismar C; Abdelnoor, Ricardo V; Nascimento, Leandro C; Carazzolle, Marcelo F; Pereira, Gonçalo AG; Margis, Rogério

doi:10.1186/1471-2164-12-307

BMC Genomics

Table 4 Families of conserved soybean miRNAs.

From: Identification of novel soybean microRNAs involved in abiotic and biotic stresses

Group^a	miRNA ID	miRNA ID sequence	Size(nt)	Ch	Start	End	Arm	Members registered in miRBase^b
5	gma-MIR156d	UUGACAGAAGAUAGAGAGCAC	21	Gm08	3891365	3891489	5'	a,b,c,d,e,f,g
3	gma-MIR156h	UUGACAGAAGAUAGAGAGCAC	21	Gm02	7812526	7812628	5'
3	gma-MIR156i	UUGACAGAAGAUAGAGAGCAC	21	Gm05	38621690	38621813	5'
3	gma-MIR156j	UUGACAGAAGAGAGUGAGCAC	21	Gm06	4699149	4699240	5'
3	gma-MIR156k	UUGACAGAAGAUAGAGAGCAC	21	Gm07	9347139	9347259	5'
3	gma-MIR156l	UUGACAGAAGAUAGAGAGCAC	21	Gm09	37843750	37843864	5'
3	gma-MIR156m	UUGACAGAAGAGAGUGAGCAC	21	Gm14	10664512	10664600	5'
3	gma-MIR156n	UUGACAGAAGAGAGUGAGCAC	21	Gm17	37759446	37759535	5'
5	gma-MIR159a-3p	UUUGGAUUGAAGGGAGCUCUA	21	Gm09	37672410	37672586	3'	a(3'),b(3'),c,d
4	gma-MIR159a-5p	GAGCUCCUUGAAGUCCAAUUG	21	Gm09	37672410	37672586	5'
5	gma-MIR159b-3p	AUUGGAGUGAAGGGAGCUCCA	21	Gm07	5386107	5386292	3'
4	gma-MIR159b-5p	GAGUUCCCUGCACUCCAAGUC	21	Gm07	5386107	5386292	5'
3	gma-MIR159e-3p	UUUGGAUUGAAGGGAGCUCUA	21	Gm07	9524917	9525127	3'
3	gma-MIR159e-5p	GAGCUCCUUGAAGUCCAAUU	20	Gm07	9524917	9525127	5'
3	gma-MIR159f-3p	AUUGGAGUGAAGGGAGCUCCA	21	Gm16	2794128	2794307	3'
3	gma-MIR159f-5p	GAGUUCCCUGCACUCCAAGUC	21	Gm16	2794128	2794307	5'
5	gma-MIR162a	UCGAUAAACCUCUGCAUCCAG	21	Gm06	20176238	20176339	3'	a
3	gma-MIR162b	UCGAUAAACCUCUGCAUCCAG	21	Gm05	7692594	7692698	3'
3	gma-MIR162c	UCGAUAAACCUCUGCAUCCAG	21	Gm17	10181489	10181607	3'
5	gma-MIR166a-3p	UCGGACCAGGCUUCAUUCCCC	21	Gm16	1912570	1912715	3'	a(3'),b*
4	gma-MIR166a-5p	GGAAUGUUGUCUGGCUCGAGG	21	Gm16	1912570	1912715	5'
3	gma-MIR166c-3p	UCGGACCAGGCUUCAUUCCCC	21	Gm02	14340767	14340863	3'
3	gma-MIR166c-5p	GGAAUGUCGUCUGGUUCGAG	20	Gm02	14340767	14340863	5'
3	gma-MIR166d-3p	UCGGACCAGGCUUCAUUCCCG	21	Gm08	14990547	14990731	3'
3	gma-MIR166d-5p	GGAAUGUUGUUUGGCUCGAGG	21	Gm08	14990547	14990731	5'
3	gma-MIR166e-3p	UCGGACCAGGCUUCAUUCCCG	21	Gm15	3688764	3688931	3'
3	gma-MIR166e-5p	GGAAUGUUGUUUGGCUCGAGG	21	Gm15	3688764	3688931	5'
3	gma-MIR166f	UCUCGGACCAGGCUUCAUUCC	21	Gm20	43105394	43105500	3'
5	gma-MIR167c	UGAAGCUGCCAGCAUGAUCUG	21	Gm07	39778512	39778886	5'	a,b,c,d,e,f,g
