High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

Mica, Erica; Piccolo, Viviana; Delledonne, Massimo; Ferrarini, Alberto; Pezzotti, Mario; Casati, Cesare; Del Fabbro, Cristian; Valle, Giorgio; Policriti, Alberto; Morgante, Michele; Pesole, Graziano; Pè, M Enrico; Horner, David S

doi:10.1186/1471-2164-10-558

Table 1 Expression of mature- and pre-miRNAs in Vitis vinifera

From: High throughput approaches reveal splicing of primary microRNA transcripts and tissue specific expression of mature microRNAs in Vitis vinifera

miRNA	Sequence	Expression data				miRNA	Sequence	Expression data
		A	B	C	D			A	B	C	D
MIR156A	TGACAGAAGAGAGGGAGCAC	2229	____	N	__I___	MIR171G	TTGAGCCGAACCAATATCACC	0	__RC	N	RLI*___
MIR156B	TGACAGAAGAGAGTGAGCAC	835876	___C	N	______	MIR172A	AGAATCTTGATGATGCTGCAT	3450	_S_C	N	______
MIR156C	TGACAGAAGAGAGTGAGCAC	835876	____	N	______	MIR172B	AGAATCTTGATGATGCTGCAT	73450	____	N	______
MIR156D	TGACAGAAGAGAGTGAGCAC	835876	LSRC	N	______	MIR172D	AGAATCTTGATGATGCTGCAT	73450	____	N	_LIBgBv_
MIR156E	TGACAGAGGAGAGTGAGCAC	251	____	N	______	MIR172C	GAATCTTGATGATGCTGCAG	1	____	N	_LIBgBv_
MIR156F	TTGACAGAAGATAGAGAGCAC	30	_S__	N	RLIBgBvBm	MIR319B	TTGGACTGAAGGGAGCTCCCT	1	____	N	RLIBgBvBm
MIR156G	TTGACAGAAGATAGAGAGCAC	30	LS_C	N	RLIBgBvBm*	MIR319C	TTGGACTGAAGGGAGCTCCCT	1	_S__	N	RLIBgBvBm
MIR156I	TTGACAGAAGATAGAGAGCAC	30	_S__	N	RLIBg*BvBm	MIR319E	TTTGGACTGAAGGGAGCTC	1	_S_C	Y	RLIBgBvBm
MIR156H	TGACAGAAGAGAGAGAGCAT	69	LS__	Y	______	MIR319G	ATTGGACTGAAGGGAGCTCCC	0	___C	N	RLIBgBvBm
MIR159A	CTTGGAGTGAAGGGAGCTCTC	0	____	N	RLIBgBvBm	MIR319F	TTGGATTGAAGGGAGCTCCCT	1	_S__	N	RLIBgBvBm*
MIR159B	CTTGGAGTGAAGGGAGCTCTC	0	____	N	RLIBgBvBm	MIR390	AAGCTCAGGAGGGATAGCGCC	141	_S__	N	RLIBgBvBm
MIR159C	TTTGGATTGAAGGGAGCTCT	124	LSRC	N	RLIBgBvBm	MIR393A	TTCCAAAGGGATCGCATTGAT	14983	____	Y	RLIBgBvBm
MIR160A	TGCCTGGCTCCCTGAATGCCA	276	____	N	RLIBgBvBm*	MIR393B	TCCAAAGGGATCGCATTGATC	398	LS__	Y	RLIBgBvBm
MIR160B	TGCCTGGCTCCCTGAATGCCA	276	____	Y	RLIBgBvBm	MIR394A	TTGGCATTCTGTCCACCTCC	748	_S__	N	______
MIR160E	TGCCTGGCTCCCTGAATGCCA	276	____	Y	RLIBgBvBm	MIR394B	TTGGCATTCTGTCCACCTCC	748	LS_C	N	______
MIR160C	TGCCTGGCTCCCTGTATGCCA	130	_SRC	N	RLIBgBvBm*	MIR394C	TTGGCATTCTGTCCACCTCC	748	____	N	______
MIR160D	TGCCTGGCTCCCTGTATGCCA	130	____	N	RLIBgBvBm	MIR395A	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR160F	TGCCTGGCTCCCTGTATGCCA	130	____	N	RLIBgBv*Bm	MIR395B	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR162	TCGATAAACCTCTGCATCCAG	1	LS_C	Y	RLIBgBvBm	MIR395C	TGAAGTGTTTGGGGGAACTC	198	____	N	RLI*BgBvBm
