Additional file 1 of De novo full-length transcriptome analysis of two ecotypes of Phragmites australis (swamp reed and dune reed) provides new insights into the transcriptomic complexity of dune reed and its long-term adaptation to desert environments

Additional file 1: Supplementary Table S1. Iso-Seq library RNA quality detection. Supplementary Table S2. Summary of Subreads reads in SMRT Cells. Supplementary Table S3. Summary of the quality of each library Circular consensus sequencing (CCS) reads. Supplementary Table S4. RNA-seq and ISO-seq transcriptome database comparison results. Supplementary Table S5. LncRNA prediction and ncRNA annotation statistical results. Supplementary Table S6. These public databases showed the annotation results of the SR full-length transcripts. Supplementary Table S7. These public databases showed the annotation results of the DR full-length transcripts. Supplementary Table S8. These public databases showed the annotation results of the All full-length transcripts. Supplementary Table S9. Expressed sequence tag-SSR (EST-SSR) identification in All_UniTransModels using MISA. Supplementary Table S10. Primers designed by Primer 3.0 based on EST-SSR motifs in All_UniTransModels. Supplementary Table 11. Distribution of alternative splice types in SR and DR.Green fill indicates swamp reed, yellow fill indicates dune reed. Supplementary Table 12. Differential expression of genes (DEGs) involved in SR and DR. Blue fill indicates DEGs between the two wild type reeds (wDR and wSR) and grey fill indicates DEGs between reeds (cDR and cSR) after homogenous culture. Supplementary Table 13. Differentially expressed genes involved in the identified transcription factors (TFs). Blue fill indicates transcription factors differentially expressed between the two wild type reeds (wDR and wSR) and grey fill indicates transcription factors differentially expressed between reeds (cDR and cSR) after homogenous culture. Supplementary Table 14. PaLhc gene family identified in Phragmites australis. Supplementary Table 15. Differentially expressed genes involved in the light-harvesting chlorophyll a/b-binding genes.