Additional file 2 of Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice
Creators: name: Yang, Xiaoyu
name: Song, Bo
name: Cui, Jie
name: Wang, Lina
name: Wang, Shuoshuo
name: Luo, Linlin
name: Gao, Lei
name: Mo, Beixin
name: Yu, Yu
name: Liu, Lin
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 2: Fig. S1 Ribosome profiles along 15–60% (W/V) sucrose gradients in ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). (A-B) Profiles of ribosomes from NB under normal condition (0 h, A) or after 24-h salt stress (24 h, B). (C-D) Profiles of ribosomes from SR86 under normal condition (0 h, C) or after 24-h salt stress (24 h, D). Ribosome profiles are obtained by recording absorbance at 254 nm during sucrose gradient fractionation (from the top to the bottom of gradient). Fig. S2 Size distribution, periodicity and coverage on genomic elements of ribosome-protected mRNA fragments (RPFs) in ribo-seq libraries of ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). (A) Size (in nucleotide, nt) distribution of RPFs in ribo-seq libraries of NB and SR86 under normal (0 h) and salt stress (24 h) conditions. (B) Periodicity (in Hz) analysis of RPFs in ribo-seq libraries of NB and SR86 under normal (0 h) and salt stress (24 h) conditions by the F-score test implemented in “Multitaper”, an R package. The horizontal dashed line indicates the cutoff for significant periodicity (P-value = 0.001) and the vertical dashed line shows the position of 1/3, the expected frequency (3-nt periodicity) of RPFs. (C) The percentage distribution of RPFs on exon, intron, 5′ UTR and 3′ UTR in the ribo-seq libraries of NB and SR86 under normal (0 h) and salt stress (24 h) conditions. “rep 1”, “rep 2” and “rep 3” represent the three biological repeats. Fig. S3 Metagene analysis of ribosome-protected mRNA fragments (RPFs) in ribo-seq libraries of ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). (A-D) Metagene analysis of RPFs in ribo-seq libraries of NB under normal (0 h, repeat 2 for A and repeat 3 for B) and salt stress (24 h, repeat 2 for C and repeat 3 for D) conditions. (E-H) Metagene analysis of RPFs in ribo-seq libraries of SR86 under normal (0 h, repeat 2 for E and repeat 3 for F) and salt stress (24 h, repeat 2 for G and repeat 3 for H) conditions. Lines at positions of frame 0 (the main frame based on the annotated start codon), 1 and 2 are colored in purple, cyan and orange, respectively. Fig. S4 Clustering analysis of transcriptomic datasets from ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). (A) Clustering analysis of transcriptomic datasets from NB under normal (0 h) and salt stress (24 h) conditions. (B) Clustering analysis of transcriptomic datasets from SR86 under normal (0 h) and salt stress (24 h) conditions. “rep 1”, “rep 2” and “rep 3” represent the three biological repeats. The color schemes indicate Euclidean distances between samples measured by DESeq2-normalized read counts. Fig. S5 Comparison of ribosome-protected mRNA fragment (RPF) distribution along gene coding sequences in ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). (A-B) The coefficient of RPF depth of translationally up-regulated genes between normal (0 h) and salt stress (24 h) conditions (grey line) is compared to the expectation of complete concordance between the two conditions (orange line) in NB (A) and SR86 (B). (C-D) The coefficient of RPF depth of translationally down-regulated genes between normal (0 h) and salt stress (24 h) conditions (grey line) is compared to the expectation of complete concordance between the two conditions (orange line) in NB (C) and SR86 (D). The relative depth of RPFs displays as the mean of three biological repeats. Fig. S6 tRNA abundance in RNA-seq libraries of ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). (A) tRNA abundance proxied by the percentage of reads mapped to each tRNA loci in NB and SR86 under normal (0 h) and salt stress (24 h) conditions. (B) The correlation between the strength of ribosome stalling and tRNA abundance.