(A) Time line of the developmental transitions probed in this study, illustrating the presence of maternal and zygotic mRNAs (pink and purple, respectively). (B) Relationship between mean poly(A)-tail length and relative translational efficiency (TE) at the indicated developmental stage (top), and the relationship between tail-length and TE changes observed between adjacent stages (bottom). For each stage, tail-length and TE measurements were from the same sample. In the top panels, results are plotted for all mRNAs that had ≥100 poly(A)-tail length measurements (tags), ≥10.0 reads per million mapped reads (RPM) in the RNA-seq data, and >0 RPM in the ribosome-profiling data. In each sample, TE values (log2) were median centered by subtracting the median TE value of that sample from each value (median values in stage 14 oocytes, 0–1 hr embryos, 2–3 hr embryos, 3–4 hr embryos, and 5–6 hr embryos were –0.2523, –0.1329, 0.4799, 0.6469, and 0.6447, respectively). In the bottom panels, results are plotted for all mRNAs that had ≥100 poly(A) tags and ≥10.0 RPM in the RNA-seq data of both samples, and ≥10.0 RPM in the ribosome-profiling data of one of the two samples and >0 RPM in the other. TE fold-change values (log2) were median centered for each comparison (median values, 0.2027, –0.0047, 0.0701, and –0.003 from left to right). The Spearman correlation coefficient (Rs) and number of mRNAs (n) are shown in each plot. The TE data for stage 14 oocytes were from Kronja et al. (2014b). (C) Abundance and TE of zelda, stat92E, smaug, and bicoid mRNA at the indicated developmental stages (RPKM is reads per kilobase per million mapped reads). TE values (log2) for each stage were median centered as described above, using the median values (log2) reported in the legends of Figure 1B and Figure 2. The data for stage 14 were from Kronja et al. (2014b). If no RPF reads were observed in a sample, TEs were calculated using a pseudocount of 1 read. Points for which TE is based on either a single read or pseudocount are in grey, as are the lines connecting to them. Other TEs were based on ≥25 RPF reads, except the TEs for bicoid in stage 14 oocytes and 3–4 hr embryos (3 and 9 reads, respectively) and the TE for smaug in stage 13 oocytes (11 reads).