Supplemental Table S2: Known conserved miRNAs identified in the Gossypium hirsutum uninfected (UIL) and CLRDV-infected (IL) libraries, their potential targets and their evolutionary relationships.

Ghr-miRNA family / Sequence 5`to 3' / Size / Reads / Reads / Targeted genes or ESTsa / Targeted proteinb / Conserved
UIL / IL / Ghrc / Ath / Pth / Vvi / Osa / Ppt
Ghr-miR156a / UGACAGAAGAGAGUGAGCAC / 20 / - / 51.10 / CO092899
TC246550
DR462234 / Squamosa-promoter binding protein*C,D,E / 14 / 14 / 11 / 9 / 18 / 3
Ghr-miR156a / UUGACAGAAGAGAGUGAGCAC / 21 / 37.97 / 110.72 / TC239557 / Squamosa-promoter binding protein*C,D,E
Ghr-miR157a / UGACAGAAGAUAGAGAGCAC / 20 / 8.43 / 6.62 / CO092899 / Unknown / 2 / 5 / *** / - / - / -
Ghr-miR157b / UUGACAGAAGAUAGAGAGCAC / 21 / 67.50 / 690.87 / TC239557 / Squamosa-promoter binding protein*B,C,D,E
Ghr-miR159b / UUGGAUUGAAGGGAGCUCUA / 20 / 5788.47 / 1932.54 / TC279858 / Unknown / 5 / 3 / 6 / 3 / 7 / -
Ghr-miR159a / UUUGGAUUGAAGGGAGCUCUA / 21 / 798534.62 / 109335.57 / TC279858 / ATP synthase F0*C
Ghr-miR159a / UUUGGAUUGAAUGGGAGCUCUA / 22 / 2.10 / - / TC276768
ES828901 / Glutathione reductase
Tubulin beta
Ghr-miR160a / GCCUGGCUCCCUGUAUGCCA / 20 / 23.20 / 23.65 / TC268754 / Auxin response factor*B,C,D,E / 3 / 3 / 8 / 6 / 8 / 9
Ghr-miR160a / UGCCUGGCUCCCUGUAUGCCA / 21 / 978.80 / 893.39 / TC246307 / Auxin response factor*B,C,D,E
Ghr-miR162a / CGAUAAACCUCUGCAUCCAG / 20 / - / 16.08 / TC245007
TC236055 / Alcohol dehydrogenase*E / 2 / 2 / 3 / 1 / 3 / -
Ghr-miR162a / UCGAUAAACCUCUGCAUCCAG / 21 / 374.43 / 500.64 / TC237985; TC267453 / LETM1-like protein; Auxin transport protein
Ghr-miR164a / GGAGAAGCAGGGCACGUGCA / 20 / 15.82 / 0.94 / CO109521 / NAC domain transcription factor*C,D,E / 5 / 3 / 6 / 4 / 6 / -
Ghr-miR164a / UGGAGAAGCAGGGCACGUGCA / 21 / 50.62 / 125.87 / CO109521 / NAC domain transcription factor*C,D,E
Ghr-miR165a / UCGGACCAGGCUUCUUCCCC / 20 / 1.05 / - / TC255842 / Alpha-glucosidase / 1 / 2 / *** / 1 / - / -
Ghr-miR165b / UCGGACCAGGCUUCAUCCCC / 20 / - / 2.83 / TC267202
TC267202 / HD-ZIP transcription factor*C,D,E
Ghr-miR165a / UCGGACCAGGCUUCAUCCCCC / 21 / 23.20 / 16.08 / TC267202 / HD-ZIP transcription factor*C,D,E
Ghr-miR166a / CGGACCAGGCUUCAUUCCCC / 20 / 87.54 / 221.45 / ES808067 / HD-ZIP transcription factor*B,C,D,E / 12 / 7 / 17 / 8 / 14 / 13
Ghr-miR166b / CGGACCAGGCUUCAUUCCCG / 20 / 109.69 / 113.56 / ES808067
ES810681 / HD-ZIP transcription factor*B,C,D,E
Ghr-miR166h / UCGGACCAGGCUUCAUUCCCG / 21 / 10751.07 / 18055.38 / ES808067 / HD-ZIP transcription factor*B,C,D,E
Ghr-miR166e / UCGGACCAGGCUUCAUUCCCCU / 22 / 42.19 / 28.39 / ES808067
ES810681 / HD-ZIP transcription factor*B,C,D,E
