Table 3.
List of reliable Vitis vinifera miRNAs from known miRNA precursors identified in Cabernet Sauvignon and Sangiovese derived small RNA libraries.
| Family | miRNA | Chra | Starta | Enda | Stranda | 5p Sequence | ntb | Abundance 5pc | 3p Sequence | ntb | Abundance 3pc |
|---|---|---|---|---|---|---|---|---|---|---|---|
| vvi−miR156 | vvi-miR156b | 4 | 5,357,061 | 5,357,310 | − | TGACAGAAGAGAGTGAGCAC | 20 | 10,561 | |||
| vvi-miR156c | 4 | 848,207 | 848,307 | − | TGACAGAAGAGAGTGAGCAC | 20 | 10,561 | ||||
| vvi-miR156d | 11 | 7,623,202 | 7,623,334 | − | TGACAGAAGAGAGTGAGCAC | 20 | 10,561 | TGCTCACCTCTCTTTCTGTCAGC | 23 | 1089 | |
| vvi-miR156e | 11 | 1,504,195 | 1,504,301 | − | TGACAGAGGAGAGTGAGCAC | 20 | 234 | ||||
| vvi-miR156f | 14 | 26,463,671 | 26,463,773 | + | TTGACAGAAGATAGAGAGCAC | 21 | 26,445 | ||||
| vvi-miR156g | 17 | 3,046,310 | 3,046,441 | − | TTGACAGAAGATAGAGAGCAC | 21 | 26,445 | GCTCTCTAGACTTCTGTCATC | 21 | 901 | |
| vvi-miR156i | 14 | 19,727,139 | 19,727,358 | − | TTGACAGAAGATAGAGAGCAC | 21 | 26,445 | ||||
| vvi-miR159 | vvi-miR159c | 17 | 2,609,190 | 2,609,409 | − | GAGCTCCTTGAAGTCCAATAG | 21 | 1644 | TTTGGATTGAAGGGAGCTCTA | 21 | 198,072 |
| vvi−miR162 | vvi-miR162 | 17 | 4,716,504 | 4,716,636 | + | GGATGCAGCGGTTCATCGATC | 21 | 365 | TCGATAAACCTCTGCATCCAG | 21 | 130,641 |
| vvi-miR164 | vvi-miR164a | 7 | 3,287,472 | 3,287,590 | − | TGGAGAAGCAGGGCACGTGCA | 21 | 198 | |||
| vvi-miR164c | 8 | 1,008,0445 | 10,080,636 | + | TGGAGAAGCAGGGCACGTGCA | 21 | 198 | CATGTGCCCCTCTTCCCCATC | 21 | 976 | |
| vvi-miR164d | 14 | 1,414,567 | 1,414,682 | − | TGGAGAAGCAGGGCACGTGCA | 21 | 198 | ||||
| vvi−miR166 | vvi-miR166a | 8 | 3,302,784 | 3,302,939 | − | AATGAGGTTTGATCCAAGATC | 21 | 1886 | TCTCGGACCAGGCTTCATTCC | 21 | 1,172,737 |
| vvi-miR166b | 12 | 17,937,384 | 17,937,510 | + | TCGGACCAGGCTTCATTCCTC | 21 | 10,941 | GGAATGTTGGCTGGCTCGAGG | 21 | 120,762 | |
| vvi-miR166c | 15 | 16,978,558 | 16,978,745 | − | GGAATGTTGTCTGGCTCGAGG | 21 | 54,367 | TCGGACCAGGCTTCATTCCCC | 21 | 17,706,997 | |
| vvi-miR166d | 16 | 21,405,202 | 21,405,388 | − | GATTGTTGTCTGGCTCGAGGC | 21 | 2661 | TCGGACCAGGCTTCATTCCCC | 21 | 17,706,997 | |
| vvi-miR166e | 2 | 2,255,708 | 2,255,901 | + | GGAATGTTGTCTGGCTCGAGG | 21 | 54,367 | TCGGACCAGGCTTCATTCCCC | 21 | 17,706,997 | |
| vvi-miR166f | 7 | 19,450,000 | 19,450,127 | + | GGAATGTTGGCTGGCTCGAGG | 21 | 10,941 | TCGGACCAGGCTTCATTCCCC | 21 | 17,706,997 | |
| vvi-miR166g | 7 | 453,844 | 453,971 | − | GGAATGTTGTCTGGTTCGAGA | 21 | 262 | TCGGACCAGGCTTCATTCCCC | 21 | 17,706,997 | |
| vvi-miR166h | 5 | 6,741,189 | 6,741,288 | − | TCGGACCAGGCTTCATTCCCC | 21 | 17,706,997 | ||||
| vvi-miR167 | vvi-miR167b | 14 | 7,137,373 | 7,137,501 | + | TGAAGCTGCCAGCATGATCT- | 21 | 1143 | AGATCATGTGGCAGTTTCACC | 21 | 536 |
