Figure S1 Evolutionary relationships of RBG subclasses in Arabidopsis (a) and B. rapa (b). Optimal...
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Transcript of Figure S1 Evolutionary relationships of RBG subclasses in Arabidopsis (a) and B. rapa (b). Optimal...
Figure S1 Evolutionary relationships of RBG subclasses in Arabidopsis (a) and B. rapa (b). Optimal neighbor-joining trees with sum of branch lengths = 6.35903127 (a) = 5.93848788 (b) are shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and missing data were eliminated. The analysis involved 19 (a) and 26 (b) amino acid sequences with a total of 74 (a) and 89 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).
AT2G21660 AtRBGA3
AT4G39260 AtRBGA6
AT3G26420 AtRBGB2
AT1G60650 AtRBGB1
AT5G04280 AtRBGB3
AT3G13224 AtRBGD3
AT5G40490 AtRBGD5
AT1G17640 AtRBGD1
AT2G33410 AtRBGD2
AT4G14300 AtRBGD4
AT3G23830 AtRBGA4
AT4G13850 AtRBGA5
AT1G18630 AtRBGA1
AT1G74230 AtRBGA2
AT5G61030 AtRBGA7
AT2G17870
AT4G36020
AT2G21060
AT4G3868099
96
100
100
99
99
71
41
98
95
70
49
52
63
46
47
0.2
Bra011869 BrRBGA1
Bra010693 BrRBGA11
Bra001972 BrRBGA7
Bra030284 BrRBGA4
Bra031210 BrRBGA13
Bra032933 BrRBGB1
Bra025205 BrRBGB3
Bra014000 BrRBGA9
Bra013997 BrRBGA10
Bra037056 BrRBGA5
Bra008142 BrRBGA2
Bra015926 BrRBGA8
Bra012986 BrRBGA3
Bra035944 BrRBGA12
Bra025674 BrRBGA6
Bra005798 BrRBGB2
Bra025568 BrRBGD2
Bra039380 BrRBGD6
Bra010757 BrRBGD5
Bra005496 BrRBGD4
Bra022938 BrRBGD1
Bra021850 BrRBGD3
Bra011655
Bra017742
Bra030325
Bra031159
99
97
100
73100
99
100
93
100
65
100
100
97
99
96
76
86
48
33
5394
78
98
0.2
(a) (b)
Subclass IVc
Subclass IVc
Figure S2 Evolutionary relationships of RBG subclasses in rice (a) and maize (b). Optimal neighbor-joining trees with sum of branch lengths = 5.17050276 (a) = 5.17937492 (b) are shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and miss -ing data were eliminated. The analysis involved 14 (a) and 20 (b) amino acid sequences with were a total of 103 (a) and 92 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).
Os08g0320100 OsRBGD2
Os08g0492100 OsRBGD3
Os10g0470900 OsRBGD4
Os02g0221500 OsRBGD1
Os03g0681900 OsRBGB1
Os03g0836200 OsRBGB2
Os03g0670700 OsRBGA2
Os12g0632000 OsRBGA6
Os01g0916600 OsRBGA1
Os12g0502200 OsRBGA5
Os07g0602600 OsRBGA3
Os10g0321700 OsRBGA4
Os02g0121100
Os08g0129200100
96
64
99
79
100
96
69
48
37
45
0.2
GRMZM2G152526 ZmRBGD1
GRMZM2G050218 ZmRBGD3
AC198361.3 FGT004 ZmRBGD2
GRMZM2G167505 ZmRBGD5
GRMZM2G139643 ZmRBGD4
GRMZM2G167356 ZmRBGD6
GRMZM2G064518 ZmRBGD7
GRMZM2G104481 ZmRBGD8
GRMZM2G082931 ZmRBGB3
GRMZM2G083783 ZmRBGB1
GRMZM2G161242 ZmRBGB4
GRMZM5G874478 ZmRBGB2
GRMZM2G080603 ZmRBGA1
GRMZM2G165901 ZmRBGA3
GRMZM2G042118 ZmRBGA5
GRMZM2G131167 ZmRBGA4
GRMZM2G150521 ZmRBGA2
GRMZM2G009448 ZmRBGA6
GRMZM2G389768
GRMZM5G895313100
100
100
100
95
100
80
97
76
100
97
81
71
86
41
73
59
0.2
(a) (b)
Subclass IVc
Subclass IVc
Figure S3 Evolutionary relationships of RBGA members based on RRM sequences. Optimal neighbor-joining tree with sum of branch lengths = 3.93304551 is shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as per-centages. All positions containing gaps and missing data were excluded. The analysis involved 32 amino acid sequences, with a total of 73 positions in the fi-nal dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).