Ghr-miR167b / GAUCAUGUGGCAGUUUCACC / 20 / 305.87 / 50.15 / TC251916
ES804906
EE592949 / Unknown / 8 / 5 / 8 / 5 / 13 / 1
Ghr-miR167c / UGAAGCUGCCAGCAUGAUCUC / 21 / 24.25 / 304.74 / DW226555 / LIM domain protein
Ghr-miR167g / GAAGCUGCCAGCAUGAUCUGG / 21 / 974.58 / 207.26 / ES834701
TC243185 / Auxin response factor*C,D
Ghr-miR167b / UGAAGCUGCCAGCAUGAUCUGG / 22 / 746.76 / 2682.09 / AW730640 / Unknown
Ghr-miR168c / CGCUUGGUGCAGGUCGGGAA / 20 / 3.16 / 6.62 / TC241943 / Unknown / 4 / 3 / 2 / 1 / 5 / -
Ghr-miR168b / UCGCUUGGUGCAGGUCGGGAA / 21 / 122.35 / 105.99 / CO084924 / Argonaute 1*C,D
Ghr-miR169a / UAGCCAAGAAUGACUUGCCU / 20 / - / 22.71 / TC233472 / Nuclear transcription factor Y*A,D / 14 / 15 / 32 / 25 / 17 / -
Ghr-miR169a / CAGCCAAGGAUGACUUGCCGG / 21 / 45.35 / 10.41 / TC269356 / Nuclear transcription factor Y*A,D
Ghr-miR169j / UAGCCAAGGAUGACUUGCCUG / 21 / 2.10 / 17.03 / TC233472 / Nuclear transcription factor Y*A,D
Ghr-miR169d / UAGCCAAGGAUGACUUGCCUGC / 22 / 14.76 / 9.46 / TC233472 / Nuclear transcription factor Y*A,D
Ghr-miR170 / UGAUUGAGCCGUGUCAAUAUC / 21 / - / 4.73 / TC270345 / Scarecrow-like protein*C / 1 / 3 / - / - / 2 / -
Ghr-miR171a / GAUUGAGCCGUGCCAAUAUC / 20 / 16.87 / 2.83 / TC270345
ES822760 / Scarecrow-like protein*C / 8 / 6 / 14 / 9 / 11 / 2
Ghr-miR171b / UGAUUGAGCCGUGCCAAUAUC / 21 / 139.22 / 3510.19 / TC270345
ES822760 / Scarecrow-like protein*C
Ghr-miR171c / UGAUUGAGCCGUGCCAAUAUCA / 22 / - / 1.89 / TC270345
ES822760 / Scarecrow-like protein*C
Ghr-miR172c / GAAUCUUGAUGAUGCUGCAU / 20 / 18.98 / 8.51 / TC251161
TC267470 / APETALA-2 transcription factor*D,E / 7 / 7 / 9 / 4 / 8 / -
Ghr-miR172d / CUUGAUGAUGCUGCAUCGGC / 20 / 4.21 / 11.35 / TC249346
TC275039 / APETALA-2 transcription factor*D,E
Ghr-miR172f / UCUUGAUGAUGCUGCAUCGGC / 21 / 93.87 / 724.94 / TC249346 / APETALA-2 transcription factor*D,E
Ghr-miR172a / AUCUUGAUGAUGCUGCAUCGGC / 22 / - / 3.78 / TC249346
TC275039
TC259821 / APETALA-2 transcription factor*D,E
Ghr-miR319b / UUGGACUGAAGGGAGCUCCC / 20 / 1005.17 / 13.24 / TC237076 / Unknown / 4 / 3 / 9 / 5 / 2 / 7
Ghr-miR319a / UUGGACUGAAGGGAGCUCCCU / 21 / 692.97 / 28.39 / DR452774 / SPIa/RYanodine receptor (SPRY)
Ghr-miR390a / AGCUCAGGAGGGAUAGCGCC / 20 / 23.20 / 29.33 / TC242082
TC275010 / Unknown*C / 5 / 2 / 4 / 1 / 1 / 4
Ghr-miR390a / AAGCUCAGGAGGGAUAGCGCC / 21 / 178.25 / 177.92 / TC242082
TC275010 / Unknown*C
Ghr-miR391b / UUCGCAGGAGAGAUAGCGCC / 20 / - / 0.94 / ES833985 / Unknown*A / 1 / 1 / - / - / - / -
Ghr-miR393 / CCAAAGGGAUCGCAUUGAUC / 20 / 1.05 / 0.94 / TC260618 / Auxin signaling F-box*C,D,E,F / 6 / 2 / 4 / 2 / 3 / -
