Comprehensive Genomic Analysis, Expression Profiling and Their Possible Regulative Role

Supplemental Tables:

Supplemental Table S1. Domain footprints, alignment details, and features of MdAGO proteins analyzed by CDD (http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi) to verify the presence of the Argonaute catalytic domain.

Query / Hit type / E-Value / Bitscore / Accession / Short name
MdAGO6 / Specific / 1.9507e-10 / 58.8678 / cd02846 / PAZ_argonaute_like
4.31138e-73 / 244.83 / cl00628 / Piwi-like superfamily
MdAGO2 / Specific / 3.36274e-20 / 88.143 / cd02846 / PAZ_argonaute_like
2.5234e-175 / 520.633 / cl00628 / Piwi-like superfamily
MdAGO1.3 / specific / 4.91219e-42 / 150.93 / cd02846 / PAZ_argonaute_like
0 / 637.348 / cl00628 / Piwi-like superfamily
MdAGO1.2 / specific / 1.41728e-42 / 152.471 / cd02846 / PAZ_argonaute_like
0 / 627.333 / cl00628 / Piwi-like superfamily
MdAGO10.2 / specific / 1.49342e-37 / 137.834 / cd02846 / PAZ_argonaute_like
0 / 613.466 / cl00628 / Piwi-like superfamily
MdAGO7.1 / specific / 2.14802e-26 / 105.862 / cd02846 / PAZ_argonaute_like
0 / 563.39 / cl00628 / Piwi-like superfamily
MdAGO7.2 / specific / 1.33883e-27 / 109.329 / cd02846 / PAZ_argonaute_like
0 / 555.686 / cl00628 / Piwi-like superfamily
MdAGO1.1 / specific / 7.71928e-43 / 153.242 / cd02846 / PAZ_argonaute_like
superfamily / 0 / 574.176 / cl00628 / Piwi-like superfamily
MdAGO4.1 / specific / 3.59044e-31 / 119.344 / cd02846 / PAZ_argonaute_like
superfamily / 1.14932e-170 / 506.766 / cl00628 / Piwi-like superfamily
MdAGO10.1 / specific / 6.85313e-28 / 110.099 / cd02846 / PAZ_argonaute_like
superfamily / 0 / 622.711 / cl00628 / Piwi-like superfamily

Supplemental Table S2. Best hits for each putative apple AGO protein, using local BLAST against apple ESTa assemblies.

Gene / GenBank Accession No. / Score / E-value / Gene / GenBank Accession No. / Score / E-value
MDP0000161046
MDP0000069525
MDP0000886537
MDP0000191579
MDP0000071268
MDP0000232035
MDP0000774227 / DR994838
EB112784
DT002215
CN866241
DT003505
GO518856
GO518856 / 1090
1229
1266
941
1229
802
1223 / 0
0
0
0
0
0
0 / MDP0000868788
MDP0000260407
MDP0000928339
MDP0000209079
MDP0000215105
MDP0000176861
MDP0000272708 / CN914704
CN888574
CO900338
CN931220
GO504980
CN889758
CN945801 / 924
1096
800
684
1192
1232
1291 / 0
0
0
0
0
0
0

aDownloaded from NCBI database.

Supplemental Table S3. GenBank Accession Numbers or Locus ID for AGOs from Vitis vinifera (Vv)b, Oryza sativa (Os)b, Solanum lycopersicum (Sl)b, and Arabidopsis thaliana (At)a.