3	gma-MIR167h	UGAAGCUGCCAGCAUGAUCUG	21	Gm20	44765096	44765173	5'
5	gma-MIR168a	UCGCUUGGUGCAGGUCGGGAA	21	Gm09	41353226	42353350	5'	a
3	gma-MIR168b	UCGCUUGGUGCAGGUCGGGAA	21	Gm01	48070311	48070420	5'
5	gma-MIR169a	CAGCCAAGGAUGACUUGCCGG	21	Gm09	35771804	35771924	5'	a,b,c,d,e
3	gma-MIR169f-3p	UUUCGACGAGUUGUUCUUGGC	21	Gm02	46876643	46876727	3'
3	gma-MIR169f-5p	UAGCCAAGAAUGACUUGCCGG	21	Gm02	46876643	46876727	5'
3	gma-MIR169g	CAGCCAAGAAUGACUUGCCGG	21	Gm09	5263992	5264096	5'
3	gma-MIR169h	CAGCCAAGAAUGACUUGCCGG	21	Gm14	5324798	5324911	5'
3	gma-MIR169i	CAGCCAAGGAUGACUUGCCGG	21	Gm10	40332790	40332926	5'
3	gma-MIR169j	CAGCCAAGGAUGACUUGCCGG	21	Gm13	368563	368441	5'
3	gma-MIR169k	CAGCCAAGGGUGAUUUGCCGG	21	Gm15	14150069	14150183	5'
3	gma-MIR169l	CAGCCAAGGAUGACUUGCCGG	21	Gm17	4861963	4861816	5'
3	gma-MIR171d	UUGAGCCGUGCCAAUAUCACG	21	Gm06	48920631	48920715	3'	a,b,c*
3	gma-MIR171e	CGAUGUUGGUGAGGUUCAAUC	21	Gm13	26271135	26271232	5'
3	gma-MIR171f	CGAUGUUGGUGAGGUUCAAUC	21	Gm17	9101701	9101798	3'
4	gma-MIR172b-5p	GUAGCAUCAUCAAGAUUCAC	20	Gm13	40401688	40401809	5'	a,b(3'),c,d,e,f*
5	gma-MIR172c	GGAAUCUUGAUGAUGCUGCAG	21	Gm18	2968986	2969138	3'
3	gma-MIR172g	GCAGCACCAUCAAGAUUCAC	20	Gm10	31592576	31592689	5'
3	gma-MIR172h-3p	AGAAUCUUGAUGAUGCUGCAU	21	Gm10	43474725	43474831	3'
3	gma-MIR172h-5p	GCAGCAGCAUCAAGAUUCACA	21	Gm10	43474725	43474831	5'
3	gma-MIR172i	GCAGCAGCAUCAAGAUUCACA	21	Gm15	2892962	2893122	5'
3	gma-MIR172j	GCAGCAGCAUCAAGAUUCACA	21	Gm20	40895747	40895836	5'
3	gma-MIR319d	UUGGACUGAAGGGAGCUCCUUC	22	Gm02	43885398	43885595	3'	a,b,c*
3	gma-MIR319e	UUGGACUGAAGGGAGCUCCCU	21	Gm02	45704227	45704412	3'
3	gma-MIR319f	UUGGACUGAAGGGGAGCUCCUUC	23	Gm04	46348798	46348991	3'
3	gma-MIR319g	UUGGACUGAAGGGAGCUCCCU	21	Gm11	1374020	1374198	3'
3	gma-MIR319h	UUGGACUGAAGGGAGCUCCCU	21	Gm11	32902062	32902247	3'
3	gma-MIR319i	UUGGACUGAAGGGAGCUCCCU	21	Gm14	47959350	47959535	3'
3	gma-MIR319j	UUGGACUGAAGGGAGCUCCUUC	22	Gm14	45953433	45953649	3'
3	gma-MIR319k	UUGGACUGAAGGGAGCUCCUUC	22	Gm17	9436178	9436279	3'
3	gma-MIR319l	UUGGACUGAAGGGAGCUCCCU	21	Gm18	4278883	4279072	3'
4	gma-MIR396a-3p	UUCAAUAAAGCUGUGGGAAG	20	Gm13	26338134	26338273	3'	a,b(5'),c,d(3'),e
5	gma-MIR396a-5p	UUCCACAGCUUUCUUGAACUG	21	Gm13	26338134	26338273	5'
4	gma-MIR396b-3p	GCUCAAGAAAGCUGUGGGAGA	21	Gm13	26329931	26330056	3'
5	gma-MIR396b-5p	UUCCACAGCUUUCUUGAACUU	21	Gm13	26329931	26330056	5'