AT2G21660.1 AtRBGA3
Bra031210 BrRBGA13
Bra030284 BrRBGA4
AT4G39260.1 AtRBGA6
Bra011869 BrRBGA1
Bra010693 BrRBGA11
Bra001972 BrRBGA7
GRMZM2G080603 ZmRBGA1
GRMZM2G165901 ZmRBGA3
Os03g0670700 OsRBGA2
Os12g0632000 OsRBGA6
AT4G13850.1 AtRBGA5
Bra037056 BrRBGA5
Bra014000 BrRBGA9
Bra013997 BrRBGA10
AT3G23830.1 AtRBGA4
Os01g0916600 OsRBGA1
GRMZM2G042118 ZmRBGA5
AT1G18630.1 AtRBGA1
Bra025674 BrRBGA6
AT1G74230.1 AtRBGA2
Bra015926 BrRBGA8
Bra008142 BrRBGA2
AT5G61030.1 AtRBGA7
Bra012986 BrRBGA3
Bra035944 BrRBGA12
GRMZM2G131167 ZmRBGA4
Os07g0602600 OsRBGA3
Os10g0321700 OsRBGA4
Os12g0502200 OsRBGA5
GRMZM2G150521 ZmRBGA2
GRMZM2G009448 ZmRBGA6
10099
76100
99
82
47
90
81
29
57
100
64
49
65
46
78
47
42
83
9092
70
72
41
63
99
39
54
0.05
IV
II
III
I
Figure S4 Evolutionary relationships of RBGB members based on RRM sequences. Optimal neighbor-joining tree with sum of branch lengths = 1.83221663 is shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and miss -ing data were excluded from the analyses.The analysis involved 12 amino acid sequences, with a total of 74 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).
AT5G04280.1 AtRBG3
Bra005798 BrRBGB2
AT1G60650 AtRBGB1
Os03g0681900 OsRBGB1
GRMZM2G083783 ZmRBGB1
GRMZM2G161242 ZmRBGB4
GRMZM2G082931 ZmRBGB3
Bra032933 BrRBGB1
AT3G26420 AtRBGB2
Bra025205 BrRBGB3
Os03g0836200 OsRBGB2
GRMZM5G874478 ZmRBGB2
99
99
69
99
100
93
88
6999
0.1
I
II
Figure S5 Evolutionary relationships of RBGD members based on first (a) and second (b) RRM sequences. Optimal neighbor-joining trees with sum of branch lengths = 2.56495787 (a) and = 2.54450918 (b) are shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and missing data were excluded from the analyses. The analysis involved 23 amino acid sequences, with a total of 72 (a) and 73 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).
AT3G13224 AtRBGD3
Bra039380 BrRBGD6
Os08g0320100 OsRBGD2
GRMZM2G152526 ZmRBGD1
Os08g0492100 OsRBGD3
GRMZM2G050218 ZmRBGD3
AT5G40490 AtRBGD5
Bra025568 BrRBGD2
GRMZM2G064518 ZmRBGD7
GRMZM2G104481 ZmRBGD8
GRMZM2G139643 ZmRBGD4
Os02g0221500 OsRBGD1
GRMZM2G167356 ZmRBGD6
AT1G17640 AtRBGD1
AT4G14300 AtRBGD4
Bra010757 BrRBGD5
Bra005496 BrRBGD4
Bra022938 BrRBGD1
AT2G33410 AtRBGD2
Bra021850 BrRBGD3
AC198361.3 FGT004 ZmRBGD2
GRMZM2G167505 ZmRBGD5
Os10g0470900 OsRBGD4
3267
100
98
94
89
88
99
99
99
96
87
41
47
97
73
99
99
9678
0.05
(a)
I
III
IV
AT3G13224 AtRBGD3
Bra039380 BrRBGD6
AT5G40490 AtRBGD5
Bra025568 BrRBGD2
Os08g0320100 OsRBGD2
GRMZM2G152526 ZmRBGD1
Os08g0492100 OsRBGD3
GRMZM2G050218 ZmRBGD3
AT1G17640 AtRBGD1
GRMZM2G064518 ZmRBGD7
GRMZM2G104481 ZmRBGD8
Os02g0221500 OsRBGD1
GRMZM2G139643 ZmRBGD4
GRMZM2G167356 ZmRBGD6
AT4G14300 AtRBGD4
Bra010757 BrRBGD5
Bra005496 BrRBGD4
Bra022938 BrRBGD1
AT2G33410 AtRBGD2
Bra021850 BrRBGD3
AC198361.3 FGT004 ZmRBGD2
GRMZM2G167505 ZmRBGD5
Os10g0470900 OsRBGD4
100
99
97
99
100
79
97
59
99
31
27
72
79
99
100
67
67
67
99
76
0.05
(b)
I
III
IV
II
II
A03 A04 A05A01 A02
Figure S6 Physical positions of RBGs on Arabidopsis chromosomes. Chromosome numbers are indicated at the top of each chromosome. The image was generated automatically by submitting the IDs of AtRBGs via the chromosome map tool to the TAIR database (https://www.arabidopsis.org/jsp/ChromosomeMap/tool.jsp). Chromosome sizes are indicated by their relative lengths.