| vvi-miR167d | 20 | 7,490,493 | 7,490,606 | + | TGAAGCTGCCAGCATGATCT- | 21 | 1143 | ||||
| vvi-miR167e | 5 | 5,845,370 | 5,845,489 | + | TGAAGCTGCCAGCATGATCT- | 21 | 1143 | AGATCATGTGGCAGTTTCACC | 21 | 536 | |
| vvi−miR168 | vvi-miR168 | 2 | 17,944,786 | 17,944,947 | − | TCGCTTGGTGCAGGTCGGGAA | 21 | 43,158 | CCCGCCTTGCATCAACTGAAT | 21 | 3558 |
| vvi-miR169c | 4 | 2,265,913 | 2,266,028 | − | CAGCCAAGGATGACTTGCCGG | 21 | 5 | ||||
| vvi-miR169 | vvi-miR169c.1 | 4 | 2,265,913 | 2,266,028 | − | TGTAGGGAGTAGAATGCAGC | 20 | 1921 | |||
| vvi-miR169e | 14 | 25,082,574 | 25,082,756 | − | TAGCCAAGGATGACTTGCCT– | 22 | 3136 | ||||
| vvi-miR169g | 8 | 21,104,448 | 21,104,568 | + | CAGCCAAGGATGACTTGCCGA | 21 | 13 | *CCGGCAAGTTGTCTTTGGCTAC | 23 | 151 | |
| vvi-miR169r | 11 | 16,415,128 | 16,415,239 | + | TGAGTCAAGGATGACTTGCCG | 21 | 11 | *GGCAAGTTGACTTGACTCAGT | 22 | 1181 | |
| vvi-miR169t | 11 | 16,399,564 | 16,399,676 | + | CGAGTCAAGGATGACTTGCCGA | 22 | 14 | *GGCAAGTTGACTTGACTCAGT | 22 | 1181 | |
| vvi−miR171 | vvi-miR171b | 12 | 5,542,396 | 5,542,529 | − | —TTGAGCCGCGTCAATATCTCC | 24 | 1068 | |||
| vvi-miR171i | 17 | 893,536 | 893,632 | + | TGATTGAGCCGTGCCAATATC | 21 | 811 | ||||
| vvi-miR172 | vvi-miR172d | 8 | 12,667,173 | 12,667,279 | + | TGAGAATCTTGATGATGCTGC– | 23 | 6451 | |||
| vvi−miR2111 | vvi-miR2111 | 8 | 15,368,664 | 15,368,748 | − | TAATCTGCATCCTGAGGTCTA | 21 | 1476 | GTCCTCTGGTTGCAGATTACT | 21 | 95 |
| vvi-miR2950 | vvi-miR2950 | 7 | 14,340,406 | 14,340,517 | + | TTCCATCTCTTGCACACTGGA | 21 | 3176 | TGGTGTGCACGGGATGGAATA | 21 | 581 |
| vvi−miR319 | vvi-miR319b | 1 | 4,189,556 | 4,189,753 | + | TTGGACTGAAGGGAGCTCCC- | 21 | 9157 | |||
| vvi-miR319c | 2 | 855,548 | 855,756 | − | AGAGCTTTCTTCAGTCCACTC | 21 | 131 | TTGGACTGAAGGGAGCTCCC- | 21 | 9157 | |
| vvi-miR319e | 11 | 4,317,223 | 4,317,329 | + | TTTGGACTGAAGGGAGCTCCT | 21 | 40,107 | ||||
| vvi-miR319f | 6 | 9,137,252 | 9,137,445 | + | TTGGACTGAAGGGAGCTCCC- | 21 | 9157 | ||||
| vvi-miR319g | 17 | 3,675,979 | 3,676,209 | − | TTGGACTGAAGGGAGCTCCC- | 21 | 9157 | ||||
| vvi-miR3623 | vvi-miR3623 | 18 | 24,650,004 | 24,650,151 | + | TCACAAGTTCATCCAAGCACCA | 22 | 108,278 | GTGCTTGGACGAATTTGCTAAG | 22 | 20,404 |
| vvi−miR3627 | vvi-miR3627 | 14 | 28,302,559 | 28,302,681 | − | TTGTCGCAGGAGAGACGGCACT | 22 | 2444 | TCGCCGCTCTCCTGTGACAAG | 21 | 12,342 |
| vvi-miR3629 | vvi-miR3629a | 13 | 18,253,987 | 18,254,170 | + | CGCATTTTCTCAGCAGCCAAG | 21 | 1 | TGGCTGCTGAGAAAATGTAGG- | 22 | 371 |
| vvi-miR3629c | 17 | 822,209 | 822,338 | + | TGGCTGCTGAGAAAATGTAGG- | 22 | 371 | ||||
| vvi−miR3632 | vvi-miR3632 | 14 | 23,394,889 | 23,395,015 | + | GGATTGGGGGCCGATGGAAAGG | 22 | 887 | TTTCCCAGACCCCCAATACCAA | 22 | 1578 |
| vvi-miR3633 | vvi-miR3633a | 17 | 5,521,913 | 5,522,060 | + | GGAATGGATGGTTAGGAGAG | 20 | 45,786 | TTCCTATACCACCCATTCCCTA | 22 | 1469 |