MIR164A	TGGAGAAGCAGGGCACGTGCA	13841	____	N	RLIBg__	MIR395D	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR164C	TGGAGAAGCAGGGCACGTGCA	13841	L___	N	RLIBg__	MIR395E	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR164D	TGGAGAAGCAGGGCACGTGCA	13841	____	N	RLIBg__	MIR395F	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR164B	TGGAGAAGCAGGGCACATGCT	1	____	N	_LI*Bg__	MIR395L	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR166A	TCGGACCAGGCTTCATTCCT	181	LSRC	Y	RLIBgBvBm	MIR395 M	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR166B	TCGGACCAGGCTTCATTCCT	181	LS__	N	RLIBgBvBm	MIR395G	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR166C	TCGGACCAGGCTTCATTCCCC	219273	LSRC	N	RLIBgBvBm	MIR395H	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR166D	TCGGACCAGGCTTCATTCCCC	219273	_S__	N	RLIBgBvBm	MIR395I	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR166E	TCGGACCAGGCTTCATTCCCC	219273	_SRC	N	RLIBgBvBm*	MIR395J	TGAAGTGTTTGGGGGAACTC	198	_S__	N	RLIBgBvBm
MIR166F	TCGGACCAGGCTTCATTCCCC	219273	____	N	RLIBgBvBm	MIR395K	TGAAGTGTTTGGGGGAACTC	198	____	N	RLIBgBvBm
MIR166G	TCGGACCAGGCTTCATTCCCC	219273	____	N	RLIBgBvBm*	MIR395N	CTGAAGAGTCTGGAGGAACTC	0	____	N	_L____
MIR166H	TCGGACCAGGCTTCATTCCCC	219273	_S_C	N	RLIBgBvBm	MIR396B	TTCCACAGCTTTCTTGAACTT	2204	LS_C	N	RL_Bg__
MIR167A	TGAAGCTGCCAGCATGATCTG	166	L_RC	N	RLIBgBvBm	MIR396A	TTCCACAGCTTTCTTGAAC	810	_S__	N	RL_Bg__
MIR167B	TGAAGCTGCCAGCATGATCTA	4965	L__C	Y	RLIBgBvBm	MIR396C	TTCCACAGCTTTCTTGAAC	810	____	N	RL_Bg__
MIR167C	TGAAGCTGCCAGCATGATCT	89	____	N	RLIBgBvBm	MIR396D	TTCCACAGCTTTCTTGAAC	810	_S_C	N	RL_Bg__
MIR167D	TGAAGCTGCCAGCATGATCTA	4965	LS__	N	RLIBgBvBm	MIR397A	ATTGAGTGCAGCGTTGATGAA	714	LS_C	N	R__Bg__
MIR167E	TGAAGCTGCCAGCATGATCTA	4965	____	N	RLIBgBvBm	MIR397B	ATTGAGTGCAGCGTTGATGAA	714	____	N	R__Bg__
MIR168	TCGCTTGGTGCAGGTCGGGAA	5	LSRC	Y	RLIBgBvBm	MIR398A	TTCTCAGGTCACCCCTTTGGG	13	_SRC	N	RL_Bg__
MIR169B	TGAGCCAAGGATGGCTTGCCG	0	____	N	_L__BvBm	MIR398B	CTCATGTGTTCTCAGGTCGCC	15	LSRC	N	R__Bg__
MIR169H	TGAGCCAAGGATGGCTTGCCG	0	____	N	_L__BvBm	MIR398C	CTCATGTGTTCTCAGGTCGCC	15	LSRC	N	R__Bg__
MIR169A	CAGCCAAGGATGACTTGCCGG	675	____	N	_LIBgBvBm	MIR399A	TGCCAAAGGAGAATTGCCCTG	106	L___	N	R_I___
MIR169C	CAGCCAAGGATGACTTGCCGG	675	____	N	_LIBgBvBm	MIR399H	TGCCAAAGGAGAATTGCCCTG	106	L___	N	R_I___
MIR169J	CAGCCAAGGATGACTTGCCGG	675	____	N	_LIBgBvBm	MIR399B	TGCCAAAGGAGAGTTGCCCTG	34	____	N	R__Bg_Bm
MIR169K	CAGCCAAGGATGACTTGCCGG	675	____	N	_LIBgBvBm	MIR399C	TGCCAAAGGAGAGTTGCCCTG	34	____	N	R__Bg_Bm
MIR169S	CAGCCAAGGATGACTTGCCGG	675	____	N	_LI*BgBvBm	MIR399I	CAAAGGAGAGTTGCCCTG	1	L_RC	N	R__Bg_Bm
MIR169W	CAGCCAAGGATGACTTGCCGG	675	____	N	_LIBgBvBm	MIR399D	TGCCAAAGGAGATTTGCTCGT	0	____	N	______
MIR169L	GAGCCAAGGATGACTTGCCGT	0	____	N	_LIBgBvBm	MIR399E	TGCCAAAGGAGATTTGCCCGG	0	___C	N	______
MIR169 M	AGCCAAGGATGACTTGCCGGC	16	____	N	_LIBgBvBm*	MIR399F	TGCCGAAGGAGATTTGTCCTG	0	____	N	______
MIR169N	AGCCAAGGATGACTTGCCGGC	16	____	N	_LIBgBvBm*	MIR399G	TGCCAAAGGAGATTTGCCCCT	0	____	N	R_I__Bm
MIR169O	GAGCCAAGGATGACTTGCCGC	0	____	N	_LIBgBvBm	MIR403A	TTAGATTCACGCACAAACTCG	0	____	N	RLIBgBvBm
MIR169P	AGCCAAGGATGACTTGCCG	16	____	N	_LIBgBvBm	MIR403B	TTAGATTCACGCACAAACTCG	0	____	N	RLIBgBvBm
MIR169Q	AGCCAAGGATGACTTGCCG	16	____	N	_LIBgBvBm	MIR403C	TTAGATTCACGCACAAACTCG	0	___C	N	RLIBgBvBm
MIR169E	TAGCCAAGGATGACTTGCCTG	8	L___	N	_LIBgBvBm	MIR403D	TTAGATTCACGCACAAACTCG	0	____	N	RLIBgBvBm