v
v
v
v
v
A09
BrRBGA12
BrRBGA13
A08
BrRBGA11
BrRBGA9BrRBGA10
BrRBGD7
A07
BrRBGA8
BrRBGA7
A03
BrRBGD1
BrRBGB2
BrRBGA3
A06
BrRBGA6
BrRBGB3
A04
BrRBGD3
BrRBGD2
BrRBGA4
A05
BrRBGD4
BrRBGA5
LF
MF1MF2Centromere
A01
BrRBGA1
A02
BrRBGB1
BrRBGA2
Figure S7 Physical positions of RBGs on B. rapa chromosomes. Chromosome numbers are indicated at the top of each chromosome. The image was prepared manually using chromosomal coordinates and subgenomic and genomic block information obtained from the Brassica database (http://brassicadb.org/brad/). Chromosome sizes are indicated by their relative lengths. The genome structure is adapted and modified from Cheng et al. (2013). Chromosomes without RBGs are not shown.
A02 A03 A07 A08 A10 A12A01
Figure S8 Physical positions of RBGs on rice chromosomes. Chromosome numbers are indicated at the top of each chromosome. The image was generated automatically by submitting the IDs of OsRBGs via the map tool to the Oryzabase database (http://viewer.shigen.info/oryzavw/maptool/MapTool.do). Chromosome sizes are indicated by their relative lengths. Chromosomes without RBGs are not shown.
AT1G18630_AtRBGA1
68.1% similarity to AT1G74230; 60.6% similarity to AT4G13850AT1G74230_AtRBGA2
58.7% similarity to AT3G23830AT2G21660_AtRBGA3
69.6% similarity to AT1G18630; 59.4% similarity to AT3G2383078.2% similarity to AT4G39260; 62.8% similarity to AT5G61030
AT3G23830_AtRBGA4
AT4G13850_AtRBGA5
72.1% similarity to AT3G23830; 41.7% similarity to AT5G61030AT4G39260_AtRBGA6
71.4% similarity to AT1G18630; 56.3% similarity to AT3G23830AT5G61030_AtRBGA7
AT1G17640_AtRBGD1
AT2G33410_AtRBGD2
AT3G13224_AtRBGD3
AT4G14300_AtRBGD4
72.2% similarity to AT2G3341078.8% similarity to AT2G33410
AT5G40490_AtRBGD5
Figure S9 Recombination signatures in AtRBGs. Genes were analyzed for recombination signatures using all available recombina-tion detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35. Subclasses with no recombi -nation signatures are not shown.
Bra011869_BrRBGA1
Bra008142_BrRBGA2
59.0% similarity to Bra035944Bra012986_BrRBGA3
Bra030284_BrRBGA4
Bra037056_BrRBGA5
Bra025674_BrRBGA6
Bra001972_BrRBGA7
Bra015926_BrRBGA8
55.4% similarity to Bra035944Bra014000_BrRBGA9
Bra013997_BrRBGA10
Bra010693_BrRBGA11
Bra035944_BrRBGA12
Bra031210_BrRBGA13
Bra022938_BrRBGD1
Bra025568_BrRBGD2
Bra021850_BrRBGD3
Bra005496_BrRBGD4
Bra010757_BrRBGD5
71.0% similarity to Bra025568; 66.7% similarity to Bra02293868.6% similarity to Bra021850
Bra039380_BrRBGD6
Figure S10 Recombination signatures in BrRBGs. Genes were analyzed for recombination signatures using all available recombi-nation detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35. Subclasses with no recom-bination signatures are not shown.
Os01g0916600_OsRBGA1
Os03g0670700_OsRBGA2
90.2% similarity to OsRBGA6; 80.6% similarity to OsRBGA5Os07g0602600_OsRBGA3
68.0% similarity to OsRBGA1Os10g0321700_OsRBGA4
63.7% similarity to OsRBGA3; 53.6% similarity to OsRBGA666.7% similarity to OsRBGA1
Os12g0502200_OsRBGA5
73.2% similarity to OsRBGA3; 55.6% similarity to OsRBGA273.2% similarity to OsRBGA3; 65.1% similarity to OsRBGA2
62.6% similarity to OsRBGA4Os12g0632000_OsRBGA6
Os02g0221500_OsRBGD1
90.6% similarity to OsRBGD2 57.8% similarity to OsRBGD2; 47.4% similarity to OsRBGD4Os08g0320100_OsRBGD2
Os08g0492100_OsRBGD3
76.8% similarity to OsRBGD1 72.1% similarity to OsRBGD272.1% similarity to OsRBGD2; 56.0% similarity to OsRBGD1
Os10g0470900_OsRBGD4
Figure S11 Recombination signatures in OsRBGs. Genes were analyzed for recombination signatures using all available recombi-nation detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35. Subclasses with no recom-bination signatures are not shown.