| vvi-miR3633b | 17 | 5,521,557 | 5,521,691 | + | GGAATGGGTGGCTGGGATCT | 20 | 10,270 | GTTCCCATGCCATCCATTCCTA | 22 | 5610 | |
| vvi−miR3634 | vvi-miR3634 | 17 | 5,681,202 | 5,681,314 | − | GGCATATGTGTGACGGAAAGA | 21 | 1563 | TTTCCGACTCGCACTCATGCCGT | 23 | 753,254 |
| vvi-miR3635 | vvi-miR3635 | 18 | 27,357,619 | 27,357,780 | + | GGCATGTGTGGGGCATAATAG | 21 | 289 | ATTATGTCCCACACATGCCTC | 21 | 399 |
| vvi−miR3636 | vvi-miR3636 | 16 | 5,414,817 | 5,414,967 | − | TCGGTTTGCTTCTTTGATAGATTC | 24 | 352 | — TGTCGGAGAAGCAAGTCGGAGAGT |
24 | 4495 |
| vvi-miR3640 | vvi-miR3640 | 16 | 11,986,842 | 11,987,014 | + | ACCTGATTGGTGATGCTTTTTTGG | 24 | 1321 | —- AAAGGCATCATCAATCAGGTAATG |
24 | 1203 |
| vvi−miR390 | vvi-miR390 | 6 | 8,159,519 | 8,159,657 | + | AAGCTCAGGAGGGATAGCGCC | 21 | 5046 | |||
| vvi-miR393 | vvi-miR393a | 16 | 17,247,172 | 17,247,327 | − | TCCAAAGGGATCGCATTGATC | 21 | 5152 | ATCATGCTATCCCTTAGGAAC | 21 | 775 |
| vvi-miR393b | 13 | 4,265,132 | 4,265,213 | + | TCCAAAGGGATCGCATTGATC | 21 | 5152 | ||||
| vvi−miR394 | vvi-miR394a | 12 | 17,122,005 | 17,122,092 | − | TTGGCATTCTGTCCACCTCC– | 22 | 412 | |||
| vvi-miR394b | 18 | 1,413,038 | 141,3130 | − | TTGGCATTCTGTCCACCTCC | 20 | 412 | ||||
| vvi-miR395 | vvi-miR395a | 1 | 6,527,921 | 6,528,019 | + | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |||
| vvi-miR395c | 1 | 6,499,899 | 6,500,020 | − | GTTCCCTTGACCACTTCACTG | 21 | 5850 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395d | 1 | 6,512,760 | 6,512,848 | + | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | ||||
| vvi-miR395e | 1 | 6,505,233 | 6,505,354 | + | GTTCCCTTGACCACTTCACTG | 21 | 5850 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395f | 1 | 6,489,527 | 6,489,642 | + | GTTCCCCTGACCACTTCACTG | 21 | 4729 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395h | 1 | 6,566,637 | 6,566,758 | + | GTTCCCTTGACCACTTCACTG | 21 | 5850 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395i | 1 | 6,562,627 | 6,562,742 | + | GTTCCCCTGACCACTTCACTG | 21 | 4729 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395j | 1 | 6,553,011 | 6,553,126 | + | GTTCCCCTGACCACTTCACTG | 21 | 4729 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395k | 1 | 6,536,764 | 6,536,885 | + | GTTCCCTTGACCACTTCACTG | 21 | 5850 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi-miR395l | 1 | 6,559,083 | 6,559,199 | + | GTTCCCCTGACCACTTCACTG | 21 | 4729 | CTGAAGTGTTTGGGGGAACTC | 21 | 6899 | |
| vvi−miR396 | vvi-miR396a | 9 | 7,372,499 | 7,372,649 | − | TTCCACAGCTTTCTTGAACTA | 21 | 15,069 | AAGAAAGCTGTGGGAGGACATGGC | 24 | 2147 |
| vvi-miR396b | 11 | 5,246,778 | 5,246,913 | + | TTCCACAGCTTTCTTGAACTT | 21 | 85,683 | GTTCAAGAAAGCTGTGGGAAA | 21 | 6917 | |