Gene / Accession No. or Locus ID / Gene / Accession No. or Locus ID
VvAGO1 VvAGO2a VvAGO2b VvAGO3
VvAGO4
VvAGO5
VvAGO6
VvAGO7
VvAGO8
VvAGO9 VvAGO10a
VvAGO10b VvAGO11
OsAGO1a
OsAGO1b
OsAGO1c
OsAGO1d
OsAGO2
OsAGO3
OsAGO4a
OsAGO4b
OsAGO14
OsMEL1
OsAGO13
OsAGO16
SHL4
OsPNH1
OsAGO17
OsAGO12 / GSVIVT01029383001
GSVIVT01026261001
GSVIVT01026264001
GSVIVT01026268001
GSVIVT01037488001
GSVIVT01031430001
GSVIVT01001941001
GSVIVT01012490001
GSVIVT01025868001
GSVIVT01033726001
GSVIVT01018054001
GSVIVT01015464001
GSVIVT01030512001
LOC_Os02g45070
LOC_Os04g47870
LOC_Os02g58490
LOC_Os06g51310
LOC_Os04g52540
LOC_Os04g52550
LOC_Os01g16870
LOC_Os04g06770
LOC_Os01g16850
LOC_Os03g58600
LOC_Os03g57560
LOC_Os07g16224
LOC_Os03g33650
LOC_Os06g39640
LOC_Os02g07310
LOC_Os03g47820 / OsAGO11
OsAGO18
OsAGO15
SlAGO1a
SlAGO1b
SlAGO10a
SlAGO10b
SlAGO5
SlAGO7
SlAGO2a
SlAGO2b
SlAGO3
SlAGO6
SlAGO4a
SlAGO4b
SlAGO4c
SlAGO4d
SlAGO15
AtAGO2
AtAGO3
AtAGO1
AtAGO7
AtAGO4
AtAGO5
AtAGO6
AtAGO8
AtAGO9
AtAGO10 / LOC_Os03g47830
LOC_Os07g28850
LOC_Os07g09020
Solyc06g072300
Solyc03g098280
Solyc09g082830
Solyc03g111760
Solyc06g074730
Solyc01g010970
Solyc02g069260
Solyc02g069270
Solyc02g069280
Solyc07g049500
Solyc01g008960
Solyc06g073540
Solyc06g073530
Solyc01g096750
Solyc12g006790
AT1G69440
AT1G31290
AT1G48410
AT5G43810
AT2G27040
AT2G27880
AT2G32940
AT5G21030
AT5G21150
AT1G31280

aData source: bData source: http://phytozome.jgi.doe.gov/pz/portal.html

Supplemental Table S4. Details of cis-acting elements in promoters of apple AGO genes.

