Identification of the Hevea brasiliensisAP2/ERF superfamily by RNA sequencing

Duan, Cuifang; Argout, Xavier; Gébelin, Virginie; Summo, Marilyne; Dufayard, Jean-François; Leclercq, Julie; Kuswanhadi; Piyatrakul, Piyanuch; Pirrello, Julien; Rio, Maryannick; Champion, Antony; Montoro, Pascal

doi:10.1186/1471-2164-14-30

BMC Genomics

Table 10 List of putative targets of conserved miRNAs and their mode of inhibition predicted both by psRNATarget server ( http://plantgrn.noble.org/psRNATarget/ ) and by MIRANDA included in the LeARN pipeline

From: Identification of the Hevea brasiliensisAP2/ERF superfamily by RNA sequencing

microRNA family		Target gene		UPE	Free energy	miRNA size	miRNA aligned fragment	Target aligned fragment	Inhibition	MiR position	miR position binding with respect to CDS
Name	Accession No	Gene name	Contig accession No			No bases				bp
miR156	acc_480780	HbAP2-9	hevea_454_rep_c24306	24.478	−24.41	23	UGACAGAAGAGAGAGAGCACAUC	UACUCUCUUUUUUCUGCCAA	Cleavage	1001-1020	Inside CDS & after AP2 domain
miR159	acc_19665	HbERF-IXc2	hevea_454_c72747	13.691	−25.86	23	UUUUGAUUGAAGGGAGCUCUAAU	GAGCACCCUUCAAUUAAG	Cleavage	297-314	Inside CDS & after AP2 domain
miR159	acc_19665	HbERF-VI-L1	hevea_454_rep_c17780	16.359	−27.80	23	UUUUGAUUGAAGGGAGCUCUAAU	GUUCUAGCUUCCUUCAAGCAGAG	Cleavage	50-72	outside CDS, 5’UTR & before AP2 domain
miR172	acc_502684	HbAP2-18	hevea_454_rep_c22185	15.621	−21.57	21	UAGCAUCAUCAAGAUUUUUAU	AAGAGAAUCCUGAUGAUGCUG	Cleavage	1473-1493	Inside CDS & after AP2 domain
miR172	acc_502684	HbAP2-20	hevea_454_rep_c45080	17.625	−24.25	21	UAGCAUCAUCAAGAUUUUUAU	AUGAGAAUCCUGAUGAUGCUG	Cleavage	990-1010	Inside CDS & after AP2 domain
miR393	acc_112860	HbAP2-4	hevea_454_c60993	24.258	−22.79	25	UUCCAAAGGGAUCGCAUUGAUUAUC	AGCAAUGUUAUUCCUUUGGC	Cleavage	198-217	Inside CDS & before AP2 domain
miR395	acc_262739	HbERF-IXc3	hevea_454_c37716	15.053	−24.47	25	CUGAAGUGUUUGGGGGACCUCAUC	GAGAAAGUUCUCCAAUCACUUCAA	Translation	243-266	Inside CDS & after AP2 domain
miR396	acc_7978	HbRAV-2	hevea_454_rep_c13430	22.097	−22.40	24	CCACAGCUUUCUUGAACUGCAAUC	GAGUUCAAGAAAGCGGUU	Cleavage	562-579	Inside CDS & after AP2 domain
miR408	acc_135004	HbERF-IXb1	hevea_454_c13287	14.501	−23.60	23	UGCACUGCCUCUUCCCUGCCAUC	AAGAGAAGAGGCAGUACA	Cleavage	118-135	Inside CDS & cut AP2 domain
miR408	acc_184014	HbERF-VIIa9	hevea_454_rep_c64305	24.62	−28.45	24	UACACUGCCUCUUCCCUGGCUAUC	UGCGAGCAGGAGGAGAGGCAGU	Cleavage	207-228	Inside CDS & before AP2 domain
miR408	acc_184014	HbERF-VIIa13	hevea_454_rep_c8113	24.62	−28.45	24	UACACUGCCUCUUCCCUGGCUAUC	UGCGAGCAGGAGGAGAGGCAGU	Cleavage	518-539	Inside CDS & before AP2 domain
miR894	S_seq_24257	HbERF-IIa2	hevea_454_rep_c7563	15,655	−19,42	16	UGUUUCACGUCGGGUU	AACCUGACUUGAACCA	Cleavage	760-775	Inside CDS & after AP2 domain
miR894	S_seq_73030	HbAP2-6	hevea_454_rep_c16078	18,933	−22,38	17	CGUUUAACGUCGGGUUC	GAAGCCGAUGUUGAACA	Cleavage	694-710	3’ region & after CDS