Ghr-miR393c / UCCAAAGGGAUCGCAUUGAUC / 21 / 49.57 / 17.98 / TC242082 TC275010 / Auxin signaling F-box*C,D,E,F
Ghr-miR393a / UCCAAAGGGAUCGCAUUGAUCC / 22 / 21.09 / 139.12 / TC260618
TC276922
TC272798 / Auxin signaling F-box*C,D,E,F
Ghr-miR394a / UUGGCAUUCUGUCCACCUCC / 20 / 31.64 / 157.10 / TC260238 / F-box / 1 / 2 / 2 / 3 / 1 / -
Ghr-miR395a / UGAAGUGUUUGGGGGAACUC / 20 / 99.14 / 10.41 / TC245081
TC235159
TC276235 / ATP sulfurases (APS)*A,C,D / 5 / 6 / 10 / 14 / 24 / 1
Ghr-miR395a / CUGAAGUGUUUGGGGGAACUC / 21 / 6757.78 / 1059.96 / TC238357 / ATP sulfurases (APS) *A,C,D
Ghr-miR395 / CUGAAGUGUUUUGGGGGAACUC / 22 / 1.05 / - / TC266217 / 40S ribosomal protein
Ghr-miR396a / UCCACAGCUUUCUUGAACUU / 20 / 4.21 / 2.83 / TC271568 / Chromatin remodeling complex / 9 / 2 / 7 / 4 / 13 / -
Ghr-miR396b / UUCCACAGCUUUCUUGAACUG / 21 / 117.07 / 184.54 / TC271568 / Chromatin remodeling complex
Ghr-miR396c / UUCCACAGCUUUCUUGAACUU / 21 / 111.80 / 235.65 / TC271568 / Chromatin remodeling complex
Ghr-miR396 / UUCCACAGCUUUCUUGAACUGU / 22 / - / 1.89 / TC271568 / Chromatin remodeling complex
Ghr-miR396 / AAGAAAGCUGUGGGAGAAGAUGGC / 24 / - / 0.94 / TC271568 / Chromatin remodeling complex
Ghr-miR397a / UUGAGUGCAGCGUUGAUGAA / 20 / 9.49 / 1.89 / DW241123
TC233218
DW224951 / Laccase / 5 / 2 / 3 / 2 / 4 / -
Ghr-miR397c / AUUGAGUGCAGCGUUGAUGA / 20 / 1.05 / 6.62 / TC256899
TC279559
TC267962 / Laccase/copper ion binding proteins*C,D,E
Ghr-miR397b / UCAUUGAGUGCAGCGUUGAUG / 21 / 203.56 / 969.11 / TC256899 / Laccase/copper ion binding proteins*C,D,E
Ghr-miR398a / GUGUUCUCAGGUCGCCCCUG / 20 / 2.10 / 4.73 / TC240242
CO094618 / Unknown / 2 / 3 / 3 / 3 / 2 / -
Ghr-miR398a / UGUGUUCUCAGGUCGCCCCUG / 21 / 30.58 / 268.77 / TC240242
CO094618 / Unknown
Ghr-miR399a / GCCAAAGGAGAGUUGCCCUG / 20 / 5.27 / - / TC270765
DW479470 / S-acyltransferase
Inorganic phosphate transporter / 14 / 6 / 12 / 9 / 11 / -
Ghr-miR399c / GCCAAAGGAGAUUUGCCCCG / 20 / - / 2.83 / TC239324 / MYB transcription factor*D,E
Ghr-miR399f / UGCCAAAGGAGAUUUGCCCGG / 21 / 95.98 / 42.58 / TC236756 / MYB transcription factor*D,E
Ghr-miR403a / UAGAUUCACGCACAAACUCG / 20 / 1.05 / 34.07 / TC249834 / Argonaute protein / 2 / 1 / 3 / 6 / - / -
Ghr-miR403b / UUAGAUUCACGCACAAACUCG / 21 / 85.43 / 295.27 / TC249834 / Argonaute protein
Ghr-miR408a / UGCACUGCCUCUUCCCUGGC / 20 / 6.32 / 2.83 / TC247338
TC244871 / Copper binding protein 3*C,D,E / 4 / 1 / 1 / 1 / 1 / 2
Ghr-miR408c / AUGCACUGCCUCUUCCCUGGC / 21 / 105.47 / 246.06 / TC246381 / Plastocyanin-like domain
Ghr-miR414 / GGACGAGGAUGAUGACGAUG / 20 / 1.05 / - / DV437895 / CCCH-type zinc finger / 8 / 1 / - / - / 1 / 1
Ghr-miR472 / UUGCCUACUCCACCCAUGCC / 20 / 1.05 / 0.94 / NP673173 / NBS-type resistance protein*D,E / 1 / 1 / 2 / - / - / -
