1. 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 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 73 100 99 100 93 100 65 100 97 99 96 76 86 48 33 53 94 78 98 0.2 (a)(b) Subclass IVc

2. 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 missing 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 Os08g0129200 100 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 GRMZM5G895313 100 95 100 80 97 76 100 97 81 71 86 41 73 59 0.2 (a)(b) Subclass IVc

3. 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 percentages. All positions containing gaps and missing data were excluded. The analysis involved 32 amino acid sequences, with a total of 73 positions in the final 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 100 99 76 100 99 82 47 90 81 29 57 100 64 49 65 46 78 47 42 83 90 92 70 72 41 63 99 39 54 0.05 IV II III I

4. 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 missing 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 69 99 100 93 88 69 99 0.1 I II

5. 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 32 67 100 98 94 89 88 99 96 87 41 47 97 73 99 96 78 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 99 76 0.05 (b) I III IV II

6. A03A04A05 A01 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

7. v v v v v A09 BrRBGA12 BrRBGA13 A08 BrRBGA11 BrRBGA9 BrRBGA10 BrRBGD7 A07 BrRBGA8 BrRBGA7 A03 BrRBGD1 BrRBGB2 BrRBGA3 A06 BrRBGA6 BrRBGB3 A04 BrRBGD3 BrRBGD2 BrRBGA4 A05 BrRBGD4 BrRBGA5 LF MF 1 MF 2 Centromere 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/

8. A02A03A07A08A10 A12 A01 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

9. AT1G18630_AtRBGA1 68.1% similarity to AT1G74230; 60.6% similarity to AT4G13850 AT1G74230_AtRBGA2 58.7% similarity to AT3G23830 AT2G21660_AtRBGA3 69.6% similarity to AT1G18630; 59.4% similarity to AT3G23830 78.2% similarity to AT4G39260; 62.8% similarity to AT5G61030 AT3G23830_AtRBGA4 AT4G13850_AtRBGA5 72.1% similarity to AT3G23830; 41.7% similarity to AT5G61030 AT4G39260_AtRBGA6 71.4% similarity to AT1G18630; 56.3% similarity to AT3G23830 AT5G61030_AtRBGA7 AT1G17640_AtRBGD1 AT2G33410_AtRBGD2 AT3G13224_AtRBGD3 AT4G14300_AtRBGD4 72.2% similarity to AT2G33410 78.8% similarity to AT2G33410 AT5G40490_AtRBGD5 Figure S9 Recombination signatures in AtRBGs. Genes were analyzed for recombination signatures using all available recombination detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35. Subclasses with no recombination signatures are not shown.

10. Bra011869_BrRBGA1 Bra008142_BrRBGA2 59.0% similarity to Bra035944 Bra012986_BrRBGA3 Bra030284_BrRBGA4 Bra037056_BrRBGA5 Bra025674_BrRBGA6 Bra001972_BrRBGA7 Bra015926_BrRBGA8 55.4% similarity to Bra035944 Bra014000_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 Bra022938 68.6% similarity to Bra021850 Bra039380_BrRBGD6 Figure S10 Recombination signatures in BrRBGs. Genes were analyzed for recombination signatures using all available recombination detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35. Subclasses with no recombination signatures are not shown.

11. Os01g0916600_OsRBGA1 Os03g0670700_OsRBGA2 90.2% similarity to OsRBGA6; 80.6% similarity to OsRBGA5 Os07g0602600_OsRBGA3 68.0% similarity to OsRBGA1 Os10g0321700_OsRBGA4 63.7% similarity to OsRBGA3; 53.6% similarity to OsRBGA6 66.7% similarity to OsRBGA1 Os12g0502200_OsRBGA5 73.2% similarity to OsRBGA3; 55.6% similarity to OsRBGA2 73.2% similarity to OsRBGA3; 65.1% similarity to OsRBGA2 62.6% similarity to OsRBGA4 Os12g0632000_OsRBGA6 Os02g0221500_OsRBGD1 90.6% similarity to OsRBGD257.8% similarity to OsRBGD2; 47.4% similarity to OsRBGD4 Os08g0320100_OsRBGD2 Os08g0492100_OsRBGD3 76.8% similarity to OsRBGD172.1% similarity to OsRBGD2 72.1% 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 recombination detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35. Subclasses with no recombination signatures are not shown.

