Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

Baksa, Ivett; Nagy, Tibor; Barta, Endre; Havelda, Zoltán; Várallyay, Éva; Silhavy, Dániel; Burgyán, József; Szittya, György

doi:10.1186/s12864-015-2209-6

Table 2 Targets of conserved and other known miRNAs in Nicotiana benthamiana ^a

From: Identification of Nicotiana benthamiana microRNAs and their targets using high throughput sequencing and degradome analysis

miRNA family	miRNA sequence	Gene ID	Clevage position	Category	Normalized abundance^a	Annotation
Conserved miRNAs and their targets
Nb_miR156	TGACAGAAGAGAGTGAGCAC	comp77119_c0_seq6 2667_2942	1787	0	2,40	Squamosa promoter-binding-like protein 6
Nb_miR156	TGACAGAAGAGAGTGAGCAC	comp69399_c0_seq4 393_944	650	2	1,28	Squamosa promoter-binding-like protein 16
Nb_miR159	TTTGGATTGAAGGGAGCTCTA	comp71582_c0_seq2 1_1230	673	0	40,63	No annotation^b
Nb_miR159	TTTGGATTGAAGGGAGCTCTA	comp69815_c0_seq4 1_894	601	0	0,39	Transcription factor GAMYB
Nb_miR159	TTTGGATTGAAGGGAGCTCTA	comp73942_c0_seq1 927_2375	1839	0	2,14	Transcription factor GAMYB
Nb_miR160	TGCCTGGCTCCCTGTATGCCA	comp78286_c0_seq3 693_2783	2065	0	307,20	Auxin response factor 18
Nb_miR160	TGCCTGGCTCCCTGTATGCCA	comp79462_c0_seq1 2477_3379	2658	0	6,41	Auxin response factor 16
Nb_miR164	TGGAGAAGCAGGGCACGTGCA	comp72325_c0_seq2 310_1305	994	0	3,43	Protein CUP-SHAPED COTYLEDON 2
Nb_miR165/166	TCGGACCAGGCTTCATTCCCC	comp80060_c0_seq5 1298_3817	1868	0	51,20	Homeobox-leucine zipper protein REVOLUTA
Nb_miR165/166	TCGGACCAGGCTTCATTCCTC	comp79517_c0_seq6 1043_3556	1601	0	246,61	Homeobox-leucine zipper protein ATHB-15
Nb_miR165/166	TCGGACCAGGCTTCATTCCTC	comp79347_c3_seq8 336_611	546	1	1,60	No annotation^b
Nb_miR167	AGATCATGTGGTAGCTTCACC	comp79742_c0_seq4 124_2421	1700	2	5,90	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase^b
Nb_miR167	AGATCATGTGGTAGCTTCACC	comp74516_c0_seq2 292_2619	1160	2	3,54	Subtilisin-like protease^b
Nb_miR168	TCGCTTGGTGCAGGTCGGGACC	comp79927_c1_seq7 1_243	876		1,60	Protein argonaute 1A
Nb_miR169	TAGCCAAGGATGACTTGCCT	comp72459_c1_seq2 1230_1673	1724	2	0,19	Nuclear transcription factor Y subunit A-5/CCAAT-binding transcription factor
Nb_miR169	TAGCCAAGGATGACTTGCCT	comp72338_c0_seq4 1046_1396	1439	2	0,29	Nuclear transcription factor Y subunit A-5/CCAAT-binding transcription factor
Nb_miR169	TAGCCAAGGATGACTTGCCT	comp73705_c1_seq8 1254_1739	1836	1	3,15	Nuclear transcription factor Y subunit A-8/CCAAT-binding transcription factor
Nb_miR169	TAGCCAAGGATGACTTGCCT	comp67524_c0_seq9 544_1167	1246	0	1,96	Nuclear transcription factor Y subunit A-10/CCAAT-binding transcription factor
Nb_miR171	TTGAGCCGCGCCAATATCACG	comp76988_c0_seq2 277_1911	896	0	26,05	Scarecrow-like protein 15
Nb_miR171	TTGAGTCGCGCCAATATCACT	comp80119_c0_seq4 672_2573	1552	0	34,34	Scarecrow-like protein 6
Nb_miR171	TTGAGTCGCGCCAATATCACT	comp75200_c0_seq2 459_2717	1696	0	109,89	Scarecrow-like protein 6
Nb_miR172	AGAATCTTGATGATGCTGCAG	comp78340_c2_seq4 552_1409	2200	0	4,42	Floral homeotic protein APETALA 2
Nb_miR319	TTGGACTGAAGGGAGCTCCCT	comp68096_c0_seq1 79_1191	1046	0	1,02	Transcription factor TCP4
Nb_miR319	TTGGACTGAAGGGAGCTCCCT	comp73714_c2_seq12 2093_2317	2006		0,98	Transcription factor TCP2
Nb_miR393	TCCAAAGGGATCGCATTGATCC	comp80206_c0_seq2 468_4724	4235	2	0,29	No annotation^b
Nb_miR394	TTGGCATTCTGTCCACCTCC	comp60101_c0_seq1 5351_5605	5291	2	2,16	Tripeptidyl-peptidase 2^b
