Figure S1 Evolutionary relationships of RBG subclasses in Arabidopsis (a) and B. rapa (b). Optimal neighbor-joining trees with sum of branch lengths =

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Figure S1 Evolutionary relationships of RBG subclasses in Arabidopsis (a) and B. rapa (b). Optimal neighbor-joining trees with sum of branch lengths = (a) = (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 AT4G Bra BrRBGA1 Bra BrRBGA11 Bra BrRBGA7 Bra BrRBGA4 Bra BrRBGA13 Bra BrRBGB1 Bra BrRBGB3 Bra BrRBGA9 Bra BrRBGA10 Bra BrRBGA5 Bra BrRBGA2 Bra BrRBGA8 Bra BrRBGA3 Bra BrRBGA12 Bra BrRBGA6 Bra BrRBGB2 Bra BrRBGD2 Bra BrRBGD6 Bra BrRBGD5 Bra BrRBGD4 Bra BrRBGD1 Bra BrRBGD3 Bra Bra Bra Bra (a)(b) Subclass IVc

Figure S2 Evolutionary relationships of RBG subclasses in rice (a) and maize (b). Optimal neighbor-joining trees with sum of branch lengths = (a) = (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). Os08g OsRBGD2 Os08g OsRBGD3 Os10g OsRBGD4 Os02g OsRBGD1 Os03g OsRBGB1 Os03g OsRBGB2 Os03g OsRBGA2 Os12g OsRBGA6 Os01g OsRBGA1 Os12g OsRBGA5 Os07g OsRBGA3 Os10g OsRBGA4 Os02g Os08g GRMZM2G ZmRBGD1 GRMZM2G ZmRBGD3 AC FGT004 ZmRBGD2 GRMZM2G ZmRBGD5 GRMZM2G ZmRBGD4 GRMZM2G ZmRBGD6 GRMZM2G ZmRBGD7 GRMZM2G ZmRBGD8 GRMZM2G ZmRBGB3 GRMZM2G ZmRBGB1 GRMZM2G ZmRBGB4 GRMZM5G ZmRBGB2 GRMZM2G ZmRBGA1 GRMZM2G ZmRBGA3 GRMZM2G ZmRBGA5 GRMZM2G ZmRBGA4 GRMZM2G ZmRBGA2 GRMZM2G ZmRBGA6 GRMZM2G GRMZM5G (a)(b) Subclass IVc

Figure S3 Evolutionary relationships of RBGA members based on RRM sequences. Optimal neighbor-joining tree with sum of branch lengths = 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). AT2G AtRBGA3 Bra BrRBGA13 Bra BrRBGA4 AT4G AtRBGA6 Bra BrRBGA1 Bra BrRBGA11 Bra BrRBGA7 GRMZM2G ZmRBGA1 GRMZM2G ZmRBGA3 Os03g OsRBGA2 Os12g OsRBGA6 AT4G AtRBGA5 Bra BrRBGA5 Bra BrRBGA9 Bra BrRBGA10 AT3G AtRBGA4 Os01g OsRBGA1 GRMZM2G ZmRBGA5 AT1G AtRBGA1 Bra BrRBGA6 AT1G AtRBGA2 Bra BrRBGA8 Bra BrRBGA2 AT5G AtRBGA7 Bra BrRBGA3 Bra BrRBGA12 GRMZM2G ZmRBGA4 Os07g OsRBGA3 Os10g OsRBGA4 Os12g OsRBGA5 GRMZM2G ZmRBGA2 GRMZM2G ZmRBGA IV II III I

