Additional file 1 of Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)
Creators: name: Xu, Yong-Chao
name: Zhang, Jie
name: Zhang, Dong-Yan
name: Nan, Ying-Hui
name: Ge, Song
name: Guo, Ya-Long
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Plant Biology

description: Additional file 1: Fig. S1. Pearson correlation coefficient of 18 strand-specific RNA-seq (ssRNA-seq) datasets. Gene expression levels (estimated as FPKM [Fragments Per Kilobase of transcript per Million mapped reads] values) were used for this analysis. Three replicates were performed for each accession. NC and NP indicate Nipponbare (cultivated rice; Nip) samples under control and drought stress conditions, respectively; BJ278C and BJ278P represent BJ278 (O. nivara; wild rice) samples under control and drought stress conditions, respectively; BJ89C and BJ89P represent BJ89 (O. nivara; wild rice) samples under control and drought stress conditions, respectively. Fig. S2. Principal component analysis (PCA) of FPKM data of Nip, BJ89, and BJ278 obtained under drought stress and control treatments. NC and NP indicate Nip samples under control and drought stress conditions, respectively; BJ278C and BJ278P represent BJ278 samples under control and drought stress conditions, respectively; BJ89C and BJ89P represent BJ89 samples under control and drought stress conditions, respectively. Fig. S3. Number of exons in long intergenic noncoding RNAs (lincRNAs), long noncoding NATs (lncNATs), and mRNAs. Fig. S4. Expression levels (log2FPKM) of different RNAs in Nip, BJ89, and BJ278. NC and NP indicate Nip samples under control and drought stress conditions, respectively; BJ278C and BJ278P represent BJ278 samples under control and drought stress conditions, respectively; BJ89C and BJ89P represent BJ89 samples under control and drought stress conditions, respectively. Red triangles represent coefficient of variation. Fig. S5. Venn diagram of NAT pairs expressed in Nip, BJ89 and BJ278. Fig. S6. Gene Ontology (GO) enrichment analysis based on differentially expressed genes (DEGs) under drought stress. Most GO terms were related to primary metabolic pathways. Colors indicate P-values of GO terms. Fig. S7. Venn diagram of differentially expressed NAT pairs under drought stress in Nip, BJ89 and BJ278. Fig. S8. Venn diagram of discordant NAT pairs under drought stress in Nip, BJ89, and BJ278. Fig. S9. Venn diagram of upregulated concordant NAT pairs under drought stress in Nip, BJ89, and BJ278. Fig. S10. Venn diagram of downregulated concordant NAT pairs under drought stress in Nip, BJ89, and BJ278. Fig. S11. The expression level of randomly selected two concordant NAT pairs that could design strand-specific primers. The relative expression level of Os02t0258800–01 (a, sense transcript) and MSTRG.6860.1 (b, antisense transcript) were both increased after PEG treatment. The relative expression level of BJ278 were increased in both Os02t0504000–01(c, sense transcript) and MSTRG.7513.1 (d, antisense transcript) after treatment but the transcripts in Nip showed no difference between control and treatment. “***” indicated that the p-value was less than 0.001. Fig. S12. Venn diagram of coding–noncoding NAT pairs of which enriched in GO terms related to drought stress in Nip, BJ89, and BJ278. Fig. S13. Sequence alignments of 10 coding–noncoding NAT pairs related to GO enrichment terms for the drought stress response. The top sequence was sense transcript and the sequence below was antisense transcript. Table S1. Statistics of paired-end reads generated by ssRNA-seq analysis of 18 cDNA libraries of Nipponbare (Nip), BJ89, and BJ278 samples treated with or without drought stress. Table S7. List of primers used in this study for quantitative PCR.