SRX3373466 inflorescence SRP124598 PRJNA417185 After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryoticmRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre). Then the enrichedmRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted intocDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTPand buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired,poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected byagarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000 by Gene DenovoBiotechnology Co. (Guangzhou, China) SRS2670721 SAMN07978389 inflorescence RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 4000 SRX3373467 scape SRP124598 PRJNA417185 After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryoticmRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre). Then the enrichedmRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted intocDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTPand buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired,poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected byagarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000 by Gene DenovoBiotechnology Co. (Guangzhou, China) SRS2670720 SAMN07978388 scape RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 4000 SRX3373468 root SRP124598 PRJNA417185 After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryoticmRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre). Then the enrichedmRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted intocDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTPand buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired,poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected byagarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000 by Gene DenovoBiotechnology Co. (Guangzhou, China) SRS2670723 SAMN07978387 root RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 4000 SRX3373469 leaf SRP124598 PRJNA417185 After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads, while prokaryoticmRNA was enriched by removing rRNA by Ribo-ZeroTM Magnetic Kit (Epicentre). Then the enrichedmRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted intocDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTPand buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit, end repaired,poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected byagarose gel electrophoresis, PCR amplified, and sequenced using Illumina HiSeqTM 4000 by Gene DenovoBiotechnology Co. (Guangzhou, China) SRS2670722 SAMN07978386 leaf RNA-Seq TRANSCRIPTOMIC cDNA Illumina HiSeq 4000