GRMZM2G080603_ZmRBGA1
GRMZM2G150521_ZmRBGA2
62.6% similarity to ZmRBGA3; 53.8% similarity to ZmRBGA4GRMZM2G165901_ZmRBGA3
GRMZM2G131167_ZmRBGA4
49.2% similarity to ZmRBGA1GRMZM2G042118_ZmRBGA5
GRMZM2G009448_ZmRBGA6
61.3% similarity to ZmRBGA3; 50.0% similarity to ZmRBGA4
GRMZM2G083783_ZmRBGB1
GRMZM5G874478_ZmRBGB2
GRMZM2G082931_ZmRBGB3
62.5% similarity to ZmRBGB1GRMZM2G161242_ZmRBGB4
95.8% similarity to ZmRBGB1
GRMZM2G152526_ZmRBGD1
AC198361.3_FGT004_ZmRBGD2
GRMZM2G050218_ZmRBGD3
67.4% similarity to ZmRBGD1GRMZM2G139643_ZmRBGD4
78.4% similarity to ZmRBGD8; 37.7% similarity to ZmRBGD2 77.6% similarity to ZmRBGD7GRMZM2G167505_ZmRBGD5
GRMZM2G167356_ZmRBGD6
79.0% similarity to ZmRBGD7GRMZM2G064518_ZmRBGD7
78.9% similarity to ZmRBGD6; 52.3% similarity to ZmRBGD5GRMZM2G104481_ZmRBGD8
79.9% similarity to ZmRBGD6; 48.3% similarity to ZmRBGD5
Figure S12 Recombination signatures in ZmRBGs. Genes were analyzed for recombination signatures us-ing all available recombination detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35.
Os07g0602600 OsRBGA3
Os10g0321700 OsRBGA4
Os12g0502200 OsRBGA5
AT1G74230 AtRBGA2
AT5G61030 AtRBGA7
AT1G18630 AtRBGA1
AT3G23830 AtRBGA4
Os01g0916600 OsRBGA1
AT4G13850 AtRBGA5
AT2G21660 AtRBGA3
AT4G39260 AtRBGA6
Os03g0670700 OsRBGA2
Os12g0632000 OsRBGA6
AT5G55670
Os09g0476100
Os08g049030088
100
99
95
98
85
46
48
47
82
36
51
24
0.1
Figure S13 Evolutionary relationships of RBGA and CPS 6-like proteins of Arabidopsis and rice based on full-length (a) and RRM (b) sequences. Optimal neighbor-joining trees with sum of branch lengths = 3.47310449 (a) and 3.57240316 (b) are shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and missing data were excluded. The analysis involved 16 amino acid sequences, with a total of 89 (a) and 73 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013). Accessions in red are CPS 6-like proteins.