Figure S4 Evolutionary relationships of RBGB members based on RRM sequences. Optimal neighbor-joining tree with sum of branch lengths = 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). AT5G AtRBG3 Bra BrRBGB2 AT1G60650 AtRBGB1 Os03g OsRBGB1 GRMZM2G ZmRBGB1 GRMZM2G ZmRBGB4 GRMZM2G ZmRBGB3 Bra BrRBGB1 AT3G26420 AtRBGB2 Bra BrRBGB3 Os03g OsRBGB2 GRMZM5G ZmRBGB 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 = (a) and = (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 Bra BrRBGD6 Os08g OsRBGD2 GRMZM2G ZmRBGD1 Os08g OsRBGD3 GRMZM2G ZmRBGD3 AT5G40490 AtRBGD5 Bra BrRBGD2 GRMZM2G ZmRBGD7 GRMZM2G ZmRBGD8 GRMZM2G ZmRBGD4 Os02g OsRBGD1 GRMZM2G ZmRBGD6 AT1G17640 AtRBGD1 AT4G14300 AtRBGD4 Bra BrRBGD5 Bra BrRBGD4 Bra BrRBGD1 AT2G33410 AtRBGD2 Bra BrRBGD3 AC FGT004 ZmRBGD2 GRMZM2G ZmRBGD5 Os10g OsRBGD (a) I III IV AT3G13224 AtRBGD3 Bra BrRBGD6 AT5G40490 AtRBGD5 Bra BrRBGD2 Os08g OsRBGD2 GRMZM2G ZmRBGD1 Os08g OsRBGD3 GRMZM2G ZmRBGD3 AT1G17640 AtRBGD1 GRMZM2G ZmRBGD7 GRMZM2G ZmRBGD8 Os02g OsRBGD1 GRMZM2G ZmRBGD4 GRMZM2G ZmRBGD6 AT4G14300 AtRBGD4 Bra BrRBGD5 Bra BrRBGD4 Bra BrRBGD1 AT2G33410 AtRBGD2 Bra BrRBGD3 AC FGT004 ZmRBGD2 GRMZM2G ZmRBGD5 Os10g OsRBGD (b) I III IV II

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 ( Chromosome sizes are indicated by their relative lengths.

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 ( 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.

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 ( 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 AT4G13850 AT1G74230_AtRBGA2 58.7% similarity to AT3G23830 AT2G21660_AtRBGA3 69.6% similarity to AT1G18630; 59.4% similarity to AT3G % 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 AT2G % 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.

Bra011869_BrRBGA1 Bra008142_BrRBGA2 59.0% similarity to Bra Bra012986_BrRBGA3 Bra030284_BrRBGA4 Bra037056_BrRBGA5 Bra025674_BrRBGA6 Bra001972_BrRBGA7 Bra015926_BrRBGA8 55.4% similarity to Bra 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 Bra % similarity to Bra 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.

Os01g _OsRBGA1 Os03g _OsRBGA2 90.2% similarity to OsRBGA6; 80.6% similarity to OsRBGA5 Os07g _OsRBGA3 68.0% similarity to OsRBGA1 Os10g _OsRBGA4 63.7% similarity to OsRBGA3; 53.6% similarity to OsRBGA6 66.7% similarity to OsRBGA1 Os12g _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 Os12g _OsRBGA6 Os02g _OsRBGD1 90.6% similarity to OsRBGD257.8% similarity to OsRBGD2; 47.4% similarity to OsRBGD4 Os08g _OsRBGD2 Os08g _OsRBGD3 76.8% similarity to OsRBGD172.1% similarity to OsRBGD2 72.1% similarity to OsRBGD2; 56.0% similarity to OsRBGD1 Os10g _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.

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 AC _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.

Os07g OsRBGA3 Os10g OsRBGA4 Os12g OsRBGA5 AT1G74230 AtRBGA2 AT5G61030 AtRBGA7 AT1G18630 AtRBGA1 AT3G23830 AtRBGA4 Os01g OsRBGA1 AT4G13850 AtRBGA5 AT2G21660 AtRBGA3 AT4G39260 AtRBGA6 Os03g OsRBGA2 Os12g OsRBGA6 AT5G55670 Os09g Os08g 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 = (a) and (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. Os07g OsRBGA3 Os10g OsRBGA4 Os12g OsRBGA5 AT1G74230 AtRBGA2 AT5G61030 AtRBGA7 AT1G18630 AtRBGA1 AT3G23830 AtRBGA4 Os01g OsRBGA1 AT4G13850 AtRBGA5 AT2G21660 AtRBGA3 AT4G39260 AtRBGA6 Os03g OsRBGA2 Os12g OsRBGA6 AT5G55670 Os09t Os08t (a) (b)

