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Table 2 The abundantly expressed Southern rice black-streaked dwarf virus-derived siRNAs and their predicted targets confirmed by RT-qPCR

From: Characteristics of siRNAs derived from Southern rice black-streaked dwarf virus in infected rice and their potential role in host gene regulation

vsiRNA No.a)

ID of predicted

target gene

Expectation

score b)

Target Accessibility

(UPE) b)

Alignment

Inhibition manner

Putative function of rice target gene

vsiRS1_1

LOC_Os08g29710.1

3.0

14.152

miRNA 20 GCGUCUCACAUAGAGCUAAU 1

.::::: :::::::.::::

Target 1652 UGCAGAUUGUAUCUUGAUUU 1671

Cleavage

galactosyltransferase family protein

 

LOC_Os06g39650.1

3.0

19.7

miRNA 20 GCGUCUCACAUAGAGCUAAU 1

.::::.::::: ::.::::.

Target 1557 UGCAGGGUGUAGCUUGAUUG 1576

Translation

pentatricopeptide

vsiRS2_1

LOC_Os02g07310.1

2.5

20.512

miRNA 21 UCACAAUAGUAUAAGAUACCU 1

.:: :::::::.::::.:::.

Target 2336 GGUAUUAUCAUGUUCUGUGGG 2356

Cleavage

AGO17

vsiRS3_1

LOC_Os09g25330.1

3.0

7.741

miRNA 22 CUAAGAAGUUAA-GACGCAGAUU 1

: :::::.:::: ::::::.:::

Target 158 GUUUCUUUAAUUGCUGCGUUUAA 180

Translation

Bric-a-Brac, Tramtrack, Broad Complex BTB domain with non-phototropic hypocotyl 3 NPH3 domain, BTBN19

vsiRS4_2

LOC_Os01g63710.2

3.0

11.886

miRNA 20 UGUCAAACGUAACAGAGCAU 1

:::::::::::::: :: ::

Target 1668 ACAGUUUGCAUUGUAUCUUA 1687

Cleavage

Putative DNA replication initiation protein, CDC6

 

LOC_Os03g51270.1

3.0

14.253

miRNA 20 UGUCAAACGUAACAGAGCAU 1

:::: :: :::: :::::::

Target 1029 ACAGCUUACAUUUUCUCGUA 1048

Cleavage

F-box domain containing protein, OsFBX108

vsiRS5_1

LOC_Os03g36790.2

3.0

21.375

miRNA 20 GUCUUAACUCAGUGCUCACA 1

::::::: :::..::::::

Target 204 CAGAAUUCAGUUGCGAGUGC 223

Cleavage

tobamovirus multiplication protein

vsiRS5_3

LOC_Os07g35750.1

2.5

18.456

miRNA 20 CACAACAGACGAACAAGCAC 1

::::::: ::::::::.:::

Target 3702 GUGUUGU-UGCUUGUUUGUG 3720

Cleavage

DUF26 kinases homologous to DUF26 containing loci,

TKL_IRAK_DUF26-ld.3

vsiRS6_1

LOC_Os07g36280.1

2.5

16.42

miRNA 22 UUGCUAGUGA-AACAAGAGAGUU 1

:: ::::::: :::::.::::::

Target 1053 AAAGAUCACUGUUGUUUUCUCAA 1075

Cleavage

F-box domain containing protein, OsFBX241

 

LOC_Os05g50890.3

3.0

23.237

miRNA 22 UUGCUAGUGAAACAAGAGAGUU 1

..::.::.:::: :::::::..

Target 319 GGCGGUCGCUUUCUUCUCUCGG 340

Translation

Probable indole-3-acetic acid-amido synthetase,

OsGH3.5

vsiRS7_1

LOC_Os02g54500.1

2.5

14.148

miRNA 20 AGGAUGUCUUACAAUAAGUU 1

:: ::::::::::::::: :

Target 3812 UCAUACAGAAUGUUAUUCUA 3831

Cleavage

WD40-like, putative, expressed

 

LOC_Os08g12780.1

3

17.599

miRNA 21 AAGGAUGUCUUACAAUAAGUU 1

:::::.:::.: ::::::::

Target 1935 UUCCUGCAGGAAAUUAUUCAA 1955

Translation

chloroplast envelope membrane protein

vsiRS8_1

LOC_Os06g25560.1

2.5

13.472

miRNA 20 CAGCUACAUCUAAGAUCACU 1

:.::::: :::::::::::

Target 454 CUUGAUGUUGAUUCUAGUGA 473

Cleavage

retrotransposon protein

 

LOC_Os04g11830.1

3.0

16.405

miRNA 20 CAGCUACAUCUAAGAUCACU 1

:: :::::.:: :.::::::

Target 1708 GUGGAUGUGGAAUUUAGUGA 1727

Translation

TCP family transcription factor

vsiRS8_2

LOC_Os12g40279.2

2.5

17.285

miRNA 20 AGGAUGAGCACGGUAACGCU 1

::.::::: :::.::::::.

Target 3774 UCUUACUCUUGCUAUUGCGG 3793

Cleavage

protein kinase domain containing protein

vsiRS9_3

LOC_Os06g20050.1

3.0

18.094

miRNA 20 CGGUUCAGGUUAACUAGACA 1

::::::.:::::::: :::

Target 2505 UCCAAGUUCAAUUGAUAUGU 2524

Cleavage

leucine-rich repeat receptor protein

kinase EXS precursor

vsiRS9_3

LOC_Os05g07820.1

3.0

17.222

miRNA 20 CGGUUCAGGUUAACUAGACA 1

:.:.:::::: :::::::::

Target 586 GUCGAGUCCA-UUGAUCUGU 604

Translation

NBS type disease resistance protein

vsiRS10_1

LOC_Os08g40170.2

3.0

19.095

miRNA 21 UCGCGGGCUAGAAUAGGUAUU 1

::.:.:.::::::.:::::..

Target 723 AGUGUCUGAUCUUGUCCAUGG 743

Cleavage

cyclin-dependent kinase B2-1

  1. a) vsiRS2_1: 5’-UCCAUAGAAUAUGAUAACACU-3’, (+) 856–876 nt, GC% = 28.6%, 58 reads. See Table 1 for the information of other vsiRNAs. b) Calculated using psRNATarget (http://plantgrn.noble.org/psRNATarget/) [48]