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).