Os07g0602600 OsRBGA3
Os10g0321700 OsRBGA4
Os12g0502200 OsRBGA5
AT1G74230 AtRBGA2
AT5G61030 AtRBGA7
AT1G18630 AtRBGA1
AT3G23830 AtRBGA4
Os01g0916600 OsRBGA1
AT4G13850 AtRBGA5
AT2G21660 AtRBGA3
AT4G39260 AtRBGA6
Os03g0670700 OsRBGA2
Os12g0632000 OsRBGA6
AT5G55670
Os09t0476100
Os08t049030098
100
99
86
96
84
51
53
44
39
73
56
36
0.1
(a) (b)
AT1G74230 AtRBGA2
Bra015926 BrRBGA8
Bra008142 BrRBGA2
AT5G61030 AtRBGA7
Bra012986 BrRBGA3
Bra035944 BrRBGA12
Os10g0321700 OsRBGA4
Os07g0602600 OsRBGA3
GRMZM2G131167 ZmRBGA4
Os12g0502200 OsRBGA5
GRMZM2G150521 ZmRBGA2
GRMZM2G009448 ZmRBGA6
AT3G23830 AtRBGA4
Os01g0916600 OsRBGA1
GRMZM2G042118 ZmRBGA5
AT4G13850 AtRBGA5
Bra037056 BrRBGA5
Bra014000 BrRBGA9
Bra013997 BrRBGA10
AT1G18630 AtRBGA1
Bra025674 BrRBGA6
Os03g0670700 OsRBGA2
Os12g0632000 OsRBGA6
GRMZM2G165901 ZmRBGA3
GRMZM2G080603 ZmRBGA1
Bra001972 BrRBGA7
AT2G21660 AtRBGA3
Bra031210 BrRBGA13
Bra030284 BrRBGA4
AT4G39260 AtRBGA6
Bra011869 BrRBGA1
Bra010693 BrRBGA11
AT5G06210.1 mtRBP
GRMZM2G113513 T01
AT2G37510.1 mtRBP
GRMZM2G077797 T01
AT5G54580.1 mtRBP
GRMZM2G003897 T01
AT3G08000.1 mtRBP
GRMZM2G470862 T01
Os09g0476100 CPS 6-like
100
80
99
99
100
99
75100
100
77
68
84
95
88
81
62
50
77
60
99
100
47
7996
89
50
51
37
38
80
62
95
17
31
39
4432
52
0.1
(a)
AT2G21660 AtRBGA3
Bra031210 BrRBGA13
Bra030284 BrRBGA4
AT4G39260 AtRBGA6
Bra011869 BrRBGA1
Bra010693 BrRBGA11
Bra001972 BrRBGA7
GRMZM2G080603 ZmRBGA1
GRMZM2G165901 ZmRBGA3
Os03g0670700 OsRBGA2
Os12g0632000 OsRBGA6
AT1G18630 AtRBGA1
Bra025674 BrRBGA6
AT2G37510.1 mtRBP
GRMZM2G077797 T01
AT5G54580.1
GRMZM2G003897 T01
AT1G74230 AtRBGA2
Bra015926 BrRBGA8
Bra008142 BrRBGA2
AT5G61030 AtRBGA7
Bra012986 BrRBGA3
Bra035944 BrRBGA12
Os10g0321700 OsRBGA4
Os07g0602600 OsRBGA3
GRMZM2G131167 ZmRBGA4
Os12g0502200 OsRBGA5
GRMZM2G150521 ZmRBGA2
GRMZM2G009448 ZmRBGA6
AT3G23830 AtRBGA4
Os01g0916600 OsRBGA1
GRMZM2G042118 ZmRBGA5
AT4G13850 AtRBGA5
Bra037056 BrRBGA5
Bra014000 BrRBGA9
Bra013997 BrRBGA10
AT3G08000.1
GRMZM2G470862 T01
Os09t0476100-01 CPS 6-like
AT5G06210.1
GRMZM2G113513 T01
99
77
99
99
98
74
99
100
99
62
92
84
93
81
75
50
38
60
57
99
99
7293
88
47
53
85
38
41
32
46
58
43
30
23
7
19
2
0.1
(b) Figure S14 Evolutionary relation-ships of RBGAs and mtRBA pro-teins based on full-length (a) and RRM (b) sequences. Optimal neighbor-joining trees with sum of branch lengths = 6.92084677 (a) and 6.64434195 (b) are shown. Trees were generated under a Pois-son model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions con-taining gaps and missing data were excluded. The analysis involved 41 amino acid sequences, with a total of 82 (a) and 73 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013). AT2G37510.1, AT3G08000.1, AT5G06210.1, AT5G54580 and their orthologs in maize—GRMZM2G077797_T01, GRMZM2G470862_T01, GR-MZM2G113513_T01 and GR-MZM2G003897_T01—are putative mitochondrial RNA binding pro-teins. CPS-6 like protein was used as an outgroup to improve bootstrap values.
Figure S15 Evolutionary relationships of RBGB, U11/U12-31K and TAF 15B members based on full-length (a) and RRM (b) sequences. Optimal neighbor-joining trees with sum of branch lengths = 5.31320179 (a) and 3.83218815 (b) are shown. Trees were generated under a Pois -son model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and missing data were excluded. The analysis involved 20 amino acid sequences, with a total of 43 (a) and 74 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).
