SRX2170074 GSM2315803 SRP089989 SRS1697764 GSM2315803 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315803 GEO Accession GSM2315803 SRX2170075 GSM2315805 SRP089989 SRS1697765 GSM2315805 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315805 GEO Accession GSM2315805 SRX2170076 GSM2315806 SRP089989 SRS1697766 GSM2315806 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315806 GEO Accession GSM2315806 SRX2170077 GSM2315808 SRP089989 SRS1697767 GSM2315808 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315808 GEO Accession GSM2315808 SRX2170078 GSM2315810 SRP089989 SRS1697768 GSM2315810 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315810 GEO Accession GSM2315810 SRX2170079 GSM2315812 SRP089989 SRS1697769 GSM2315812 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315812 GEO Accession GSM2315812 SRX2170080 GSM2315814 SRP089989 SRS1697770 GSM2315814 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315814 GEO Accession GSM2315814 SRX2170081 GSM2315816 SRP089989 SRS1697771 GSM2315816 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315816 GEO Accession GSM2315816 SRX2170082 GSM2315819 SRP089989 SRS1697772 GSM2315819 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315819 GEO Accession GSM2315819 SRX2170083 GSM2315821 SRP089989 SRS1697773 GSM2315821 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315821 GEO Accession GSM2315821 SRX2170084 GSM2315823 SRP089989 SRS1697774 GSM2315823 Bisulfite-Seq GENOMIC RANDOM Three randomly chosen biological replicates from each CO2 treatment were gently filtered onto 5 µm polycarbonate filters (Whatman) during the middle of the photoperiod, immediately flash frozen, and stored in liquid nitrogen until extraction DNA extraction. DNA was extracted from frozen filters with the FastDNA Spin Kit for Soil (MP Biomedicals, Santa Ana, CA, USA) following the manufacturer’s protocol. Extracted DNA was then sent to the USC Epigenome Center for library construction and sequencing. Briefly, ~100 ng of DNA was bisulfite treated with the Zymo Gold kit (Zymo Research) and libraries were constructed using the Ovation Ultra-Low Methyl-Seq library kit (NuGEN) followed by sequencing on the NextSeq (Illumina). NextSeq 500 gds 302315823 GEO Accession GSM2315823