Ghr-miR472a / UCUUGCCUACUCCACCCAUGC / 21 / 8.43 / 21.76 / NP673173 / NBS-type resistance protein*D,E
Ghr-miR472a / UCUUGCCUACUCCACCCAUGCC / 22 / 186.69 / 773.20 / NP673173 / NBS-type resistance protein*D,E
Ghr-miR479a / CGAGCCGAAUCAAUAUCACUC / 21 / - / 28.39 / TC232119 / GRAS family transcription factor / 1 / - / 1 / 1 / - / -
Ghr-miR479a / CGUGAUAUUGGUUCGGCUCAUC / 22 / 6.32 / 34.07 / TC232019
DN780454 / Plastid-lipid-associated
Scarecrow-like
Ghr-miR482a / UCUUUCCAAUUCCUCCCAUU / 20 / - / 1.89 / ES794432 / Actin / 6 / - / 2 / 1 / - / -
Ghr-miR482a / UCUUUCCAAUUCCUCCCAUUC / 21 / 1.05 / 4.73 / ES794432 / Actin
Ghr-miR482a / UCUUUCCUACUCCUCCCAUUCC / 22 / 123.40 / 762.79 / TC276311
NP831319 / NBS-type resistance protein*E
Ghr-miR535a / GACAAUGAGAGAGAGCACGC / 20 / 238.37 / 6.62 / CO118493 / Presenilin-1 / 1 / - / - / 5 / 1 / 4
Ghr-miR535b / UGACAAUGAGAGAGAGCACGC / 21 / 372.32 / 242.27 / CO118493 / Presenilin-1
Ghr-miR535 / UGACAAUGAGAGAGAGCACGCU / 22 / - / 0.94 / CO118493 / Presenilin-1
Ghr-miR779 / GAUUGGAAAUUUCGUUGACU / 20 / 1.05 / - / DR454462
FG551714 / NSFL1 cofactor p47 / 1 / 1 / - / - / - / -
Ghr-miR827b / UUAGAUGACCAUCAACAAACA / 21 / 3.16 / 17.98 / CO088990; TC250696 / Unknown*E / 4 / 1 / 1 / - / 3 / -
Ghr-miR828a / UCUUGCUCAAAUGAGUAUUCC / 21 / - / 0.94 / TC235742 / MYB transcription factor*E / 1 / 1 / 1 / 2 / - / -
Ghr-miR828a / UCUUGCUCAAAUGAGUAUUCCA / 22 / 2.10 / 37.85 / TC235742 / MYB transcription factor*E
Ghr-miR845b / CGGCUCUGAUACCAAUUGAUG / 21 / - / 1.89 / DT464811 / Growth-regulating factor 1 / 2 / 2 / - / 5 / - / -
Ghr-miR894a / CGUUUCACGUCGGGUUCACC / 20 / 5.27 / 1.89 / TC268166
TC263658
TC253043 / Nuclear pore complex / 2 / - / - / - / - / 1
Ghr-miR2947a*1 / UACCGUGCCCAUGACUGUAG / 20 / 143.44 / 42.58 / CO105636 / Unknown / - / - / - / - / - / -
Ghr-miR2947a*1 / AUACCGUGCCCAUGACUGUAG / 21 / 637.06 / 252.68 / CO105636 / Unknown
Ghr-miR2947a*1 / UAUACCGUGCCCAUGACUGUAG / 22 / 23914.35 / 7386.63 / CO105636 / Unknown
Ghr-miR2948a / UGUGGGAGAGUUGGGCAAGA / 20 / 2.10 / 5.67 / EV497230
TC231731
TC233607 / Cytochrome P450 / 1 / - / - / - / - / -
Ghr-miR2948a / UGUGGGAGAGUUGGGCAAGAA / 21 / 8.43 / 12.30 / TC231731 / Cytochrome P450
Ghr-miR2948a / UGUGGGAGAGUUGGGCAAGAAU / 22 / 266.85 / 477.93 / EV497230
TC231731 / Cytochrome P450
Ghr-miR2949a / UUUUGAACUGGAUUUGCCGA / 20 / 2.10 / 1.89 / TC244560
TC273521 / Unknown / 4 / - / - / - / - / -
Ghr-miR2949b / ACUUUUGAACUGGAUUUGCC / 20 / - / 3.78 / TC244560
TC273521 / Unknown
Ghr-miR2949b / CUUUUGAACUGGAUUUGCCGA / 21 / 33.75 / 10.41 / TC244560
TC273521 / Unknown
