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




Os03g0681900 OsRBGB1


Os03g0670700 OsRBGA2






Os02g0121100

Os08g0129200100

96

64

99

79

100

96

69

48

37

45

0.2

GRMZM2G152526 ZmRBGD1


AC198361.3 FGT004 ZmRBGD2






GRMZM2G082931 ZmRBGB3




GRMZM2G080603 ZmRBGA1






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





AT4G13850.1 AtRBGA5

Bra037056 BrRBGA5

Bra014000 BrRBGA9

Bra013997 BrRBGA10

AT3G23830.1 AtRBGA4



AT1G18630.1 AtRBGA1

Bra025674 BrRBGA6

AT1G74230.1 AtRBGA2

Bra015926 BrRBGA8

Bra008142 BrRBGA2

AT5G61030.1 AtRBGA7

Bra012986 BrRBGA3

Bra035944 BrRBGA12







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





Bra032933 BrRBGB1

AT3G26420 AtRBGB2

Bra025205 BrRBGB3



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





AT5G40490 AtRBGD5

Bra025568 BrRBGD2






AT1G17640 AtRBGD1

AT4G14300 AtRBGD4

Bra010757 BrRBGD5

Bra005496 BrRBGD4

Bra022938 BrRBGD1

AT2G33410 AtRBGD2

Bra021850 BrRBGD3




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





AT1G17640 AtRBGD1






AT4G14300 AtRBGD4

Bra010757 BrRBGD5

Bra005496 BrRBGD4

Bra022938 BrRBGD1

AT2G33410 AtRBGD2

Bra021850 BrRBGD3




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.

https://www.arabidopsis.org/jsp/ChromosomeMap/tool.jsp

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.

http://brassicadb.org/brad/

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.

http://viewer.shigen.info/oryzavw/maptool/MapTool.do

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



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


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


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


76.8% similarity to OsRBGD1 72.1% similarity to OsRBGD272.1% similarity to OsRBGD2; 56.0% similarity to OsRBGD1


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


62.6% similarity to ZmRBGA3; 53.8% similarity to ZmRBGA4GRMZM2G165901_ZmRBGA3


49.2% similarity to ZmRBGA1GRMZM2G042118_ZmRBGA5


61.3% similarity to ZmRBGA3; 50.0% similarity to ZmRBGA4

GRMZM2G083783_ZmRBGB1



62.5% similarity to ZmRBGB1GRMZM2G161242_ZmRBGB4

95.8% similarity to ZmRBGB1

GRMZM2G152526_ZmRBGD1

AC198361.3_FGT004_ZmRBGD2


67.4% similarity to ZmRBGD1GRMZM2G139643_ZmRBGD4

78.4% similarity to ZmRBGD8; 37.7% similarity to ZmRBGD2 77.6% similarity to ZmRBGD7GRMZM2G167505_ZmRBGD5


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.




AT1G74230 AtRBGA2

AT5G61030 AtRBGA7

AT1G18630 AtRBGA1

AT3G23830 AtRBGA4


AT4G13850 AtRBGA5

AT2G21660 AtRBGA3

AT4G39260 AtRBGA6



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.




AT1G74230 AtRBGA2

AT5G61030 AtRBGA7

AT1G18630 AtRBGA1

AT3G23830 AtRBGA4


AT4G13850 AtRBGA5

AT2G21660 AtRBGA3

AT4G39260 AtRBGA6



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







AT3G23830 AtRBGA4



AT4G13850 AtRBGA5

Bra037056 BrRBGA5

Bra014000 BrRBGA9

Bra013997 BrRBGA10

AT1G18630 AtRBGA1

Bra025674 BrRBGA6





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





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







AT3G23830 AtRBGA4



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







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







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



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





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






NP_112556 Hs-hnRNPAB RRM2

NP_112738 Hs-hnRNPD0 RRM2

NP_112740 Hs-hnRNPDL RRM2


sp|P22626|ROA2 Hs-hnRNPA2/B1 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


Bra014000 BrRBGA9

Bra013997 BrRBGA10

CAA80599 Hs-hnRNPG NP_001271 Hs-CIRBP

NP_006734 Hs-RBM3


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

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99

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91

56

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0.2

(a) AT5G55550 AtRBGD-R RRM1

AT4G26650 AtRBGD-R RRM1









AT3G15010 UBA2 RRM1

AT3G56860 UBA2 RRM1

AT2G41060 UBA2 RRM1100

99

100

98

97

77

57

58

49

93

0.1

(b)











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

99

97

69100

75100

100

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9197

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55

48

89

75

5861

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76

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6485

89

98

57 97

8999

4879

100

7069

100

6999

62

69 97

99

3487

0.1

AT3G13224 AtRBGD3

Bra039380 BrRBGD6





AT5G40490 AtRBGD5

Bra025568 BrRBGD2

AT1G17640 AtRBGD1









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.

figure s1 evolutionary relationships of rbg subclasses in arabidopsis (a) and b. rapa (b). optimal...

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