AT5G04280 AtRBGB3
Bra005798 BrRBGB2
AT1G60650 AtRBGB1
Os03g0681900 OsRBGB1
GRMZM2G083783 ZmRBGB1
GRMZM2G161242 ZmRBGB4
GRMZM2G082931 ZmRBGB3
Os03g0836200 OsRBGB2
GRMZM5G874478 ZmRBGB2
Bra032933 BrRBGB1
AT3G26420 AtRBGB2
Bra025205 BrRBGB3
AT3G10400.1 U11/U1231K protein
Brara.E03019.1Brassica rapa FPscU11/U1231K protein
Os09t0549500 U11/U1231K protein
GRMZM2G053223 U11/U1231K protein
GRMZM2G048551 U11/U1231K protein
AT5G58470.1 TAB15b
Os01t0164400-01 TAB15b
GRMZM2G097775 TAB15b 98
100
100
52
76
98
99
99
75
94
96
88
41
61
53
16
23
0.2
(a) AT5G04280 AtRBGB3
Bra005798 BrRBGB2
AT1G60650 AtRBGB1
Os03g0681900 OsRBGB1
GRMZM2G083783 ZmRBGB1
GRMZM2G161242 ZmRBGB4
GRMZM2G082931 ZmRBGB3
Os03g0836200 OsRBGB2
GRMZM5G874478 ZmRBGB2
Bra032933 BrRBGB1
AT3G26420 AtRBGB2
Bra025205 BrRBGB3
AT3G10400.1 U11/U1231K protein
Brara.E03019.1Brassica rapa FPsc
Os09t0549500
GRMZM2G053223
GRMZM2G048551
AT5G58470.1 TAB15b
Os01t0164400-01
GRMZM2G097775 93
100
100
60
71
100
100
99
66
99
99
90
93
72
76
69
99
0.1
(b)
Figure S16 Evolutionary relationships between RBGs of Arabidopsis and CIRBP, RBM3, hnRNP G, hnRNP A/B and hnRNP D proteins of human (Hs) based on RRM sequences. Optimal neighbor-joining trees with sum of branch lengths = 6.45241954 (a) and 6.92555617 (b) are shown. Trees were generated under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade repre -sent bootstrap support values expressed as percentages. All positions containing gaps and missing data were excluded. The analysis involved 20 amino acid sequences, with a total of 71 (a) and 72 (b) positions in the final dataset. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013). Accession numbers of selected human proteins are GenBank Ids.
AT1G74230 AtRBGA2
AT5G61030 AtRBGA7
AT3G23830 AtRBGA4
AT4G13850 AtRBGA5
AT1G18630 AtRBGA1
AT1G60650 AtRBGB1
AT5G04280 AtRBGB3
AT3G26420 AtRBGB2
AT2G21660 AtRBGA3
AT4G39260 AtRBGA6
CAA80599 Hs-hnRNPG
NP_001271 Hs-CIRBP
NP_006734 Hs-RBM3
NP_112420 Hs-hnRNPA1 RRM1
NP_919223 Hs-hnRNPA3 RRM1
NP_006796 Hs-hnRNPA0 RRM1
sp|P22626|ROA2 Ha-HnRNPA2/B1 RRM1
NP_112738 Hs-hnRNPD0 RRM1
NP_112740 Hs-hnRNPDL RRM1
NP_112556 Hs-hnRNPAB RRM1
AT2G33410 AtRBGD2 RRM1
AT4G14300 AtRBGD4 RRM1
AT1G17640 AtRBGD1 RRM1
AT3G13224 AtRBGD3 RRM1
AT5G40490 AtRBGD5 RRM1100
88
54
100
99
41
100
87
99
99
68
62
98
96
49
91
48
6390
30
34
43
0.1
(a)
AT1G74230 AtRBGA2
AT5G61030 AtRBGA7
AT3G23830 AtRBGA4
AT4G13850 AtRBGA5
AT1G18630 AtRBGA1
CAA80599 Hs-hnRNPG
NP_001271 Hs-CIRBP
NP_006734 Hs-RBM3
AT1G60650 AtRBGB1
AT5G04280 AtRBGB3
AT3G26420 AtRBGB2
AT2G21660 AtRBGA3
AT4G39260 AtRBGA6
AT3G13224 AtRBGD3 RRM2
AT5G40490 AtRBGD5 RRM2
AT1G17640 AtRBGD1 RRM2
AT2G33410 AtRBGD2 RRM2
AT4G14300 AtRBGD4 RRM2
NP_112556 Hs-hnRNPAB RRM2
NP_112738 Hs-hnRNPD0 RRM2
NP_112740 Hs-hnRNPDL RRM2
NP_006796 Hs-hnRNPA0 RRM2
sp|P22626|ROA2 Hs-hnRNPA2/B1 RRM2
NP_112420 Hs-hnRNPA1 RRM2
NP_919223 Hs-hnRNPA3 RRM2
61
100
45
100
100
76
99
60
54
91
74
99
63
98
92
93
63
54
97
33
38
33
0.1
(b)
Figure S17 Evolutionary relationships of RBGA, RBGD, UBA2 proteins of Arabidopsis and B. rapa, and human hnRNP A/B and hnRNP D pro-teins based on full-length sequences. The optimal neighbor-joining tree with sum of branch lengths = 7.64650837 is shown. The tree was generated in MEGA6 (Tamura et al. 2013) under a Poisson model, with uniform rates and complete deletion op-tions. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and missing data were excluded. The analysis involved 48 amino acid se-quences, with a total of 65 positions in the final dataset. Accession numbers of selected human pro-teins are GenBank Ids.