Ghr-miR2949c / ACUUUUGAACUGGAUUUGCCG / 21 / 26.36 / 71.92 / TC244560
TC273521 / Unknown
Ghr-miR2949a / ACUUUUGAACUGGAUUUGCCGA / 22 / 3394.18 / 4329.77 / TC244560
TC273521 / Unknown
Ghr-miR2950 / UGGUGUGCAGGGGGUGGAAUA / 21 / 6.32 / - / TC242859 / Subtilisin-like protease / 1 / - / - / - / - / -
Ghr-miR3476a / GAACUGGGUUUGUUGGCUGC / 20 / 4033.36 / 394.64 / AW729461 / Unknown / 1 / - / - / - / - / -
Ghr-miR3476a / UGAACUGGGUUUGUUGGCUGC / 21 / 71625.98 / 21039.38 / TC276560; TC238923 / Unknown
Ghr-miR3476 / UGAACUGGGUUUUGUUGGCUGC / 22 / 7.38 / 0.94 / CO084248
C249639 / Unknown

Note: Only the 5’ to 3’ sequences of the most representative mature miRNAs are represented for each family. The number of reads is expressed as reads per 10 million. aG. hirsutum putative target genes or ESTs identified using psRNATarget CGI Release 11 showing scores ≤ 3 as calculated according to [3]. b BlastN at NCBI with E-values ≤ 10-4. C The numbers of isoforms identified in the plant microRNA database (PMRD) and additional miRNAs identified in Zhang et al. (2007); Barozai et al. (2008); Kwak et al. (2009); Pang et al. (2009); Ruan et al. (2009). *1 Ghr-miR2947 was identified against Gossypium arboreum. “-” means no information available. “***” means articles did not discriminate miR156 from miR157 and miR165 from miR166. *A, *B, *C, *D, *E and *F indicate similar target proteins as references [Zhang et al. (2007); Barozai et al. (2008); Ruan et al. (2009); Kwak et al. (2009); Pang et al. (2009) and Qiu et al. (2007) respectively. Abbreviations: Ghr (Gossypium hirsutum), Ath (Arabidopsis thaliana), Ptc (Populus trichocarpa), Vvi (Vitis vinifera), Osa (Orysa sativa), and Ppt (Physcomitrella patens). Query 4. Abdurakhmonov et al (2008): BMC Plant Biol. 8:93 (all of these papers are on line only). Amin et al. (2011): Virology J. 8:143. Artico et al. (2010): BMC Plant Biol. 10:49. Bazzini et al. (2009): BMC Plant Biol. 9:152. Fahlgren et al. (2007):PLoS One 14;2(2):e219. Boyko et al. (2010): PLoS One 3;5(3):e9514. Buhtz et al. (2010): BMC Plant Biol. 10:64. Cho et al. (2008):PLoS Genet. 4(12):e1000314. Hu et al. (2011): PLoS One 6(5):e19549. Jay et al. (2010): the correct is 2011: PLoS Pathog. 7(5):e1002035. Klevebring et al. (2009): BMC Genomics 20;10:620. Kwak et al. (2009): BMC Genomics 29;10:457. Naqvi et al. (2010): Virol J. 7:281. Pang et al. (2009): Genome Biol. 10(11):R122. Silva et al. (2008): Virol J. 5:123; (2011): BMC Mol Biol 12:40. Szittya et al. (2008): BMC Genomics 9:593. Todesco et al. (2010): PLoS Genet. 6(7):e1001031. Varkonyi-Gasic and Hellens (2010): Methods Mol Biol. 631:109-122. Zhang et al. (2009): BMC Genomics 10:449.