Cis-element / Sequence / Number of cis-elements / Function
MdAGO
1.1 / MdAGO
5.1 / MdAGO
10.2 / MdAGO
2 / MdAGO
7.1 / MdAGO
4.1 / MdAGO
6 / MdAGO
8
5'UTR Py-rich stretch
A-box
ABRE
ACE
AE-box
ARE
AT1-motif
ATCC motif
ATCT motif
AuxRR-core
Box-4
Box-I
Box II
Box-III
Box-W1
C-box
CAAT-box
CAT-box
CATT-motif
CCGTCC-box
CGTCA motif
CCAAT-box
ELI-box3
ERE
G-Box
G-box
GA motif
GAG motif
GARE motif
GATA-motif
GATT-motif
GC motif
GT1 motif
GCN4 motif
HD-Zip 1
HD-Zip 2
HSE
LTR
I-box
MBS
MRE
O 2 –site
P-box
Skn-1 motif
Sp1
TA-rich region
TATA-box
TC-rich repeats
TCA element
TGA element
TCT motif
TGACG motif
W-box
chs-CMA1a
as-2-box
Circadian
rbcS-CMA7a
WUN-motif
W box / TTTCTTCTCT
CCGTCC
CACGTG
AAAACGTTTA
AGAAACAA
TGGTTT
AATTATTTTTTATT
CAATCCTC
AATCTAATCC
GGTCCAT
ATTAAT
TTTCAAA
TGGTAATAA
CATTTACACT
TTGACC
ACGAGCACCGCC
CCAAT
GCCACT
GCATTC
CCGTCC
CGTCA
CAACGG
AAACCAATT
ATTTCAAA
CACGTG
CACGAC
AAGGAAGA
GGAGATG
AAACAGA
AAGGATAAGG
CTGCAGATTTCT
CCCCCG
GGTTAA
CAAGCCA
CAAT(A/T)ATTG
CAAT(G/C)ATTG
AAAAAATTTC
CCGAAA
AAGATAAGA
CAACTG
AACCTAA
GATGACATGG
CCTTTTG
GTCAT
CC(G/A)CCC
TATA……TATA
TATA
ATTTTCTTCA
GAGAAGAATA
AACGAC
TCTTAC
TGACG
TTGACC
TTACTTAA
GATAATGATG
CAANNNNATC
GTCGATAAGG
AAATTTCCT
TTGACC / 1
0
0
0
0
2
0
1
0
0
1
1
0
0
0
0
25
0
1
0
1
0
0
1
1
1
0
0
0
0
0
0
0
0
0
0
2
0
1
3
1
1
1
1
0
0
48
0
2
0
0
1
0
0
1
1
1
0
0 / 2
0
0
0
1
2
0
0
0
0
1
3
0
0
1
0
23
1
0
0
1
0
0
0
5
0
0
0
0
0
0
2
1
2
0
0
0
2
0
0
0
0
0
5
3
0
17
0
1
0
0
2
1
0
0
0
0
0
0 / 1
0
2
0
3
1
1
0
1
0
1
1
0
1
0
0
20
0
1
0
0
0
0
0
2
3
0
3
1
0
0
0
0
0
0
0
1
0
0
0
0
0
2
0
0
0
40
0
1
1
1
0
0
0
1
1
0
0
0 / 5
1
0
0
0
1
0
0
0
1
1
2
0
1
0
0
37
0
0
1
2
0
1
0
3
0
1
2
1
0
0
0
1
1
0
0
1
2
2
1
0
1
0
4
1
0
62
1
1
1
1
2
0
0
0
1
1
0
0 / 5
0
0
1
0
1
0
1
2
0
0
5
1
1
0
0
30
0
0
0
1
0
0
1
0
1
2
2
1
1
0
0
2
0
0
0
1
1
0
1
0
0
1
2
0
1
74
2
2
0
0
1
0
1
1
2
0
0
0 / 0
0
1
0
3
6
0
0
0
0
2
1
0
0
0
0
28
0
0
0
0
0
0
0
3
1
0
0
1
0
0
0
0
0
0
0
0
2
0
0
0
1
0
3
0
0
69
1
1
0
1
0
0
1
0
2
0
0
0 / 1
1
0
0
1
1
0
0
1
0
3
0
0
0
0
1
28
0
0
1
1
1
0
0
0
0
0
0
1
0
1
0
0
2
0
0
1
2
0
3
0
0
1
3
0
0
36
1
0
1
1
1
0
0
0
0
0
1
0 / 1
0
2
2
0
3
0
0
0
0
1
0
0
0
1
0
29
0
1
0
1
0
1
0
3
3
0
0
0
0
0
0
0
2
1
1
1
0
0
0
0
1
1
1
0
2
70
3
0
0
2
1
0
0
0
2
0
0
1 / High transcription levels
Cis-acting regulatory element
Abscisic acid-responsive
Light-responsive
Part of module for light response
Anaerobic induction
Part of light-responsive module
Part of conserved DNA module involved in light response
Part of conserved DNA module involved in light response
Auxin-responsiveness
Part of conserved DNA module involved in light response
Light-responsive
Part of light-responsive element
Protein binding site Common
Fungal elicitor-responsive element
Involved in light response
Cis-acting element in promoter and enhancer regions
Cis-acting regulatory element related to meristem expression
Part of light-responsive element
Meristem-specific activation
MeJA-responsive
MYBHv1 binding site involved in light response
Elicitor-responsive element
Ethylene-responsive
Light-responsive
Light-responsive
Part of light-responsive element
Part of light-responsive element
Gibberellin-responsive
Part of light-responsive element
Part of light-responsive element
Anoxic-speciﬁc inducibility
Light-responsive
Endosperm expression
Palisade mesophyll cells differentiation
Leaf morphology development
Heat stress-responsive
Low temperature-responsive
Part of light-responsive element
MYB binding site involved in drought inducibility
MYB binding site involved in light response
Regulation of zein metabolism
Gibberellin-responsive
Endosperm expression
Light-responsive
Enhancer
Core promoter element around –30 bp of
transcription start
Defense- and stress-responsive
Salicylic acid-responsive
Part of auxin-responsive element
Part of light-responsive element
MeJA-responsive
Wounding- and pathogen-responsive
Part of light-responsive element
Shoot-speciﬁc expression and light-responsiveness
Circadian control
Part of light-responsive element
Wound-responsive element
Circadian control