The generation and analysis of transcriptome data of developing embryo and endosperm
To systematically investigate the dynamics of the rice seed transcriptome over development, we generated RNA-Seq libraries of three different seed tissues of the wild type WYJ3 (WT) and its notched-belly mutant (NB) from 8 different time points, including 16 embryos, 16 upper endosperms and 16 bottom endosperms (Figure 1). In total, we detected 20820 genes expressed in at least one of the 48 samples. Among them, 18171 genes were expressed in both embryo and endosperm, while only 1969 and 680 genes were specifically expressed in embryo and endosperm, respectively (Figure 2a). Subsequently, the mRNA datasets from different tissues were compared to get a more specific look into the individual characteristics of the embryo and endosperm during seed development. Results showed that most of genes are expressed in seed tissues during the early phase of seed development (Figure 2b). Within endosperm, both genotypes showed higher gene activity in upper part of endosperm (EnU) than the bottom part (EnB). In addition, embryo samples had higher number of expressed genes as compared to those of the endosperm throughout seed development (Figure 2c).