Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development

Gao, Chao; Wang, Pengfei; Zhao, Shuzhen; Zhao, Chuanzhi; Xia, Han; Hou, Lei; Ju, Zheng; Zhang, Ye; Li, Changsheng; Wang, Xingjun

doi:10.1186/s12864-017-3587-8

Table 1 Known and novel miRNA families identified in peanut gynorphore

From: Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development

Well-conserved	Mature sequence	Length(nt)	Star(*)	References	Conserved in other plants
miR156	UGACAGAAGAGAGUGAGCAC	20	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	UUGACAGAAGAGAGUGAGCAC	21	Yes
	UGAUAGAAGAGAGUGAGCACA	21	Yes
	UUGACAGAAGAGAGUGAGCACA	22	Yes
miR157	UUGACAGAAGAUAGAGAGCAC	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	UGACAGAAGAUAGAGAGCACA	22	Yes
	UUGACAGAAGAUAGAGAGCA	20	Yes
miR159	UUUGGAUUGAAGGGAGCUCUA	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR159	UUUGGAUUGAAGGGAGCUCU	20	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR160	UGCCUGGCUCCCUGUAUGCCA	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR162	UCGAUAAACCUCUGCAUCCAG	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR164	UGGAGAAGCAGGGCACGUGCA	21	No	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	UGGAGAAGCAGGGCACGUGC	20	No
	UGGAGAAGCAGGGCACGUGCAA	22	No
	UGGAGAAGCAGGGCACGUGCAAU	23	No
miR165	UCGGACCAGGCUUCAUUCCUC	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR165	UCGGACCAGGCUUCAUUCC	19	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR166	UCGGACCAGGCUUCAUUCCCC	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	UCUCGGACCAGGCUUCAUUCC	21	Yes
	UCGGACCAGGCUUCAUUCCC	20	Yes
	UCGGACCAGGCUUCAUUCC	19	Yes
miR167	UGAAGCUGCCAGCAUGAUCUU	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	UGAAGCUGCCAGCAUGAUCU	20	Yes
	UGAAGCUGCCAGCAUGAUCUUA	22	Yes
miR168	UCGCUUGGUGCAGGUCGGGAA	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	UCGCUUGGUGCAGGUCGGGA	20	Yes
	CGCUUGGUGCAGGUCGGGAAC	21	Yes
miR169a	AAGCCAAGGAUGACUUGCCGG	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR169b	GGCAGGUCAUCUUGUGGCUAU	21	Yes
miR169b	GGCAGGUCAUCUUGUGGCUAUA	22	Yes
miR171	GGAUAUUGGUGCGGUUCAAUG	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR171	UAUUGGUGCGGUUCAAUGAGA	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR172	AGAAUCUUGAUGAUGCUGCAU	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR172	AGAAUCUUGAUGAUGCUGCA	20	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR319	UUGGACUGAAGGGAGCUCCCU	21	Yes		Arabidopsis, Rice, Maize et al.
miR390	AAGCUCAGGAGGGAUAGCGCC	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR391	UGUCGCAGGAGAAAUAGCACC	21	No		Arabidopsis, Rice, Maize et al.
miR393	UCCAAAGGGAUCGCAUUGAUC	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR394	UUGGCAUUCUGUCCACCUCC	20	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR396	UUCCACAGCUUUCUUGAACUU	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
