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. 2019 Nov 12;20:839. doi: 10.1186/s12864-019-6169-0

Table 4.

Analysis of the major miRNA families identified in the small RNA libraries from E. curvula

miRNA family Database miRNA sequence Sequence tags found in the libraries Count in individual libraries In silico Differential expression Given name E. curvula conserved sequence
O2P1 O2P2 T3P1 T3P2
miR2275 ata-miR2275a-3p UUUGUUUUUCUCCAAUAUCUCA UUUGUUUUUCUCCAAUAUCUCA – – 1643 1266 Tanganyka ecu_miR2275a UUGUUUUUCUCCAAUAUCUC
-UUGUUUUUCUCCAAUAUCUCA 331 127 400 397 –
UUUGUUUUUCUCCAAUAUCUC- – – 198 147 Tanganyka
osa-miR2275d CUUGUUUUUCUCCAAUAUCUCA CUUGUUUUUCUCCAAUAUCUCA 9465 4392 8769 9004 –
CUUGUUUUUCUCCAAUAUCUC- 429 213 408 301 –
bdi-miR2275a UUUGGUUUCCUCCAAUGUCUCA UUUGGUUUCCUCCAAUGUCUCA 240 – 281 257 – – –
zma-miR2275a-3p UUUGUUUUCCUCCAAUAUCUCA UUUGUUUUCCUCCAAUAUCUCA 1826 893 1673 1477 – – –
UUUGUUUUCCUCCAAUAUCUC- 494 315 367 341 –
zma-miR2275c-3p UGAGUUGGAGGAAAAUAUCUCA UUCAGUUUCCUCUAAUAUCUCA 2693 1012 1732 1702 – ecu-miR2275b UUCAGUUUCCUCUAAUAUCUC
UUCAGUUUCCUCUAAUAUCUC- 698 315 378 354 –
ata-miR2275b-5p AGAGUUGGAGGAAAACAAACA AGAGUUGGAGGAAAACAAACC 53 244 321 208 – – –
miR156 gma-miR156d UUGACAGAAGAUAGAGAGCAC UUGACAGAAGAUAGAGAGCAC 2643 1110 4663 5001 – ecu-miR156a uuGACAGAAGAuAGAGAGCAC
UUGACAGAAGAUAGAGAGC-- 312 182 410 451 –
ata-MIR156d-3p GCUCACUCCUCUUUCUGUCAGC GCUCACUCCUCUUUCUGUCAGCC 1084 730 953 638 –
stu-miR156d-3p GCUCUCUAUGCUUCUGUCAUC GCUCUCUAUGCUUCUGUCAUC 3526 2339 5901 8423 – ecu-miR156b GCUCUCUAUGCUUCUGUCAUC
zma-miR156a-3p GCUCACUUCUCUCUCUGUCAGU GCUCACUUCUCUCUCUGUCAGU 335 222 547 685 –
bdi-miR156h-3p GCUCACUGCUCUUCCUGUCAUC GCUCACUACUCUUCCUGUCACC 896 530 256 323 OTA-S
miR396 vca-miR396b-5p UCCACAGGCUUUCUUGAACUA -UCCACAGGCUUUCUUGAACUA 478 152 418 432 –