12. GRMZM2G080603_ZmRBGA1 GRMZM2G150521_ZmRBGA2 62.6% similarity to ZmRBGA3; 53.8% similarity to ZmRBGA4 GRMZM2G165901_ZmRBGA3 GRMZM2G131167_ZmRBGA4 49.2% similarity to ZmRBGA1 GRMZM2G042118_ZmRBGA5 GRMZM2G009448_ZmRBGA6 61.3% similarity to ZmRBGA3; 50.0% similarity to ZmRBGA4 GRMZM2G083783_ZmRBGB1 GRMZM5G874478_ZmRBGB2 GRMZM2G082931_ZmRBGB3 62.5% similarity to ZmRBGB1 GRMZM2G161242_ZmRBGB4 95.8% similarity to ZmRBGB1 GRMZM2G152526_ZmRBGD1 AC198361.3_FGT004_ZmRBGD2 GRMZM2G050218_ZmRBGD3 67.4% similarity to ZmRBGD1 GRMZM2G139643_ZmRBGD4 78.4% similarity to ZmRBGD8; 37.7% similarity to ZmRBGD277.6% similarity to ZmRBGD7 GRMZM2G167505_ZmRBGD5 GRMZM2G167356_ZmRBGD6 79.0% similarity to ZmRBGD7 GRMZM2G064518_ZmRBGD7 78.9% similarity to ZmRBGD6; 52.3% similarity to ZmRBGD5 GRMZM2G104481_ZmRBGD8 79.9% similarity to ZmRBGD6; 48.3% similarity to ZmRBGD5 Figure S12 Recombination signatures in ZmRBGs. Genes were analyzed for recombination signatures using all available recombination detection methods (RDP, BOOtscan, MaxChi, Chimaera, SiScan, 3Seq and LARD) in RDP v4.35.

13. 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 Os08g0490300 88 100 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 Os08t0490300 98 100 99 86 96 84 51 53 44 39 73 56 36 0.1 (a) (b)

14. 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 99 100 99 75 100 77 68 84 95 88 81 62 50 77 60 99 100 47 79 96 89 50 51 37 38 80 62 95 17 31 39 44 32 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 98 74 99 100 99 62 92 84 93 81 75 50 38 60 57 99 72 93 88 47 53 85 38 41 32 46 58 43 30 23 7 19 2 0.1 (b) Figure S14 Evolutionary relationships of RBGAs and mtRBA proteins 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 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 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, GRMZM2G113513_T01 and GRMZM2G003897_T01—are putative mitochondrial RNA binding proteins. CPS-6 like protein was used as an outgroup to improve bootstrap values.

15. 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 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 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.E03019.1 Brassica 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 52 76 98 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 60 71 100 99 66 99 90 93 72 76 69 99 0.1 (b)

16. 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 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 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 RRM1 100 88 54 100 99 41 100 87 99 68 62 98 96 49 91 48 63 90 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 76 99 60 54 91 74 99 63 98 92 93 63 54 97 33 38 33 0.1 (b)

17. Figure S17 Evolutionary relationships of RBGA, RBGD, UBA2 proteins of Arabidopsis and B. rapa, and human hnRNP A/B and hnRNP D proteins 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 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 48 amino acid sequences, with a total of 65 positions in the final dataset. Accession numbers of selected human proteins 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 94 100 99 100 79 100 68 84 100 99 54 100 94 47 99 76 99 74 98 54 98 99 39 27 51 99 45 87 92 55 23 79 48 89 61 99 43 76 91 0.1

18. Figure S18 Evolutionary relationships of Arabidopsis hnRNP 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 sequences 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 UBA2b 100 99 100 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 RRM1 100 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 RRM2 100 52 39 99 97 84 91 86 69 0.1

19. Figure S19 Evolutionary relationships of plant RBGD, RBGD-R and UBA2 proteins based on full-length sequences. The optimal neighbor- joining 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 generated for each clade represent bootstrap support values expressed as percentages. All positions containing 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 69 100 75 100 99 100 91 97 100 99 100 55 48 89 75 58 61 100 76 99 97 64 85 89 98 57 97 89 99 48 79 100 70 69 100 69 99 62 69 97 99 34 87 0.1

20. 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 AT1G48920.1 100 45 77 100 90 99 100 99 41 97 89 61 48 100 99 82 99 0.2 Figure S20 Evolutionary relationships of plant RBGD and Arabidopsis nucleolin-like proteins based on full-length protein sequences. The optimal neighbor-joining tree with sum of branch lengths = 5.02599772 is shown. Trees were 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 25 amino acid sequences, with a total of 217 positions in the final dataset. Accessions in red are nucleolin-like proteins.