Bra011869 BrRBGA1
Bra010693 BrRBGA11 AT4G39260 AtRBGA6
Bra001972 BrRBGA7
Bra030284 BrRBGA4
AT2G21660 AtRBGA3 Bra031210 BrRBGA13
AT3G23830 AtRBGA4
AT4G13850 AtRBGA5 Bra037056 BrRBGA5
Bra014000 BrRBGA9
Bra013997 BrRBGA10
CAA80599 Hs-hnRNPG NP_001271 Hs-CIRBP
NP_006734 Hs-RBM3
AT1G18630 AtRBGA1 Bra025674 BrRBGA6
AT1G74230 AtRBGA2
Bra015926 BrRBGA8
Bra008142 BrRBGA2 AT5G61030 AtRBGA7
Bra012986 BrRBGA3
Bra035944 BrRBGA12
NP_112556 Hs-hnRNPAB NP_112738 Hs-hnRNPD0
NP_112740 Hs-hnRNPDL
NP_112420 Hs-hnRNPA1 NP_919223 Hs-hnRNPA3
sp|P22626|ROA2 Hs-hnRNPA2/B1
NP_006796 Hs-hnRNPA0
AT3G13224 AtRBGD3 Bra039380 BrRBGD6
AT5G40490 AtRBGD5
Bra025568 BrRBGD2
AT1G17640 AtRBGD1 AT4G14300 AtRBGD4
Bra010757 BrRBGD5
Bra005496 BrRBGD4 AT2G33410 AtRBGD2
Bra022938 BrRBGD1
Bra021850 BrRBGD3
Bra039664 Bra038113
AT3G15010 UBA2c
AT3G56860 UBA2a Bra007277
AT2G41060 UBA2b
Bra016954
99
66
100
94100
99
100
79
100
6884
100
99
54100
100
100
94
4799
7699
99
74
98
5498
99
39
27
51
99
45
87
92
55
23
79
4889
61
99
43
7691
0.1
Figure S18 Evolutionary relationships of Arabidopsis hn-RNP A/B homologs based on first RRM (a), second RRM (b) and full-length protein (c) sequences. Optimal trees with sum of branch lengths = 3.57717484 (a), 3.45614914 (b) and 4.59144754 (c) are shown. The tree was generated in MEGA6 (Tamura et al. 2013) under a Poisson model, with uniform rates and complete deletion options. Numbers generated for each clade represent bootstrap support values expressed as percentages. All positions containing gaps and missing data were excluded. The analysis involved 13 amino acid se-quences in (a), (b) and (c), with a total of 71 (a), 73 (b) and 245 (c) positions in the final dataset.
(c)
AT5G55550 AtRBGD-R
AT4G26650 AtRBGD-R
AT5G47620 AtRBGD-R
AT3G07810 AtRBGD-R
AT1G58470 AtRBGD-R
AT2G33410 AtRBGD2
AT4G14300 AtRBGD4
AT1G17640 AtRBGD1
AT3G13224 AtRBGD3
AT5G40490 AtRBGD5
AT3G15010 UBA2c
AT3G56860 UBA2a
AT2G41060 UBA2b100
100
99
100
100
97
93
91
56
100
0.2
(a) AT5G55550 AtRBGD-R RRM1
AT4G26650 AtRBGD-R RRM1
AT3G07810 AtRBGD-R RRM1
AT5G47620 AtRBGD-R RRM1
AT2G33410 AtRBGD2 RRM1
AT4G14300 AtRBGD4 RRM1
AT1G17640 AtRBGD1 RRM1
AT3G13224 AtRBGD3 RRM1
AT5G40490 AtRBGD5 RRM1
AT1G58470 AtRBGD-R RRM1
AT3G15010 UBA2 RRM1
AT3G56860 UBA2 RRM1
AT2G41060 UBA2 RRM1100
99
100
98
97
77
57
58
49
93
0.1
(b)
AT5G55550 AtRBGD-R RRM2
AT4G26650 AtRBGD-R RRM2
AT5G47620 AtRBGD-R RRM2
AT3G07810 AtRBGD-R RRM2
AT1G58470 AtRBGD-R RRM2
AT2G33410 AtRBGD2 RRM2
AT4G14300 AtRBGD4 RRM2
AT1G17640 AtRBGD1 RRM2
AT3G13224 AtRBGD3 RRM2
AT5G40490 AtRBGD5 RRM2
AT3G15010 UBA2 RRM2
AT3G56860 UBA2 RRM2
AT2G41060 UBA2 RRM2100
100
52
39
99
97
84
91
86
69
0.1
Figure S19 Evolutionary relationships of plant RBGD, RBGD-R and UBA2 proteins based on full-length sequences. The optimal neighbor-join-ing tree with sum of branch lengths = 6.47429939 is shown. The tree was generated in MEGA6 (Tamura et al. 2013) under a Poisson model, with uniform rates and complete deletion options. Numbers gen-erated for each clade represent bootstrap support values expressed as percentages. All positions con-taining gaps and missing data were excluded. The analysis involved 58 amino acid sequences, with a total of 161 positions in the final dataset. Accessions in red are RBGD-R proteins.