AT1G74230 AtRBGA2 Bra BrRBGA8 Bra BrRBGA2 AT5G61030 AtRBGA7 Bra BrRBGA3 Bra BrRBGA12 Os10g OsRBGA4 Os07g OsRBGA3 GRMZM2G ZmRBGA4 Os12g OsRBGA5 GRMZM2G ZmRBGA2 GRMZM2G ZmRBGA6 AT3G23830 AtRBGA4 Os01g OsRBGA1 GRMZM2G ZmRBGA5 AT4G13850 AtRBGA5 Bra BrRBGA5 Bra BrRBGA9 Bra BrRBGA10 AT1G18630 AtRBGA1 Bra BrRBGA6 Os03g OsRBGA2 Os12g OsRBGA6 GRMZM2G ZmRBGA3 GRMZM2G ZmRBGA1 Bra BrRBGA7 AT2G21660 AtRBGA3 Bra BrRBGA13 Bra BrRBGA4 AT4G39260 AtRBGA6 Bra BrRBGA1 Bra BrRBGA11 AT5G mtRBP GRMZM2G T01 AT2G mtRBP GRMZM2G T01 AT5G mtRBP GRMZM2G T01 AT3G mtRBP GRMZM2G T01 Os09g CPS 6-like (a) AT2G21660 AtRBGA3 Bra BrRBGA13 Bra BrRBGA4 AT4G39260 AtRBGA6 Bra BrRBGA1 Bra BrRBGA11 Bra BrRBGA7 GRMZM2G ZmRBGA1 GRMZM2G ZmRBGA3 Os03g OsRBGA2 Os12g OsRBGA6 AT1G18630 AtRBGA1 Bra BrRBGA6 AT2G mtRBP GRMZM2G T01 AT5G GRMZM2G T01 AT1G74230 AtRBGA2 Bra BrRBGA8 Bra BrRBGA2 AT5G61030 AtRBGA7 Bra BrRBGA3 Bra BrRBGA12 Os10g OsRBGA4 Os07g OsRBGA3 GRMZM2G ZmRBGA4 Os12g OsRBGA5 GRMZM2G ZmRBGA2 GRMZM2G ZmRBGA6 AT3G23830 AtRBGA4 Os01g OsRBGA1 GRMZM2G ZmRBGA5 AT4G13850 AtRBGA5 Bra BrRBGA5 Bra BrRBGA9 Bra BrRBGA10 AT3G GRMZM2G T01 Os09t CPS 6-like AT5G GRMZM2G T (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 = (a) and (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). AT2G , AT3G , AT5G , 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.

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 = (a) and (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 Bra BrRBGB2 AT1G60650 AtRBGB1 Os03g OsRBGB1 GRMZM2G ZmRBGB1 GRMZM2G ZmRBGB4 GRMZM2G ZmRBGB3 Os03g OsRBGB2 GRMZM5G ZmRBGB2 Bra BrRBGB1 AT3G26420 AtRBGB2 Bra BrRBGB3 AT3G U11/U1231K protein Brara.E Brassica rapa FPscU11/U1231K protein Os09t U11/U1231K protein GRMZM2G U11/U1231K protein GRMZM2G U11/U1231K protein AT5G TAB15b Os01t TAB15b GRMZM2G TAB15b (a) AT5G04280 AtRBGB3 Bra BrRBGB2 AT1G60650 AtRBGB1 Os03g OsRBGB1 GRMZM2G ZmRBGB1 GRMZM2G ZmRBGB4 GRMZM2G ZmRBGB3 Os03g OsRBGB2 GRMZM5G ZmRBGB2 Bra BrRBGB1 AT3G26420 AtRBGB2 Bra BrRBGB3 AT3G U11/U1231K protein Brara.E Brassica rapa FPsc Os09t GRMZM2G GRMZM2G AT5G TAB15b Os01t GRMZM2G (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 = (a) and (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_ Hs-CIRBP NP_ Hs-RBM3 NP_ Hs-hnRNPA1 RRM1 NP_ Hs-hnRNPA3 RRM1 NP_ Hs-hnRNPA0 RRM1 sp|P22626|ROA2 Ha-HnRNPA2/B1 RRM1 NP_ Hs-hnRNPD0 RRM1 NP_ Hs-hnRNPDL RRM1 NP_ Hs-hnRNPAB RRM1 AT2G33410 AtRBGD2 RRM1 AT4G14300 AtRBGD4 RRM1 AT1G17640 AtRBGD1 RRM1 AT3G13224 AtRBGD3 RRM1 AT5G40490 AtRBGD5 RRM (a) AT1G74230 AtRBGA2 AT5G61030 AtRBGA7 AT3G23830 AtRBGA4 AT4G13850 AtRBGA5 AT1G18630 AtRBGA1 CAA80599 Hs-hnRNPG NP_ Hs-CIRBP NP_ 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_ Hs-hnRNPAB RRM2 NP_ Hs-hnRNPD0 RRM2 NP_ Hs-hnRNPDL RRM2 NP_ Hs-hnRNPA0 RRM2 sp|P22626|ROA2 Hs-hnRNPA2/B1 RRM2 NP_ Hs-hnRNPA1 RRM2 NP_ Hs-hnRNPA3 RRM (b)

