Figure 1.
Most prominent GO terms assigned to the M. rosebergii developmental transcriptome.
The most prominent GO terms assigned to level 2 of biological processes (top) and levels 2 and 3 of molecular functions (middle) and cellular components (bottom) are listed, as calculated by Blast2GO software suite. A small fraction of 161 GO terms (∼1.4%) are assigned to developmental processes.
Table 1.
Number of transcripts differentially represented in the M. rosenbergii developmental transcriptomic database.
Figure 2.
Volcano plot of transcript expression differences between larval and post-larval prawns.
The magnitude of the difference in gene expression between larval and post-larval M. rosenbergii is shown on the X-axis on a log2 scale (post-larval/larval) of intensity (with minimum 2-fold change). The significance of the difference is given as the -log10 (P-value) obtained from a t test (with a minimum P-value = 0.05). The mass of transcripts that are slightly over-represented in larvae (2–8-fold) are circled. Dashed lines represent the border of 8-fold change in larvae (-8 and left) and post-larvae (8 and right).
Figure 3.
Representative pathways enriched in larvae or relative to metamorphosis.
Cell cycle (A) and DNA replication (B) pathways, Hedgehog (C) and Wnt (D) signaling pathways all have higher representation in larvae than in PLs, while in the insect hormone synthesis pathway (E), the expression pattern is more ambiguous. KO terms present in KEGG pathways but absent in the M. rosenbergii developmental transcriptome are highlighted in purple. KO terms with ≥2-fold over-expression in larvae are in green, and in pale green when the ratio falls between 1.5 and 2. Yellow denotes KO terms found in our transcriptome showing no differential representation between larvae and PLs. Red denotes KO terms with ≥2-fold over-expression in PLs, changing to pink when the ratio falls between 1.5 and 2. Blue denotes ambiguous expression between larvae and PLs. Hedgehog and Wnt signaling pathways include Patched receptor (Ptc), Wnt5 and Frizzled, whose encoding transcripts were validated using real-time RT-PCR (C and D).
Table 2.
Number of KO terms assigned to differentially represented transcripts in the M. rosenbergii developmental transcriptomic database.
Figure 4.
Relative transcript levels of key metamorphosis-related genes.
Relative transcript levels of Mr-Patched, Mr-Wnt5, Mr-Fz and Mr-CYP15A1 were quantified via real-time RT-PCR in larvae and PLs (n = 18 in each group). Different letters represent significant differences, while error bars represent SEM. Comparison of relative Mr-Patched (A), Mr-Wnt5 (B) and Mr-Fz (C) transcript levels in larvae and PLs reveals a highly significant difference (Mann-Whitney U test, P-value <0.01), supporting the ratio of ∼20 (Mr-Patched) and ∼2 (Mr-Wnt5 and Mr-Fz) in favor of the larval group compared with PLs, as calculated by the RPM ratio obtained with the transcriptome. Comparison of relative Mr-CYP15A1 (D) transcript levels in larvae and PLs also reveals a highly significant difference (Mann-Whitney U test, P-value <0.01), supporting the higher expression levels expected in PLs, as calculated by the RPM ratio obtained with the transcriptome. However, when dividing the larval and PL groups into defined stages (Zoea 4, 7–8, 10–11, PL3, 15, 22), the overall trend is more complex, with significantly higher Mr-Patched transcript levels seen in Zoea 4, and 7–8, as compared with PL15 and PL22 and also in Zoea 10–11, as compared with PL22 (A'; Kruskal-Wallis test: H (df = 5, N = 36) = 24.06317, P-value <0.05), significantly higher Mr-Wnt5 transcript levels seen in Zoea 4, 7–8 and PL3, as compared with PL22 (B'; Kruskal-Wallis test: H (df = 5, N = 36) = 28.50751, P-value <0.01), significantly higher Mr-Fz transcript levels in Zoea 7–8, as compared with PL22 (C'; Kruskal-Wallis test: H (df = 5, N = 36) = 14.48048, P-value <0.02) and significantly higher Mr-CYP15A1 transcript levels in PL3, as compared with Zoea 4 and Zoea 7–8 (D'; Kruskal-Wallis test: H (df = 5, N = 36) = 17.66032, P-value <0.05).