miR894	S_seq_174443	HbERF-IIIe3	hevea_454_rep_c58258	21,025	−23,87	20	UCUUCGUUUCACGUCGGGUU	AAUCUGCCGUGGUACGAGGA	Cleavage	653-672	Inside CDS & after AP2 domain
miR894	S_seq_181990	HbERF-IXc5	hevea_454_rep_c36947	23,707	−25,35	20	GUUUCACAUCGGGUUCACCA	UGGAGAAAUCCAUGUGAAAU	Translation	901-920	5’ region & before CDS
miR894	S_seq_376904	HbERF-VIIa20	hevea_454_rep_c710	17,302	−27	16	GUGCGUUUCACGUCGG	UUGCCGUGAAACGCAU	Cleavage	130-145	Inside CDS & before AP2 domain
miR894	S_seq_376904	HbERF-VIIa23	hevea_454_rep_c88669	17,295	−27	16	GUGCGUUUCACGUCGG	UUGCCGUGAAACGCAU	Cleavage	73-88	Inside CDS & before AP2 domain
miR1511	S_seq_556556	HbERF-IXc6	hevea_454_rep_c18341	22,461	−27,04	19	AACCAGGCUCUGAUACCAU	AUGGCAUCAGGGUUUGGUU	Cleavage	449-467	Inside CDS & inside AP2 domain
miRn11	S_seq_275942	HbERF-VIIa2	hevea_454_rep_c40731	16,586	−26,87	16	AGUUUGGCUGGGGCGG	UCGCCUUAGCUAAACA	Cleavage	37-52	5’ region & before CDS
miRn11	S_seq_275942	HbERF-VIIIa7	hevea_454_rep_c16802	16,135	−24,03	19	AGUUUGGCUGGGGCGGCAC	GCGCAGCCCAAGCCAAACC	Translation	355-373	Inside CDS & after AP2 domain
miRn11	S_seq_11884	HbERF-IIId3	hevea_454_c39573	13,87	−31,03	16	GGGAGUUUGGCUGGGG	UCCUAGCCAAAUUCUU	Cleavage	405-420	Inside CDS & inside AP2 domain
miRn11	S_seq_11884	HbERF-Xa8	hevea_454_c51284	21,466	−28,52	15	GGGAGUUUGGCUGGG	CCUAGCCAAACUCUA	Cleavage	419-433	Inside CDS & Inside AP2 domain
miRn11	S_seq_4512	HbERF-VI5	hevea_454_c22933	4,586	−24,23	17	GAGUUUGGCUGGGGCGG	UCGUCCAAGCCCAACUC	Translation	215-231	5’ region & before CDS
miRn11	S_seq_422499	HbERF-VIIa4	hevea_454_rep_c1157	11,652	−23,53	16	GAGUUUGGCUGGGGCU	AGUCCUAUCCGAACUC	Translation	457-472	Inside CDS & before AP2 domain
miRn11	S_seq_234287	HbSoloist3	hevea_454_rep_c46638	20,623	−37,87	19	UCAGGUGGG-GAGUUUGGCU	AGCCAGACUCAUCCACCUGA	Translation	618-637	Inside CDS & after AP2 domain
miRn12	S_seq_119244	HbERF-IIa1	hevea_454_rep_c8625	11,7	−21,45	16	UUUGCAGUUCGAAAGU	AUUUUUUAACUGUAAG	Translation	982-997	5’ region & before CDS
miRn12	S_seq_7691	HbAP2-10	hevea_454_rep_c22185	23,384	−26,47	17	UUAGCAGUUCGAAAGUG	CACCCUUGAACUGCUAA	Cleavage	39-55	3’ region & after CDS
miRn12	S_seq_2869	HbERF-Xa1	hevea_454_c58761	22,067	−32,35	17	UUGGCAGU-UCGAAAGUG	UACUUUCGAUACUGCCGA	Translation	611-628	Inside CDS & inside AP2 domain
miRn14	S_seq_358709	HbERF-Ib5	hevea_454_rep_c4396	8,491	−24	26	UAGAACACAAUUAUAGGAAUCAAUAU	AUAUUGGU-CUUGUACUUGUGUUCUG	Translation	1936-1960	3’ region & after CDS

Target accessibility is represented as the maximum energy needed (UPE) to unpair the secondary structure around target site on target mRNA. The lower the energy the greater the possibility that small RNA is able to contact (and cleave) target mRNA. The lower the free energy the greater the possibility that small RNA is able to contact target mRNA. The predicted microRNA was based on a free energy threshold below −20 kcal/mol.

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ISSN: 1471-2164

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