Nb_miR395	CTGAAGTGTTTGGGGGAACTC	comp75863_c0_seq1 200_1609	553	2	0,53	ATP sulfurylase 1, chloroplastic
Nb_miR395	CTGAAGTGTTTGGGGGAACTC	comp29318_c1_seq1 108_620	254	0	1,07	Sulfate transporter 2.1
Nb_miR396	TTCCACATCTTTCTTGAACTG	comp71133_c0_seq1 1089_1355	935	2	2,10	Protein THYLAKOID FORMATION1, chloroplastic^b
Nb_miR396	TTCCACAGCTTTCTTGAACTG	comp77639_c0_seq4 942_2765	1723	0	4,42	Growth-regulating factor 6
Nb_miR396	TTCCACAGCTTTCTTGAACTG	comp67678_c0_seq1 205_573	279	0	12,19	Thioredoxin H-type 1^b
Nb_miR396	TTCCACAGCTTTCTTGAACTG	comp50987_c1_seq1 2_379	144	1	0,48	40S ribosomal protein S15^b
Nb_miR396	TTACACAGCTTTCTTGAACTG	comp69468_c0_seq1 204_1724	1425	2	0,58	Protein IQ-DOMAIN 14^b
Nb_miR396	TTCCACAGCTTTCTTGAACTG	comp77795_c0_seq2 2_1780	1546		0,58	Pentatricopeptide repeat-containing protein At5g04810, chloroplastic^b
Nb_miR396c	TTCCACAGCTTTCTTGAACTG	comp77334_c1_seq28 1342_2196	1370	0	3,74	Growth-regulating factor 5
Nb_miR396	TTCCACAGCTTTCTTAAACTG	comp79406_c0_seq1 393_3506	1932	2	0,29	No annotation^b
Nb_miR396	TTCCACAGCTTTCTTGAACTG	comp76253_c0_seq1 643_1557	767	0	0,19	Growth-regulating factor 9
Nb_miR396	TTCCACAGCTTTCTTGGACTG	comp69128_c0_seq2 114_806	521	2	0,19	DNA-directed RNA polymerase V subunit 5A-l ike^b
Nb_miR397	TCATTGAGTGCAGCGTTGATG	comp73318_c2_seq1 87_1109	883	2	4,42	Glyceraldehyde-3-phosphate dehydrogenase, cytosolic^b
Nb_miR397	TCATTGAGTGCAGCGTTGATG	comp75344_c1_seq2 127_1839	810	2	0,24	Laccase-7
Nb_miR397	TCATTGAGTGCAGCGTTGATG	comp77652_c0_seq1 1261_3177	176	2	0,29	Probable serine/threonine-protein kinase abkC^b
Nb_miR398	TATGTTCTCAGGTCGCCCCTG	comp100607_c0_seq1 102_557	78	0	9,46	Umecyanin
Nb_miR408	TGCACTGCCTCTTCCCTGGCT	comp85708_c0_seq1 121_624	630	0	15,30	Uclacyanin-2
Nb_miR408	TGCACTGCCTCTTCCCTGGCT	comp79061_c1_seq3 184_1473	2346	0	12,38	Copper-transporting ATPase PAA2, chloroplastic
Other known miRNAs and their targets
Nb_miR482	TTCCAATTCCACCCATTCCTA	comp75828_c0_seq3 249_1742	1609	2	1,07	No annotation^b
Nb_miR827	TTAGATGAACATCAACAAACT	comp75426_c0_seq1 2_226	1982	2	1,36	UPF0496 protein 4
Nb_miR4376	TACGCAGGAGAGATGATACTG	comp79500_c0_seq4 305_3562	284	2	0,98	Calcium-transporting ATPase 8, plasma membrane-type
Nb_miR6020	AAATGTTCTTCGAGTATCTTC	comp70698_c0_seq1 752_1555	996	1	0,68	GPN-loop GTPase 3 homolog^b
Nb_miR6020	AAATGTTCTTCGAGTATCTTC	comp74553_c0_seq5 265_702	596	0	1,47	No annotation^b
Nb_miR6020	AAATGTTCTTCGAGTATCTTC	comp75715_c0_seq5 271_2055	1544	2	0,27	Probable methylenetetrahydrofolate reductase^b
Nb_miR6149	TTGATACGCACCTGAATCGGG	comp80883_c0_seq1 2_310	14	2	0,27	Tubulin alpha chain^b
Nb_miR6149	TTGATACGCACCTGAATCGGG	comp75221_c0_seq2 455_1678	1646	2	1,77	Serine/threonine-protein kinase HT1^b
Nb_miR6151	TGAGTGTGAGGCGTTGGATTGA	comp84169_c0_seq1 105_1127	334	2	2,10	Probable carboxylesterase 8^b
Nb_miR6157	TGGTAGACGTAGGATTTGAAA	comp66224_c0_seq2 136_780	259		0,68	Ras-related protein RABA2b^b
Nb miR6161	TGCTGGACCGACATACTTTGT	comp74264_c0_seq1 147_1052	343	2	0,48	60S ribosomal protein L5^b

^a The abundance for the degradome fragment (tag) indicating cleavage at that position/total number of fragments x 1,000,000
^b New target in N. benthamiana for conserved and other known miRNAs

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ISSN: 1471-2164

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