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 | – | |||||