Transcriptome-wide identification and characterization of miRNAs from Pinus densata

Wan, Li-Chuan; Zhang, Haiyan; Lu, Shanfa; Zhang, Liang; Qiu, Zongbo; Zhao, Yuanyuan; Zeng, Qing-Yin; Lin, Jinxing

doi:10.1186/1471-2164-13-132

BMC Genomics

Table 1 Conserved miRNAs identified in P.densata

From: Transcriptome-wide identification and characterization of miRNAs from Pinus densata

miRNA gene	miRNA sequence (5'-3')	Arm	Length (nt)	A + U (%)	Folding energy	MFEI	RT-PCR	qPCR	*Conserved in other plants
									ath	osa	ptc	vvi	pta	pab
pde-miR159a	UUUGGUUUGAAGGGAGCUCUA^a	3'	21	53.5	-94.74	0.89	+	+	+	+	+	+	+
pde-miR162a	UCGAUAAACCUCUGCAUCCAG	3'	21	45.0	-49.10	0.80			++	+	++	++
pde-miR166a	UCGGACCAGGCUUCAUUCC	3'	19	45.8	-49.10	0.96	+	+	+	+	+	++	+	+
pde-miR166b	UCGGACCAGGCUUCAUUCC	3'	19	48.8	-43.40	1.01	+	+	+	+	+	++	+	+
pde-miR169a	CAGCCAAGGAUGACUUGCCUA^a	5'	21	58.3	-48.80	1.14	+		+	+	+	+
pde-miR171a	UGAUUGAGCCGUGCCAAUAUC	3'	21	55.2	-55.20	1.28	+	+	+	++	++	++	+
pde-miR390a	AAGCCCAGGAUGGAUAGCGCC	5'	21	53.7	-40.50	0.92		+	+	+	+	+	++
pde-miR396a	UCCCACGGCUUUCUUGAACUU^a	5'	21	55.1	-43.28	0.90			+	+	+	+	+	+
pde-miR482a	UCUUUCCUACUCCUCCCAUUCC	3'	22	52.3	-60.90	0.98	+	+	+		+	++	+	++
pde-miR482b	UCUUCCCUAUUCCUCCCAUUCC	3'	22	52.1	-60.30	1.04	+		+		+	+	+	++
pde-miR482c	GGCUUGCGAGGGUAGGAAAAG^a	5'	21	48.9	-45.20	0.90			+		+	+	+	+
pde-miR482d	CCUUUCCAACGCCUCCCAUGCC^a	3'	22	54.8	-46.50	0.76	+		+		+	+	+	+
pde-miR783	AUUCUUUGCUGGUUCAUUUUC	3'	21	57.0	-26.80	0.67	+						+
pde-miR946a	CAGCCCUUCUCCUAUCCACAA	3'	21	59.3	-71.50	1.02	+	+					++
pde-miR947	CAUCGGAAUCUGUUACUGUUUC	3'	22	48.7	-70.70	0.94	+						++	+
pde-miR949a	UCUCUAGGAAUCAAAUGUGUC^a	5'	21	47.7	-41.80	0.91	+						+
pde-miR949b	UCUCCGGGAAUCCAAUGCGCC	5'	21	46.3	-66.30	1.12	+						++
pde-miR950a	UCUGGUCCACGGUGGUUUAU^a	5'	20	57.2	-40.90	1.05	+	+					+	+
pde-miR951	UGUUCUUGACGUCUGGACCAC	5'	21	54.8	-43.00	0.83	+						++	+
pde-miR952a	AACAGAGCAUGCCAUUGGUG^a	5'	20	54.0	-232.79	0.96	+						++
pde-miR952b	AACAGAGCAUGCCAUUGGUG^a	5'	20	53.9	-214.40	0.99	+						++
pde-miR952c	AACAGAACAUGCCAUUGGUG^a	5'	20	54.2	-192.12	0.90	+						++
pde-miR1310	GGCAUCGGGGGCGUAACGCCCU	5'	22	47.0	-35.00	0.80	+						++
pde-miR1311	UCAGAGUUUUGCCAGUUCCGCC	3'	22	48.8	-43.40	0.99	+	+					++	++
pde-miR1312a	UUUGGAGAGAAAAUGGCGACAU	3'	22	62.8	-41.50	0.81	+						++
pde-miR1313	UACCACUGAAAUUGUUGUUCG^a	5'	21	58.6	-66.72	0.71	+	+					+
pde-miR1314a	CCGGCCUCGAAUGUUAGGAGAA^a	3'	22	56.2	-42.30	0.92	+	+					+
pde-miR1448	CUUUCCAACGCCUCCCAUGC^a	3'	20	54.8	-46.50	0.76	+				+
pde-miR2118a	UUUCCAACGCCUCCCAUGCCUA^a	3'	22	54.8	-46.50	0.76	+			+
pde-miR2118b	UUCCCUAUUCCUCCCAUUCCUA^a	3'	22	49.4	-42.00	0.98	+			+
pde-miR3701	UGAACAAUGCCCACCCUUCAUC^a	3'	22	59.3	-84.10	1.07	+							+
pde-miR3704a	GGUCUCGGUGGAGUUGGGAAGA^a	5'	22	53.8	-49.00	0.98	+							+
pde-miR3704b	GGUCUCGAUGGAGUUGGGAAGA^a	5'	22	54.7	-46.40	0.95	+							+
pde-miR3712	UGUGAUCAAGAUCAGACUCCCA^a	5'	22	59.4	-15.00	0.54	+							+
						0.92 ± 0.15^b

*Ath, osa, ptc, vvi, pta and pab are the abbreviations for A. thaliana, O. sativa, P. trichocarpa, Vitis vinifera, P. taeda and P. abies, respectively. The plus symbols indicate: ++, miRNAs identical to known miRNAs in other plant species; +, miRNAs homologous to known miRNAs in other plant species. ^a is a novel member of corresponding miRNA family. ^b 0.92 ± 0.15 is the average and standard deviation of MFEI values of pre-miRNAs.

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ISSN: 1471-2164

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