Fig. 2

Comparison between transcriptome and translatome of ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86). a The correlation between the changes of gene expression at transcriptional and translational levels in NB under salt stress. b The correlation between the changes of gene expression at transcriptional and translational levels in SR86 under salt stress. Genes are categorized into nine groups based on their changes in the transcriptome and/or the translatome: I) genes that are transcriptionally down-regulated but translationally up-regulated, II) genes that are only translationally up-regulated, III) genes that are transcriptionally and translationally up-regulated, IV) genes that are only transcriptionally down-regulated, V) genes that are unchanged, VI) genes that are only transcriptionally up-regulated, VII) genes that are transcriptionally and translationally down-regulated, VIII) genes that are only translationally down-regulated, and IX) genes that are transcriptionally up-regulated but translationally down-regulated. c Translational alterations under salt stress are well explained by the combined changes of transcriptome and translation efficiency in NB. d Translational alterations under salt stress are well explained by the combined changes of transcriptome and translation efficiency in SR86. The translationally up- and down-regulated genes are colored in orange and cyan, respectively. e Correlation between the measured and predicted translation efficiency in rice. The predicted translation efficiency is derived from a random forest regression, which is trained by a dataset including codon usage frequency, amino acid usage frequency, coding sequence length, GC content and transcriptional level of each gene in rice. In (c)-(e), “TE” represents translation efficiency. f The top 15 most important sequence features that contribute to rice translation efficiency. The importance of these features is measured by the Mean Decreased Accuracy (IncNodePurity). “FPKM” is short for “fragments per kilobase of transcript per million fragments mapped”