Castillo et al. Rice Archaeogenetics electronic supplementary information
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1 Castillo et al. Rice Archaeogenetics electronic supplementary information Figure S1: PCR amplification for the nuclear genome region Sh4; and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with specific primer sets, F2 and R2 primers. M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), J: Modern japonica cv. 'Nipponbare', NC: negative control (dh2o), 1-10: represent remains from Ban Non Wat V200 7: 3 Δ2 Samples (b) Sequence detected in wild rice, japonica and archaeological remains from Ban Non Wat V200 7: 3 Δ2. Wild rice: Modern O. rufipogon (EU999926); Japonica: Modern japonica cv. Nipponbare (NC_008397); Remains: from Ban Non Wat V200 7: 3 Δ2 represent 14, 15 and 19. * shows identical nucleotide sequencing to Wild rice.
2 Figure S2: PCR amplification for the nuclear genome region qsh1; and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with specific primer sets, F and R primers. M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), J: Modern japonica cv. 'Nipponbare', NC: negative control (dh2o), 1-10: represent remains from Noen U-Loke #105 Samples (b) Sequence detected in wild rice, japonica and archaeological remains from Noen U-Loke #105. Wild rice: Modern O. rufipogon (EU999846); Japonica: Modern japonica cv. Nipponbare (NC_008394); Remains: from Noen U-Loke #105 represent 2 and 9. * shows identical nucleotide sequencing to Wild rice.
3 Figure S3: PCR amplification for the nuclear genome region Waxy; and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with specific primer sets, F and R primers. M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), Wx: Modern japonica cv. 'Nipponbare', wx: Modern japonica glutinous cv. accession no. DQ280635, NC: negative control (dh2o), 1-10: represent remains from Ban Non Wat K500 4:2 GEN Δ Samples (b) Sequence detected in non-glutinous rice, glutinous rice and archaeological remains from Ban Non Wat K500 4:2 GEN Δ. Non-glutinous rice: Modern japonica cv. Nipponbare (NC_008399); Glutinous rice: accession no. DQ280635; Remains: from Ban Non Wat K500 4:2 GEN Δ represent in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical nucleotide sequencing to non-glutinous rice.
4 Figure S4: PCR amplification for exon 7 in the Rc gene; and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with specific primer sets, F and R primers. M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), rc: Modern japonica cv. 'Nipponbare', Rc: Modern indica cv. 'AC417', NC: negative control (dh2o), 1-10: represent remains from Ban Non Wat K500 4:2 GEN Δ Samples (b) Sequence detected in rice with a white and red pericarp, and archaeological remains from Ban Non Wat K500 4:2 GEN Δ. White pericarp: Modern japonica cv. Nipponbare (NC_008400); Red pericarp: Modern indica cv. 'Kasalath' (AB247503); Remains: from Ban Non Wat K500 4:2 GEN Δ represent 7 and 8. - in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical nucleotide sequencing to White pericarp.
5 Figure S5: Examples of PCR amplification for the chloroplast genome region Orf100 and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with F and R1 primer set (upper image) and F and R2 primer set (lower). M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), J: Modern japonica cv. Nipponbare, I: Modern indica cv. IR36, NC: negative control (dh2o), 1-10: represent remains from Noen U-Loke #105 Samples (b) Sequence detected in indica, japonica and archaeological remains from Noen U-Loke. Indica: Modern indica (NC_008155); Japonica: Modern japonica cv. Nipponbare (NC_001320); Remains: from Noen U-Loke represent samples 2,4,5,8 and 9. - in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical sequencing to indica.
6 Figure S6: Examples of PCR amplification for the chloroplast genome region PetN-TrnC and the sequence analysis, indicating presence of deletion characteristic of japonica rice in archaeological specimens. (a) Electrophoresis of 10 PCR products amplified with specific primer set, F and R primers. M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), J: Modern japonica cv. Nipponbare, I: Modern indica cv. IR36, NC: negative control (dh2o), 1-10: represent remains from Noen U-Loke #105 Samples (b) Sequence detected in indica, japonica and archaeological remains from Noen U-Loke. Indica: Modern indica (NC_008155); Japonica: Modern japonica cv. Nipponbare (NC_001320); Remains: from Noen U-Loke represent 2,5,9 and in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical sequencing to indica.
7 Figure S7: Examples of PCR amplification for the chloroplast genome region Rp114-Rp116 and Rp116 (the PS-ID region); and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with Rp116 specific primer set (upper) and Rp114-Rp116 specific primer sets (lower). M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), J: Modern japonica cv. 'Nipponbare', NC: negative control (dh2o), 1-10: represent remains from Ban Non Wat K500 4:2 GEN Samples (b) Sequence detected in indica, japonica and archaeological remains from Ban Non Wat K500 4:2 GEN. Indica: Modern indica (NC_008155); Japonica: Modern japonica cv. Nipponbare (NC_001320); Remains: from Ban Non Wat K500 4:2 GEN represent 1,2,4,5,6,9 and in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical nucleotide sequence to indica.
8 Figure S8: Polymorphism in a non-cording region in chromosome 6 (Ch6); and the sequence analysis. (a) Electrophoresis of PCR products amplified with specific primer sets, Ch6 F and R1 primers (upper) and Ch6 and R2 primers (lower). M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), Te: Modern temperate japonica cv. 'Nipponbare', S: Modern tropical japonica cv. 'AC220', NC: negative control (dh2o), 1-10: represent remains from Ban Non Wat K500 4:2 GEN Δ Sample (b) Sequence detected in temperate japonica, tropical japonica and archaeological remains from Ban Non Wat K500 4:2 GEN Δ. Temperate: Modern japonica cv. Nipponbare (NC_008399); Tropical: Modern japonica cv. 'AC220'; Indica: Modern indica cv. 'IR36'; Remain Te: from Ban Non Wat K500 4:2 GEN Δ represent samples 11, 12, 13, 14 and 16; Remain S: from Ban Non Wat K500 4:2 GEN Δ represent samples 14, 17, 18 and in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical nucleotide sequencing to Temperate.
9 Figure S9: PCR amplification for the nuclear genome region Acp1; and the sequence analysis. (a) Electrophoresis of 10 PCR products amplified with specific primer sets, F and R primers. M1: 100bp DNA Ladder (TaKaRa, Japan), M2: 20bp DNA Ladder (TaKaRa, Japan), J: Modern japonica cv. 'Nipponbare', I: Modern indica cv. 'IR36', NC: negative control (dh2o), 1-10: represent remains from Ban Non Wat V200 7: 4 Δ27 Samples (b) Sequence detected in indica, japonica and archaeological remains from Ban Non Wat V200 7: 4 Δ27. Indica: Modern indica cv. 'IR36'; Japonica: Modern japonica cv. Nipponbare (AL731762); Remains: from Ban Non Wat V200 7: 4 Δ27 represent 12, 14, 18 and in the sequence symbolises a gap introduced to optimise alignment, whereas * shows identical nucleotide sequencing to indica.
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