Fig. 2

In vivo RNA structure landscape in tetraploid Kronos. a Diagram showing the experimental procedures of in vivo RNA structure profiling in wheat. Seedlings were incubated with either NAI (+SHAPE) or DMSO (−SHAPE), respectively. RNA was extracted and subjected to library generation and high-throughput sequencing and analysis. b Strong agreement between SHAPE reactivity and phylogenetic structure on 18S rRNA. Nucleotides with SHAPE reactivity lower than 0.3, between 0.3 and 0.6, or over 0.6 are coloured in gray, orange, or red, respectively. A statistical comparison between SHAPE reactivity and base-pairing features in phylogenetic structure is tabulated. c Genome-wide comparison of in vivo folded RNA structure and in silico predicted structure. A high or low positive prediction value (PPV) indicates strong or weak agreement between in vivo structure and in silico structure, respectively. d Arc diagram showing ERFL1c (ethylene-responsive factor-like transcription factor, TRITD3Av1G203860) transcript with high PPV between in vivo structure and in silico structure, indicating strong agreement between in vivo structure and in silico structure on ERFL1c, every arc corresponds to one base pair. e Arc diagram showing PHYA (Phytochrome A, TRITD4Av1G095120) transcript with low PPV between in vivo structure and in silico structure, indicating weak agreement between in vivo structure and in silico structure on PHYA, otherwise in Fig. 2d. f Volcano plot showing differences of the average base-pairing probability (BPP) between the A and B subgenomes. The A subgenome homoeologs with significantly higher or lower average BPP than those in the B subgenome, or without significant differences between the A and B subgenomes are colored in blue, orange, or gray, respectively (P < 0.05, by Wilcoxon rank-sum test, NSD, no significant difference)