	GCUCAAGAAAGCUGUGGGAGA	21	Yes
	CUCAAGAAAGCUGUGGGAGA	20	Yes
miR397	UCAUUGAGUGCAGCGUUGAUG	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR398	UGUGUUCUCAGGUCACCCCUU	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR399	GGGCACCUCUUCACUGGCAUG	21	Yes	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Arabidopsis, Rice, Maize et al.
miR403	UUAGAUUCACGCACAAACUUG	21	Yes	Chi et al., 2011 [35].	Arabidopsis, Soybean et al.
miR408	CUGGGAACAGGCAGAGCAUGA	21	No	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Soybean, Maize et al.
miR414	AACAGAGCAGAACAGAACAGA	21	No		Arabidopsis, Rice et al.
miR477	UCCCUCAAAGGCUUCCAGUA	20	No		Physcomitrella patens, Grape et al.
miR477	UCCCUCAAAGGCUUCCAGUAU	21	No		Physcomitrella patens, Grape et al.
miR482a	GGAAUGGGCGGUUUGGGAUGA	21	Yes		Arabidopsis, Rice, Maize et al.
miR482b	UUCCCAAUUCCACCCAUUCCUA	22	Yes		Arabidopsis, Rice, Maize et al.
miR530	UGCAUUUGCACCUGCACUUUA	21	No		Arabidopsis, Soybean, Alfalfa et al.
miR845	CCAAGCUCUGAUACCAAUUGAUGG	24	No		Arabidopsis, Grape et al.
miR1507	CCUCGUUCCAUACAUCAUCUAA	22	Yes	Chi et al., 2011 [35].	Soybean, Alfalfa
miR1507	CCCUCGUUCCAUACAUCAUCUA	22	Yes	Chi et al., 2011 [35].	Soybean, Alfalfa
miR1509	UUAAUCAAGGGAAUCACAGUUG	22	No		Soybean, Alfalfa
miR1509	UUAAUCAAGGGAAUCACAGUU	21	No		Soybean, Alfalfa
miR1511	AACCAGGCUCUGAUACCAUGA	21	No	Chi et al., 2011 [35].	Soybean, Alfalfa
miR1515	UCAUUUUUGCAUGCAAUGAUCC	22	No	Chi et al., 2011 [35].	Soybean, Alfalfa
miR2111	AUCCUUAGGAUGCAGAUUACG	21	No	Chi et al., 2011 [35].	Soybean, Alfalfa
miR2118	UUGCCGAUUCCACCCAUGCCUA	22	No	Chi et al., 2011 [35].	Soybean, Alfalfa
miR2118	UUGCCGAUUCCACCCAUGCCU	21	No	Chi et al., 2011 [35].	Soybean, Alfalfa
miR4376	ACGCAGGAGAGAUGGCGCUAU	21	No		Soybean, Tomato et al.
miR4376	UACGCAGGAGAGAUGGCGCUA	21	No		Soybean, Tomato et al.
miR4414	AGCUGCUGACUCGUCGGUUCA	21	Yes		Soybean, Alfalfa
miR4414	AGCUGCUGACUCGUCGGUUC	20	Yes		Soybean, Alfalfa
miR5225	UCUGUCGCAGGAGAGAUGACG	21	No		Arabidopsis, Soybean, Alfalfa et al.
miR5225	UCUGUCGCAGGAGAGAUGACGC	22	No		Arabidopsis, Soybean, Alfalfa et al.
Less-conserved	Mature sequence	Length(nt)	Star(*)	References	Conservative in other plants
miR829	AAGCUCUGAUACCAAUUGAUGGUU	24	No		Arabidopsis
miR894	CGUUUCACGUCGGGUUCACCA	20	No	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Physcomitrella patens
miR1088	UGACGGAAGAAAGAGAGCACA	21	Yes		Physcomitrella patens
	UUGACGGAAGAAAGAGAGCAC	21	Yes
	UUGACGGAAGAAAGAGAGCACA	22	Yes
miR1520	AUGUUGUUAAUUGGAGGAGCGG	22	No		Soybean
miR1520	UGUUGUUAAUUGGAGGAGCGGU	22	No		Soybean
miR2084	CGUCAUCGUUGCGAUUGUGGA	21	No		Physcomitrella patens
miR2199	UGAUACACUAGCACGGGUCAC	21	No	Chi et al., 2011 [35].	Alfalfa
miR2628	GAAGAAAGAGAAUGAUGAGUAA	22	No		Alfalfa