| vvi-miR396c | 4 | 5,119,592 | 5,119,698 | − | TTCCACAGCTTTCTTGAACTG | 21 | 3900 | ||||
| vvi-miR396d | 11 | 5,253,095 | 5,253,244 | − | TTCCACAGCTTTCTTGAACT- | 21 | 7387 | GTTCAATAAAGCTGTGGGAAG | 21 | 1899 | |
| vvi-miR397 | vvi-miR397a | 20 | 11,971,890 | 11,972,015 | − | TCATTGAGTGCAGCGTTGATG | 21 | 432 | |||
| vvi−miR398 | vvi-miR398b | 6 | 16,503,544 | 16,503,633 | − | TGTGTTCTCAGGTCGCCCCTG | 21 | 16,121 | |||
| vvi-miR398c | 6 | 15,575,579 | 15,575,668 | + | TGTGTTCTCAGGTCGCCCCTG | 21 | 16,121 | ||||
| vvi-miR399 | vvi-miR399a | 10 | 2,989,435 | 2,989,561 | + | GTGTGATTCTCCTTTGGCAGA | 21 | 503 | TGCCAAAGGAGAATTGCCCTG | 21 | 1289 |
| vvi-miR399b | 16 | 15,618,708 | 15,618,845 | − | TGCCAAAGGAGAGTTGCCCTG | 21 | 2996 | ||||
| vvi-miR399c | 15 | 15,232,197 | 15,232,281 | + | TGCCAAAGGAGAGTTGCCCTG | 21 | 2996 | ||||
| vvi-miR399e | 10 | 2,992,220 | 2,992,341 | − | TGCCAAAGGAGATTTGCCCGG | 21 | 184 | ||||
| vvi-miR399h | 10 | 2,983,543 | 2,983,634 | + | TGCCAAAGGAGAATTGCCCTG | 21 | 1289 | ||||
| vvi-miR399i | 2 | 4,101,786 | 4,101,937 | + | GGGCTTCTCTCCTTCTGGCAGG | 22 | 148 | CGCCAAAGGAGAGTTGCCCTG | 21 | 113,055 | |
| vvi−miR403 | vvi-miR403a | 5 | 65,247 | 65,361 | + | TTAGATTCACGCACAAACTCG | 21 | 82,567 | |||
| vvi-miR403b | 5 | 600,176 | 600,266 | + | TTAGATTCACGCACAAACTCG | 21 | 82,567 | ||||
| vvi-miR403d | 5 | 166,467 | 166,582 | + | AGTTTGTGCGCGAATCCAACC | 21 | 201 | TTAGATTCACGCACAAACTCG | 21 | 82,567 | |
| vvi-miR403e | 5 | 168,096 | 168,213 | + | TTAGATTCACGCACAAACTCG | 21 | 82,567 | ||||
| vvi-miR403f | 7 | 4,179,658 | 4,179,795 | − | AGTTTGTGCGTGACTCTAAAA | 21 | 523 | TTAGATTCACGCACAAACTCG | 21 | 82,567 | |
| vvi-miR408 | vvi-miR408 | 7 | 5,011,920 | 5,012,056 | + | CGGGGACGAGGTAGTGCATGG | 21 | 3223 | ATGCACTGCCTCTTCCCTGGC | 21 | 6566 |
| vvi−miR477 | vvi-miR477b | 2 | 1,237,529 | 1,237,808 | + | ACTCTCCCTCAAGGGCTTCT-G | 22 | 513 | CGAAGTCTTTGGGGAGAGTGG | 21 | 3289 |
| vvi-miR479 | vvi-miR479 | 16 | 21,573,744 | 21,573,866 | + | TGTGGTATTGGTTCGGCTCATC | 22 | 4449 | CGAGCCGAACCAATATCACTC | 21 | 46,073 |
| vvi−miR482 | vvi-miR482 | 17 | 5,523,009 | 5,523,155 | + | *AATTGGAGAGTAGGAAAGCTT | 22 | 139,166 | TCTTTCCTACTCCTCCCATTCC | 22 | 42,801 |
| vvi-miR535 | vvi-miR535a | 25 | 1,392,255 | 1,392,353 | − | TGACAACGAGAGAGAGCACGC | 21 | 18,893 | |||
| vvi-miR535c | 25 | 1,346,353 | 1,346,483 | − | TGACAACGAGAGAGAGCACGC | 21 | 18,893 | GTGCTCTCTGTCGCTGTCATA | 21 | 2191 |
a
Refers to the genomic localization on the GRAPE_IGGP12Xv1 genome sequence.
b
Nucleotide, sequence length of the microRNA.
c
Sum of TP4M values from 48 libraries.
−Missing nucleotide.
Nucleotides that differ from the annotated sequence are shown in red.
*
Indicates that the most abundant sequence in our dataset does not correspond to the mature annotated miRNA, but to the star sequence.