Table 1.
– Normalized reads for potentially novel miRNAs and isoforms with variations in the sequence length of known miRNA/miRNA* detected by miRCat tool, in sRNA datasets of Col pollen and sperm cells (SC) in comparison with inflorescence tissue (Inf)
| microRNA | Sequence | SC | Pollen | Inf | psRNA target(s) |
| Variations of known miRNA/miRNA*(a) | |||||
| miR156h | UUGACAGAAGAAAGAGAGCAC | 107 | 24 | 162 | SQUAMOSA PROMOTER BINDING PROTEIN-LIKE |
| miR158b | UCCCCAAAUGUAGACAAAGCA | 248 | 1099 | 12 | AT2G46590 |
| miR161a.1 | UUGAAAGUGACUACAUCGGGGu | 5605 | 7146 | 2066 | PPR (AT5G41170) |
| miR162 | AUCGAUAAACCUCUGCAUCCAGg | 4 | 58 | 1 | DICER-LIKE 1 (AT1G01040) |
| miR165* | gGAAUGUUGUCUGGAUCGAGGA | 46 | 102 | 9 | - |
| miR167c | uUAAGCUGCCAGCAUGAUCUUGU | 10 | 0 | 2 | - |
| miR408* | ACAGGGAACAAGCAGAGCATGG | 589 | 29 | 12 | AT2G47020, AT4G02940, AT1G04210, AT1G17180, AT4G03950 |
| miR773a | TTTGCTTCCAGCTTTTGTCTCC | 82 | 524 | 22 | MET2 (AT4G14140), AT4G05390, AT4G08990 |
| miR778* | ACAAACUCGGUGUACAUAGACcaaaccaag | 116 | 316 | 2 | AT5G22380, AT1G69610 |
| miR840* | UUGUUUAGGUCCCUUAGUUUCu | 21 | 27 | 9 | - |
| miR844a | AAUGGUAAGAUUGCUUAUAAGcu | 11 | 22 | 11 | AT2G13720, AT5G44120 |
| miR852 | AAGAUAAGCGCCUUAGUUCUGA | 42 | 63 | 15 | AT5G56650, AT5G56660 |
| miR852a | AAGAUAAGCGCCUUAGUUCUGA | 32 | 107 | 7 | - |
| miR860 | ucaAUAGAUUGGACUAUGUAUAUU | 17 | 9 | 10 | AT5G26030, AT3G12640 |
| miR863a | uugAGAGCAACAAGACAUAAUAAAGAG | 2 | 11 | 0 | - |
| miR870 | AAUCUAAUUUGGUGUUUCUUCGaug | 2 | 13 | 1 | AT3G55370 |
| Potentially novel miRNAs (b) | |||||
| miR2934(c) | CAUCCAAGGUGUUUGUAGAAA† | 101 | 392 | 6 | - |
| miR4240.2(d) | AUGGCUAGAGUGACUAGACCCG | 23 | 0 | 10 | - |
| miR447a.2 | UAUGGAAGAAAUUGUAGUAUU | 84 | 42 | 152 | AT1G42630, AT1G54710 |
| miR447c.2 | CCCCUUACAAUGUCGAGUAAA | 0 | 13 | 3 | - |
| miR868.2 | UCAUGUCGUAAUAGUAGUCAC | 32 | 92 | 5 | CMT1 (AT1G80740), CMT2 (AT4G19020) |
| miR5012 | UUUUACUGCUACUUGUGUUCC | 6 | 0 | 3 | AT1G53700, AT2G37678 |
| miR5013 | UUUGUGACAUCUAGGUGCUUU | 86 | 317 | 1 | AT3G60580 |
| miR5014 | UUGUACAAAUUUAAGUGUACG | 15 | 4 | 9 | - |
| miR5015.1 | UUGGUGUUAUGUGUAGUCUUC | 17 | 20 | 0 | - |
| miR5015.2 | UCUGUUGUUGUUGGUGUUAUG | 17 | 38 | 2 | AT2G38320, AT1G12860, AT2G01760, AT5G38740 |
| miR5016 | UUCUUGUGGAUUCCUUGGAAA | 2 | 5 | 0 | - |
| miR5017 | UUAUACCAAAUUAAUAGCAAA | 4 | 5 | 67 | - |
| miR5018 | UUAAAGCUCCACCAUGAGUCCAAU | 0 | 5 | 0 | - |
| miR5019 | UGUUGGGAAAGAAAAACUCUU | 6 | 40 | 2 | AT3G58810, AT1G14510, AT4G19550 |
| miR5020a | UGGAAGAAGGUGAGACUUGCA | 15 | 53 | 0 | - |
| miR5020b | AUGGCAUGAAAGAAGGUGAGA | 158 | 711 | 1 | - |
| miR5021 | UGAGAAGAAGAAGAAGAAAA | 0 | 7 | 0 | - |
| miR5022 | GUCAUGGGGUAUGAUCGAAUG† | 17 | 56 | 0 | - |
| miR5023 | AUUGGUAGUGGAUAAGGGGGC† | 0 | 18 | 0 | AT5G24950 |
| miR5024 | AUGACAAGGCCAAGAUAUAACA | 4 | 7 | 0 | - |
| miR5025 | ACUGUAUAUAUGUAAGUGACA | 4 | 9 | 0 | AT2G48010 |
| miR5026 | ACUCAUAAGAUCGUGACACGU | 10 | 16 | 2 | - |
| miR5027 | ACCGGUUGGAACUUGCCUUAA | 10 | 27 | 3 | - |
| miR5028 | AAUUGGGUUUAUGCUAGAGUU | 92 | 443 | 8 | - |
| miR5029 | AAUGAGAGAGAACACUGCAAA† | 84 | 288 | 1 | AT2G30070, AT4G02900 |
Underlined sequences indicate the mature form annotated in ASRP(a), including missing nucleotides (lower case). These variations were preferentially detected by miRCat since they are more abundant than the annotated isoforms of known miRNAs.
(a) – Annotation as in ASRP: The Arabidopsis Small RNA Project Database (http://asrp.cgrb.oregonstate.edu/).
(b) – No correspondence found in ASRP database. Predicted foldback structures and chromosome loci presented in Table S2.
(c) – Potentially mature miRNA sequence processed from ath-MIR2934, more abundant in our SC and pollen datasets than ath-miR2934 UCUUUCUGCAAACGCCUUGGA reported in Grant-Downton et al. (2009b), but classified in our study as ath-miR2934* (Table S1).
(d) – Processed from ath-MIR4240 (Ma et al., 2010), shifted 10nt from ath-miR4240 that was not detected in our SC and pollen datasets.
† Correspondent miRNA* sequence also detected in the sRNA dataset.