Maize and Tripsacum As Model Systems to Compare Gene Expression Pattern After Fertilization

Supplementary Material

Supplementary Table 1. qRT-PCR ratio Fie/actin

Supplementary Table 2: A list of oligonucleotides for real-time RT-PCR.

Supplementary Table 3: A list of primers for RT-PCR and MSRE-PCR.

Supplementary Table 4. Number of methylated cytosines across four Fie1 regions in different tissues.

Supplementary Table 5. Number of methylated cytosines at Fie1 maternal and paternal alleles of exon 1. Hermon et al. 2

Supplementary Table 1. qRT-PCR ratio Fie/actin.

Fie1/actin Fie2/actin Samples Fie1 STDEV SE Fie2 STDEV SE Ovules 0.11 0.04 0.02 3.95 0.28 0.16 1DAP 0.02 0.02 0.01 5.25 0.55 0.32 2DAP 1.02 0.25 0.15 4.96 0.53 0.30 3DAP 7.56 1.22 0.70 5.30 0.59 0.34 4DAP 11.94 3.50 2.02 4.41 1.15 0.66 5DAP 43.54 10.64 6.14 3.58 0.98 0.57 7DAP 32.70 5.45 3.14 2.70 0.74 0.43 8DAP 35.50 11.18 6.46 2.45 0.84 0.49 9DAP 73.46 14.32 8.27 0.99 0.08 0.05 10DAP 76.72 36.78 21.23 0.95 0.65 0.38 11DAP 67.14 26.52 15.31 0.39 0.09 0.05 12DAP 62.23 18.67 10.78 0.17 0.04 0.02 STDEV –standard deviation, SE –standard error

Supplementary Table 2: A list of oligonucleotides for real-time RT-PCR.

Oligonucleotide Sequence (5’ to 3’) Fie1_F TTGGTTCAGAGTCGCCAGAT Fie1_R ACAGCAGCATCCTAACATTCAA Fie1_probe CAGCCACA Fie2_F GGGTTGCGATGGTTGAAT Fie2_R AACACCAACCATTTTGACTAGAAA Fie2_probe TTCCACCA -Actin_F CTTCGAATGCCCAGCAATGT -Actin_R GTTCGCCCACTAGCGTACAAC -Actin_probe TCGAGGCTGTTCTTT Hermon et al. 3

Supplementary Table 3: A list of primers for RT-PCR, MSRE-PCR and Bisulfate sequencing

Primers Sequence in 5’ to 3’ direction.

SC RT-PCR F-fie1 GGAACCAAAACCAGACAAGCGTAGGC R-fie1 CCTTATCGGCGACTTGCATTCCTGGTT F-fie2 ATGGACTGACCTTCCATCAAAGTTTCCAAC R-fie2 CAATGAGGACAGGAGGGC Gap1 AGGGTGGTGCCAAGAAGGTTG Gap2 GTAGCCCCACTCGTTGTCGTA SC MSRE-PCR F1-fie1 CGCCGCCACCATATAGAACCACTTATC R1-fie1 ATTGCAACTGGCGATGGC Tissue MSRE-PCR Fie1, F1 GCCGCCACCATATAGAACCACTTATC Fie1, R1 TTGCAACTGGCGATGGC Fie1, F2 ATGAGATAAGGACTCATGCCTCGAAGCCA Fie1, R2 CCCACTCACGTGCAGGTAGAAAG Fie1, F3 AGGCGAGATCTATGTCTGGGAAGTGCAGTC Fie1, R3 ATCGGCGACTTGCATTCC Fie1, F4 AATGCAAGTCGCCGATAAGGCAGACCGCAG Fie1, R4 CAACCAGCACGGAGTACGATCGATGTGAA Fie2, F5 GCGACACTAGTAACGGTCTACACCA Fie2, R5 CGCGTCCATGAAGTTGAACCCGATAG Bisulfite Sequencing Fie1, -1202 TAGTGGGAGGTGGATGTTTTATT Fie1, -1098 TCACTTACATACCTTAACTTAATTCCTTAC Fie1, -815 ATGGTATGGTTGTATAGGTGTTTTTAATTA Fie1, -604 AAAAAAATTATTTCCCCCTAATCCT Fie1, +22 GAAAGAGGTTATTTTGTGATATTATTGTT Fie1, +217 CTACTTCACATCCTAATCCTTATCATAAA Fie1, +2245 GGTTTGGGAATTATTTTAAATTAGTTTT Fie1, +2575 CACCAAACCATCTTAATACAATCAACAT Fie2, -84 GGGAAAGTAGTAGAGGAGGGGGTAGTAAT Fie2, +280 TAATTTTACCTTACCATTAATCAACAAA Hermon et al. 4

Supplementary Table 4. Number of methylated cytosines across four Fie1 regions in different tissues.

Promoter Number of CG (2 sites) CNG (2 sites) Asymmetric region 1 molecules (14 sites)

Pollen 5 9/10 (90%) 5/10 (50.00%) 0/70 (0%) Leaf 12 24/24 (100%) 8/24 (33.33%) 0/168 (0%) Embryo 15 27/30 (90%) 9/30 (30.00%) 3/210 (1.43%) Endosperm 16 18/32 (56.25%) 4/32 (13.33%) 0/224 (0%)

Promoter Number of CG (1 sites) CNG (2) Asymmetric (39) region 2 molecules Pollen 6 4/6 (66.67%) 8/12 (66.67%) 6/234 (2.56%) Leaf 16 12/16 (75.00%) 24/32 ( 75.00%) 15/624 (2.40%) Embryo 13 9/13 (69.23%) 21/26 (80.77%) 9/507 (1.78%) Endosperm 15 2/15 (13.33%) 5/30 (16.67%) 3/585 (0.51%)

Exon 1 Number of CG (10) CNG (9) Asymmetric (30) molecules Pollen 8 62/80 (77.50%) 72/54 (75.00%) 17/240 (7.08%) Leaf 14 82/140 (58.57%) 60/126 (47.62%) 15/420 (3.57%) Embryo 14 92/140 (65.71%) 62/126 (49.21%) 18/420 (4.29%) Endosperm 16 35/160 (21.88%) 21/144 (16.67%) 9/480 (1.88%)

Exons/introns Number of CG (3) CNG (11) Asymmetric (45) 6-7-8 molecules Pollen 8 23/24 (95.83%) 75/88 (85.23%) 8/360 (2.22%) Leaf 16 47/48 (97.92%) 147/176 (83.52%) 24/720 (3.33%) Embryo 16 43/48 (89.58%) 126/176 (71.59%) 8/720 (1.11%) Endosperm 16 14/48 (29.17%) 29/176 (16.48%) 3/720 (0.42%) CGG sites are counted as CG sites not as CNG. Asymmetric is defined by cytosines in the context CHH, where H=A, T, or C. Each fraction represents the number of cytosines methylated out of the total number of sites analyzed.

Supplementary Table 5. Number of methylated cytosines at Fie1 maternal and paternal alleles of exon 1.

Genotype Number of CG (10) CNG (9) Asymmetric (30) Molecules Fie1 102 29/1020 (2.84%) 30/918 (3.27%) 6/3060 (0.19%) Maternal Endosperm Fie1 14 92/140 (65.71%) 62/126 (49.21%) 7/420 (1.66%) Paternal Fie1 10 64/100 (64.00%) 51/90 (56.66%) 4/300 (1.33%) Maternal Embryo Fie1 4 28/40 (70.00%) 23/36 (63.88%) 2/120 (1.66%) Paternal