Figure S1: The proportion of the isoforms or genes covered on quinoa reference transcripts and correlation between two replicates of sequenced libraries. (a) The proportion of the isoforms or genes that covered reference transcripts; (b) correlation between two replicates of sequenced libraries. Shown are the biological replicates from CSQ5 (up) and CRQ64 (down). Figure S2: Validation of RNA-seq results by real-time RT-qPCR. The relative expression levels were calculated according to the 2-ΔΔCT method using actin as internal reference gene. Figure S3. GO enrichment of DEGs found in CRQ64 only. Figure S4. KEGG class of 2393 CRQ64-specific DEGs. Figure S5. KEGG enrichment of the genes with DAS events in CSQ5 and CRQ64. (a) KEGG enrichment of the genes with DAS events between CSQ5N and CSQ5C; (b) KEGG enrichment of the genes with DAS between CSQ64N and CSQ64C. Figure S6. KEGG enrichment of target genes of 136 LncRNAs. Table S1: Summary of ONT native RNA read statistics. Table S2: All identified novel isoforms in this transcriptome. Table S3: List of DEGs in CRQ64 and CSQ5 under cold stress. Table S4: The genes that had DAS in CRQ64 and CSQ5 under cold stress. Table S5: All identified TFs in this transcriptome. Table S6: All identified LncRNA transcripts in this transcriptome. Table S7: List of primers used in this study for RT-PCR and real-time RT-qPCR analysis.