show Abstracthide AbstractPeanut fruit development underground is a salient characteristic through which peanut is distinguished from most of other plant species, yet a comprehensive understanding of its developmental transcriptome at the whole organ level is lacking to date. In this study we report sequencing and deep analysis of messenger RNA and microRNA from 20 separated seed and shell samples representing 11 distinct developmental stages to explore the developmental dynamics of the fruit transcriptome. this study defined major characteristics of the transcriptional programs that underlie peanut pod development. Our data provide a high-resolution view of transcriptome dynamics over peanut fruit development, serve as a valuable resource for gene discovery and for unraveling the fundamental mechanisms of embryogenesis underground as well as form a transcriptional baseline for fruit development under dark conditions.