Bra026413 RBGD-R Bra019094 RBGD-R AT4G26650 RBGD-R
AT5G55550 RBGD-R Bra028973 RBGD-R
Bra029681 RBGD-R Bra001267 RBGD-R AT3G07810 RBGD-R Bra040031 RBGD-R
Os11t0637700 RBGD-R GRMZM2G014400 RBGD-R GRMZM2G022313 RBGD-R
Os07t0584500 RBGD-R GRMZM2G013065 RBGD-R GRMZM2G144890 RBGD-R
GRMZM2G162954 RBGD-R Bra021062 RBGD-R
AT5G47620 RBGD-R Bra017475 RBGD-R Bra024928 RBGD-R
Bra022145 RBGD-R AC198361.3 FGT004 ZmRBGD2 GRMZM2G167505 ZmRBGD5
Os10g0470900 OsRBGD4 AT4G14300 AtRBGD4 Bra010757 BrRBGD5
Bra005496 BrRBGD4 AT2G33410 AtRBGD2
Bra022938 BrRBGD1 Bra021850 BrRBGD3
AT1G58470 RBGD-R Bra027860 RBGD-R
AT1G17640 AtRBGD1 GRMZM2G139643 ZmRBGD4 GRMZM2G167356 ZmRBGD6
Os02g0221500 OsRBGD1 GRMZM2G064518 ZmRBGD7 GRMZM2G104481 ZmRBGD8 AT5G40490 AtRBGD5
Bra025568 BrRBGD2 Os08g0320100 OsRBGD2
GRMZM2G152526 ZmRBGD1 AT3G13224 AtRBGD3
Bra039380 BrRBGD6 Os08g0492100 OsRBGD3
GRMZM2G050218 ZmRBGD3 AT3G56860 UBA2a
Bra007277 UBA2 AT2G41060 UBA2b
Bra016954 UBA2 Os01t0265800 UBA2
GRMZM2G132465 UBA2 Bra039664 UBA2
Bra038113 UBA2 AT3G15010 UBA2c
GRMZM2G049866 UBA2 Os01t0614500 UBA2 GRMZM5G803433 UBA2
100
92
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97
69100
75100
100
99
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100
9197
100
99
100
100
55
48
89
75
5861
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76
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99
97
6485
89
98
57 97
8999
4879
100
7069
100
6999
62
69 97
99
3487
0.1
AT3G13224 AtRBGD3
Bra039380 BrRBGD6
Os08g0320100 OsRBGD2
GRMZM2G152526 ZmRBGD1
Os08g0492100 OsRBGD3
GRMZM2G050218 ZmRBGD3
AT5G40490 AtRBGD5
Bra025568 BrRBGD2
AT1G17640 AtRBGD1
GRMZM2G064518 ZmRBGD7
GRMZM2G104481 ZmRBGD8
Os02g0221500 OsRBGD1
GRMZM2G139643 ZmRBGD4
GRMZM2G167356 ZmRBGD6
AC198361.3 FGT004 ZmRBGD2
GRMZM2G167505 ZmRBGD5
Os10g0470900 OsRBGD4
AT4G14300 AtRBGD4
Bra010757 BrRBGD5
Bra005496 BrRBGD4
Bra021850 BrRBGD3
AT2G33410 AtRBGD2
Bra022938 BrRBGD1
AT3G18610.1
AT1G48920.1100
100
4577
100
100
100
90
99
100
100
100
99
41
97
89
61
48100
99
8299
0.2
Figure S20 Evolutionary relationships of plant RBGD and Arabidopsis nucleolin-like proteins based on full-length protein sequences. The opti-mal neighbor-joining tree with sum of branch lengths = 5.02599772 is shown. Trees were gener-ated in MEGA6 (Tamura et al. 2013) under a Pois-son model, with uniform rates and complete dele-tion options. Numbers generated for each clade rep-resent bootstrap support values expressed as per-centages. All positions containing gaps and missing data were excluded. The analysis involved 25 amino acid sequences, with a total of 217 positions in the final dataset. Accessions in red are nucleolin-like proteins.