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 = 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. Bra BrRBGA1 Bra BrRBGA11 AT4G39260 AtRBGA6 Bra BrRBGA7 Bra BrRBGA4 AT2G21660 AtRBGA3 Bra BrRBGA13 AT3G23830 AtRBGA4 AT4G13850 AtRBGA5 Bra BrRBGA5 Bra BrRBGA9 Bra BrRBGA10 CAA80599 Hs-hnRNPG NP_ Hs-CIRBP NP_ Hs-RBM3 AT1G18630 AtRBGA1 Bra BrRBGA6 AT1G74230 AtRBGA2 Bra BrRBGA8 Bra BrRBGA2 AT5G61030 AtRBGA7 Bra BrRBGA3 Bra BrRBGA12 NP_ Hs-hnRNPAB NP_ Hs-hnRNPD0 NP_ Hs-hnRNPDL NP_ Hs-hnRNPA1 NP_ Hs-hnRNPA3 sp|P22626|ROA2 Hs-hnRNPA2/B1 NP_ Hs-hnRNPA0 AT3G13224 AtRBGD3 Bra BrRBGD6 AT5G40490 AtRBGD5 Bra BrRBGD2 AT1G17640 AtRBGD1 AT4G14300 AtRBGD4 Bra BrRBGD5 Bra BrRBGD4 AT2G33410 AtRBGD2 Bra BrRBGD1 Bra BrRBGD3 Bra Bra AT3G15010 UBA2c AT3G56860 UBA2a Bra AT2G41060 UBA2b Bra

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 = (a), (b) and (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 (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 RRM (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 RRM

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 = 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. Bra RBGD-R Bra RBGD-R AT4G26650 RBGD-R AT5G55550 RBGD-R Bra RBGD-R Bra RBGD-R Bra RBGD-R AT3G07810 RBGD-R Bra RBGD-R Os11t RBGD-R GRMZM2G RBGD-R GRMZM2G RBGD-R Os07t RBGD-R GRMZM2G RBGD-R GRMZM2G RBGD-R GRMZM2G RBGD-R Bra RBGD-R AT5G47620 RBGD-R Bra RBGD-R Bra RBGD-R Bra RBGD-R AC FGT004 ZmRBGD2 GRMZM2G ZmRBGD5 Os10g OsRBGD4 AT4G14300 AtRBGD4 Bra BrRBGD5 Bra BrRBGD4 AT2G33410 AtRBGD2 Bra BrRBGD1 Bra BrRBGD3 AT1G58470 RBGD-R Bra RBGD-R AT1G17640 AtRBGD1 GRMZM2G ZmRBGD4 GRMZM2G ZmRBGD6 Os02g OsRBGD1 GRMZM2G ZmRBGD7 GRMZM2G ZmRBGD8 AT5G40490 AtRBGD5 Bra BrRBGD2 Os08g OsRBGD2 GRMZM2G ZmRBGD1 AT3G13224 AtRBGD3 Bra BrRBGD6 Os08g OsRBGD3 GRMZM2G ZmRBGD3 AT3G56860 UBA2a Bra UBA2 AT2G41060 UBA2b Bra UBA2 Os01t UBA2 GRMZM2G UBA2 Bra UBA2 Bra UBA2 AT3G15010 UBA2c GRMZM2G UBA2 Os01t UBA2 GRMZM5G UBA

AT3G13224 AtRBGD3 Bra BrRBGD6 Os08g OsRBGD2 GRMZM2G ZmRBGD1 Os08g OsRBGD3 GRMZM2G ZmRBGD3 AT5G40490 AtRBGD5 Bra BrRBGD2 AT1G17640 AtRBGD1 GRMZM2G ZmRBGD7 GRMZM2G ZmRBGD8 Os02g OsRBGD1 GRMZM2G ZmRBGD4 GRMZM2G ZmRBGD6 AC FGT004 ZmRBGD2 GRMZM2G ZmRBGD5 Os10g OsRBGD4 AT4G14300 AtRBGD4 Bra BrRBGD5 Bra BrRBGD4 Bra BrRBGD3 AT2G33410 AtRBGD2 Bra BrRBGD1 AT3G AT1G 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 = 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.