miR5021	UGAGAAGAAGAAGAAGAAGAA	21	No		Arabidopsis
miR5221	AGGAGAGAUGGUGUUUUGACUU	22	No		Alfalfa
miR5227	UGAAGAGAAGGGAUUUAUGAA	21	No		Alfalfa
miR5234	UGUUAUUGUGGAUGGCAGAAG	21	No		Alfalfa
miR5244	UGUCUGAUGAAGAUUGUUGGU	21	No		Alfalfa
miR5499	AAGGAAGAAUCAGUUAUGUACA	22	No		Rice
miR6300	GUCGUUGUAGUAUAGUGGUGA	21	No		Soybean
miR6475	UCUUGAGAAGUAGAGAACCGACAG	24	No		Populus trichocarpa
miR6478	CCGACCUUAGCUCAGUUGGUA	21	No		Populus trichocarpa
miR7502	UAACGGUAGAAGAAGGACUGAA	22	No		Cotton
miR7696	UUGAAUUAUGCAGAACUUAUCA	22	No		Alfalfa
miR8175	CGUUCCCCGGCAACGGCGCCA	21	No		Arabidopsis
miR9666	CGGUAGGGCUGUAUGAUGGCGA	22	No		Wheat
Peanut-specific	Mature sequence	Length(nt)	Star(*)	References	Conservative in other plants
miR3508	UAGAGGGUCCCCAUGUUCUCA	21	No	Zhao et al., 2010 [24]; Chi et al., 2011 [35].	Peanut
miR3509	UGAUAACUGAGAGCCGUUAGAUG	23	Yes	Zhao et al., 2010 [24].	Peanut
miR3511	GCCAGGGCCAUGAAUGCAGAA	21	No	Zhao et al., 2010 [24].	Peanut
miR3512	CGCAAAUGAUGACAAAUAGACA	22	No	Zhao et al., 2010 [24].	Peanut
miR3513	UGAUAAGAUAGAAAUUGUAUA	21	Yes	Zhao et al., 2010 [24].	Peanut
miR3514	UCACCGUUAAUACAGAAUCCUU	22	Yes	Zhao et al., 2010 [24].	Peanut
miR3515	AAUGUAGAAAAUGAACGGUAU	21	No	Zhao et al., 2010 [24].	Peanut
miR3516	UGCUGGGUGAUAUUGACAGAA	21	No	Zhao et al., 2010 [24].	Peanut
miR3517	UCUGACCACUGUGAUCCCGGAA	22	No	Zhao et al., 2010 [24].	Peanut
miR3518	GACCUUUGGGGAUAUUCGUGG	21	No	Zhao et al., 2010 [24].	Peanut
miR3519	UCAAUCAAUGACAGCAUUUCA	21	No	Zhao et al., 2010 [24].	Peanut
miR3520	AGGUGAUGGUGAAUAUCUUAUCUU	24	No	Zhao et al., 2010 [24].	Peanut
Novel	Mature sequence	Length(nt)	Star(*)	References	Conservative in other plants
miRn1	UUCCCAAUUCCACCCAUUCCUA	22	Yes
	UUUUCCCAAUUCCACCCAUUCC	22	Yes
miRn2	UUUUCAUUCCAUACAUCAUCUA	22	Yes
	UUUUCAUUCCAUACAUCAUCU	21	Yes
	UUUCAUUCCAUACAUCAUCUA	21	Yes
miRn3	UAGAGGGUCCCCAUGUUCUCA	21	Yes
miRn4	UGAAGCAAAGUGAUGACUCUG	21	Yes
miRn5	UGUGUGGGUUUCUGGUCUCCAC	22	Yes
miRn6	AUCCCUCGAAGGCUUCCGCUA	21	Yes
miRn7	UUAUUGUCGGACUAAGGUGUCU	22	Yes
miRn8	UUGAUGCAGUACGGACAAAAG	21	Yes
miRn9	UUUGUGUGAAAGAUCUCCGGA	21	No
miRn10	CGGUUGUGUGGAGUGCUACGG	21	No
miRn11	AGGUGCCGGUGCAUUUGCAGG	21	No
miRn12	AUGAGCUCAGUUGAAGAUUUG	21	Yes
miRn13	GGAACAAAGAGUUUGAGAUGG	21	Yes
miRn14	AAAUUGAUUGAUUAUUCCUGA	21	Yes
miRn15	UUGCUAGGAUCGUUUGGCGAU	21	Yes
miRn16	UGCUUAGGAAGGAUUGUCUUA	21	Yes
miRn17	AGGGCGUUAUGUAGGGCAUC	20	No
miRn18	UUGGUAGUAGAAGAAGGAGAU	21	No
miRn19	UCUGAAUGGGAUGAAAACGCU	21	No
miRn20a	UUUGGAAAUUCGGUACAUUAA	21	Yes
miRn20b	UUUGGAAACUCGGUACAUUAA	21	Yes
miRn21	UUACGUGUACACAAAAAAUCA	21	No
miRn22	UGAAAGUGGAAUUAAAGCAAG	21	No
miRn23	GUCGACUUUACAUGAAGUUGA	21	Yes
miRn24	UUUGGGUCUUGAGAGUACAUG	21	No

* means star sequence of miRNA

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com

BMC Genomics

Contact us