Fig. 4

Transcriptome dynamics. a Development stages of the common bean. Modified with permission from the technical guide for the bean growing by the “Instituto Interamericano de Cooperación para la Agricultura” (IICA) [33]. b Hierarchical clustering of bean samples based on expression levels of protein coding genes (PCG). The sample labels are described in Additional file 1: Table S8. c Tissue specificity of the PCGs and lncRNA genes. The bar plot represents the proportion of genes expressed in a given number of organs d The pie charts represent the distribution of organ-specific PCG and lncRNAs across organs. The color code for organs is specified in (b). e Differential PCG and lncRNA expression during development. Each bar corresponds to the number of genes differentially expressed in a given developmental stage compared with the previous one. Values above and below zero indicate the proportion of up-regulated and down-regulated genes, respectively; the number of regulated genes is shown at the tip of the corresponding bar