Researches on plant organelle genomes are intriguing due to their distinctive characteristics: both plastids and mitochondria are of bacterial endosymbiont origins with deconstructed genomes, presenting many enigmatic features gained/shared from both prokaryotes and eukaryotes in the evolution; chloroplasts and mitochondria are the two key power houses of plant cells and many components of the energy generating systems (e.g. photosystems in chloroplasts and respiratory chain in mitochondria) are encoded by both nuclear and organelle genomes; the cross-talk between nuclear and organelle gene transcription and translation is coordinately regulated with high specificity. One example is the exclusively land plant-expanded nucleus-encoded RNA-binding PPR (pentatricopeptide repeat) proteins which participate in specific RNA processing mechanisms in both organelles. All of these characteristics make the researches on plant organelles fascinating. Next generation sequencing technologies (NGS) has completed the nucleus and organelle genome sequences of many plant species, which were designated as the uncovering of “the book of life” of an organism. However, it is the transcription and dynamic coordination between nuclear and organelle genes that specify a plant cell, here we can refer to the elucidation of plant transcriptome as revealing “the legend of life”.