ecu-miR396a

ecu-miR396b

UCCACAGGCUUUCUUGAACU

CCACAGGCUUUCUUGAACUG
sbi-miR396e UUCCACAGGCUUUCUUGAACUG UUCCACAGGCUUUCUUGAACUG 379 144 299 292 –
fve-miR396e UUCCACAGGCUUUCUUGAACU -UCCACAGGCUUUCUUGAACUU- 252 76 261 176 –
ata-miR396b-5p UCCACAGGCUUUCUUGAACUG GCCACAGGCUUUCUUGAACUG 235 103 209 179 –
AUCCACAGGCUUUCUUGAACUG 454 151 380 340 –
UCCACAGGCUUUCUUUAACUG 174 51 134 126 –
GUCCACAGGCUUUCUUGAACUG 410 137 370 345 –
UCCACAGGAUUUCUUGAACUG 202 50 108 99 –
UCCACAGGCUUUCUUGCACUG 46 118 158 108 –
ata-miR396d-3p GUUCAAGAAAGCCCAUGGAAA GUUCAAGAAAGCCCAUGGAAA 114 64 142 163 –
osa-miR396e-5p UCCACAGGCUUUCUUGAACUG --UCCACAAGCUUUCUUGAAC-- 356 257 53 57 OTA-S
osa-miR396d UCCACAGGCUUUCUUGAACGG UCCACAAGCUUUCUUGAACGG 312 93 52 57 OTA-S
miR827 ssp-miR827 UUAGAUGACCAUCAGCAAACA UUAGAUGACCAUCAGCAAACA 1751 1229 2565 3373 – ecu-miR827 UUAGAUGACCAUCAGCAAACA
UUAGAUGACCAUCAGCAAAC- 166 126 205 278 –
-UAGAUGACCAUCAGCAAACA 47 29 63 98 –
bdi-miR827-5p UUUUGUUGGUUGUCAUCUAACC UUUUGUUGGUGGUCAUCUAACC 261 229 627 563 –
miR169 bdi-miR169l UAGCCAAGGAUGAAUUGCCGG CAGCCAAGGAUGAAUUGCC 243 117 27 28 OTA-S
CAGCCAAGGAUGAAUUGCCGG 4061 1758 397 570 OTA-S
vvi-MIR169y UAGCGAAGGAUGACUUGCCUA CGAGCUUGUUUACCGUUGAUAC 250 143 98 81 –
GUAUCAACGGUAAACAAGCUCGG 139 76 32 50 –
miR5072 osa-miR5072 CGAUUCCCCAGCGGAGUCGCCA ------CCCCAGCGGAGTCGCCA 419 192 438 495 –
CG-UUCCCCAGCGGAGUCGCCA 220 188 187 276 –
---UUCCCCAGCGGAGUCGCCA 225 137 238 254 –
----UCCCCAGCGGAGUCGCCA 425 199 294 454 –
--GUUCCCCAGCGGAGUCGCCA 189 157 169 231 –
---GUCCCCAGCGGAGUCGCCA 94 63 104 127 –
--GAUCCCCAGCGGAGUCGCCA 71 64 66 78 –
UCGUUCCCCAGCGGAGUCGCCA 493 270 376 – –
miR-8175 ath- miR-8175 GAUCCCCGGCAACGGCGCCA CCCCGGCAACGGCGCCA 297 224 727 623 – ecu-miR8175 UCCCCGGCAACGGCGCCA
CGAUCCCCGGCAACGGCGCCA 103 – 79 107 –
UCCCCGGCAACGGCGCCA 293 154 488 377 –
UUCGAUCCCCGGCAACGGCGCCA 56 27 54 42 –
UUCGGUCCCCGGCAACGGCGCCA 27 9 35 38 –
UUCGUUCCCCGGCAACGGCGCCA 99 42 98 99 –
MIR894 ppt-MIR894 CGUUUCACGUCGGGUUCACC UUCGUUUCACGUCGGGUUCACCA 148 157 127 237 – ecu-miR894 GUUUCACGUCGGGUUCACCA
UCGUUUCACGUCGGGUUCACCA 223 433 290 758 –
GUUUCACGUCGGGUUCACCA 238 241 242 249 –
UUUCACGUCGGGUUCACCA 353 543 1028 382 –
UUCACGUCGGGUUCACCA 1855 1718 1363 1222 –
UCACGUCGGGUUCACCA 1873 1710 1783 1468 –

The analysis is based on the identity of the miRNAs with miRNAs from miRBase. The miRNAs sequences differentially expressed in silico are indicated by the genotype name. The last columns show the names of the E. curvula miRNAs based on the names of miRNAs from the database and the consensus sequence obtained. Oligonucleotides corresponding to these sequences were used as primers to amplify sequences from cDNAs of the conserved miRNAs