5	gma-MIR396c	UUCCACAGCUUUCUUGAACUU	21	Gm13	43804777	43804893	5'
4	gma-MIR396d-5p	UUCCACAGCUUUCUUGAACUU	21	Gm17	9053051	9053155	5'
3	gma-MIR396f	UCCACAGCUUUCUUGAACUG	20	Gm14	13971419	13971566	5'
3	gma-MIR396g	UUCCACAGCUUUCUUGAACUU	21	Gm15	556707	556796	5'
3	gma-MIR396h-3p	GUUCAAUAAAGCUGUGGGAAG	21	Gm17	9044850	9044984	3'
3	gma-MIR396h-5p	UUCCACAGCUUUCUUGAACUG	21	Gm17	9044850	9044984	5'
4	gma-MIR482b-3p	UCUUCCCUACACCUCCCAUACC	22	Gm20	35360312	35360406	3'	a*,b(5')
5	gma-MIR482b-5p	UAUGGGGGGAUUGGGAAGGAAU	22	Gm20	35360312	35360406	5'
3	gma-MIR482c	AUUUGUGGGAAUGGGCUGAUUGG	23	Gm18	61452904	61453003	5'
3	gma-MIR482d-3p	UCUUCCCUACACCUCCCAUACC	22	Gm10	48569629	48569723	3'
3	gma-MIR482d-5p	UAUGGGGGGAUUGGGAAGGAAU	22	Gm10	48569629	48569723	5'
5	gma-MIR1507a	UCUCAUUCCAUACAUCGUCUGA	22	Gm13	25849777	25849883	3'	a,b
5	gma-MIR1507b	UCUCAUUCCAUACAUCGUCUG	21	Gm17	6190604	6190701	3'
5	gma-MIR1508b	UAGAAAGGGAAAUAGCAGUUG	21	Gm09	28530168	28530271	3'	a*,b
5	gma-MIR1509a	UUAAUCAAGGAAAUCACGGUCG	22	Gm17	10099759	10099869	5'	a, b*
4	gma-MIR1510b	AGGGAUAGGUAAAACAACUACU	22	Gm02	6599299	6599392	5'	a*,b(3')
5	gma-MIR1510b	UGUUGUUUUACCUAUUCCACC	21	Gm02	6599299	6599392	3'
3	gma-MIR1512b	UAACUGGAAAUUCUUAAAGCAU	22	Gm02	8618692	8618781	5'	a*
5	gma-MIR1513a	UGAGAGAAAGCCAUGACUUAC	21	Gm07	43245809	43245901	5'	a
3	gma-MIR1513b	UAUGAGAGAAAGCCAUGAC	19	Gm17	1401433	1401523	5'
3	gma-MIR1513c	AAAGCCAUGACUUACACACGC	21	Gm20	223679	223766	3'
4	gma-MIR2109a	GGAGGCGUAGAUACUCACACCU	22	Gm04	28532441	28532537	3'	a(5')*
4	gma-MIR4376a-3p	AGCAUCAUAUCUCCUGCAUAG	21	Gm13	40845925	40846034	3'	a(5')*
5	gma-MIR4413a	AAGAGAAUUGUAAGUCACUG	20	Gm19	1788518	1788617	5'	a
3	gma-MIR4413b	UAAGAGAAUUGUAAGUCACU	20	Gm13	5170460	5170527	5'
4	gma-MIR4415a-3p	UUGAUUCUCAUCACAACAUGG	21	Gm18	60474198	60474369	3'	a(5')*
3	gma-MIR4415b	UUGAUUCUCAUCACAACAUGG	21	Gm08	23142767	23142922	3'

^a The group number refers to: (3) the new miRNAs identified in the conserved soybean miRNAs families; (4) miRNAs originated from the opposite arm of miRNAs previously identified; and (5) miRNAs registered in the miRBase that were detected in our libraries. ^b * miRNAs registered in the miRBase database that were not detected in our libraries.

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ISSN: 1471-2164

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