MIR169F	CAGCCAAGGATGACTTGCCGA	317	___C	N	_LIBgBvBm*	MIR403E	TTAGATTCACGCACAAACTCG	0	____	N	RLIBgBvBm
MIR169G	CAGCCAAGGATGACTTGCCGA	317	_S__	N	_LIBgBvBm	MIR403F	TTAGATTCACGCACAAACTCG	0	_SRC	N	RLIBgBvBm
MIR169R	TGAGTCAAGGATGACTTGCCG	0	____	N	_LIBgBvBm*	MIR408	TGCACTGCCTCTTCCCTGGC	131	LSRC	Y	RLIBgBvBm
MIR169T	TGAGTCAAGGATGACTTGCCG	0	____	N	_LIBgBvBm*	MIR477A	ATCTCCCTCAAAGGCTTCCAA	0	____	N	___BgBvBm
MIR169U	TGAGTCAAGGATGACTTGCCG	0	____	N	_LIBgBvBm*	MIR479	TGTGGTATTGGTTCGGCTCATC	2	____	N	______
MIR169V	AAGCCAAGGATGAATTGCCGG	0	____	N	__IBg__	MIR482	CCTACTCCTCCCATTCC	0	LSRC	Y	______
MIR169X	TAGCCAAGGATGACTTGCCTA	1	____	Y	_LIBgBvBm	MIR535A	TGACAACGAGAGAGAGCACGCT	0	____	Y	RLIBgBvBm
MIR169Y	TAGCGAAGGATGACTTGCCTA	0	____	N	__I___	MIR535B	TGACAACGAGAGAGAGCACGCT	0	____	Y	RLIBgBvBm
MIR169I	GAGCCAAGGATGACTGGCCGT	0	____	N	_L_Bg__	MIR535C	TGACAACGAGAGAGAGCACGCT	0	____	Y	RLIBgBvBm
MIR169D	CAGCCAAGAATGATTTGCCGG	0	____	N	______	MIR535D	TGACAACGAGAGAGAGCACGCT	0	____	Y	RLIBgBvBm
MIR171B	TGATTGAGCCGCGTCAATATC	0	____	N	R_____	MIR535E	TGACAACGAGAGAGAGCACGCT	0	____	Y	RLIBgBvBm
MIR171C	TGATTGAGCCGTGCCAATATC	637	____	N	RLIBg__	MIR828A	TCTTGCTCAAATGAGTATTCCA	0	____	N	______
MIR171D	TGATTGAGCCGTGCCAATATC	637	____	N	RLIBg__	MIR828B	TCTTGCTCAAATGAGTGTTCCA	0	____	N	______
MIR171A	TGATTGAGCCGTGCCAATATC	637	_SRC	Y	RLIBg__	MIR845A	TAGCTCTGATACCAATTGATA	0	____	N	______
MIR171I	TGATTGAGCCGTGCCAATATC	637	____	N	RLIBg__	MIR845B	TAGCTCTGATACCAATTGATA	0	____	N	______
MIR171E	TGATTGAGCCGCGCCAATATC	53	___C	N	RLIBgBvBm*	MIR845C	AGGCTCTGATACCAATTGATG	0	____	N	______
MIR171H	TGGTTGAGCCGCGCCAATATC	0	____	N	RLIBgBvBm	MIR845D	TGGCTCTGATACCAATTGATGG	0	____	N	______
MIR171F	TTGAGCCGCGCCAATATCACT	0	_S__	N	RLIBgBv_	MIR845E	TGGCTCTGATACCAATTGATGG	0	____	N	______

For each predicted pre-miRNA the table reports: the mature sequence, the number of perfect matching short RNA reads observed in leaf (column A), tissues in which significant expression of the precursor was observed by Illumina whole transcriptome sequencing (column B, where L = leaf, R = root, S = stem, C = callus), the presence of 454 reads including the precursor sequence in leaf (column C, where Y = yes, N = no), and tissues where the Combimatrix oligoarray showed significant expression of the mature sequence (column D, where L = leaf, I = inflorescence, R = root, Bg = immature berry, Bv = veraison, Bm = mature berry). Asterisks indicate signal detected for precursor in that tissue. Mature miRNAs are ordered to reflect expected cases of crosshybridization for oligonucleotide arrays. For all microRNAs, chromosome, strand and coordinates of the precursor miRNA are provided (scaffold coordinates indicate that the miRNA was situated on a scaffold not incorporated into the 8.4× genome assembly).

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ISSN: 1471-2164

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