Identification of expressed genes. (A) Stage distribution of transcripts detected above the cutoff threshold of 64 reads. The total number of transcripts detected at each stage is in parentheses. PRE, precompetent; COMP, competent; POST, postlarvae; ADULT, adult stage. (B) Comparison of sequencing read counts and quantitative RT-PCR cycles for 50 selected transcripts in the four developmental stages. (C) The number of annotated versus non-annotated genes detected by sequencing. Gene annotations are based on alignment to known sequences in the UniProt database (e-value ≤ 1x10-4). Non-annotated genes have no significant matches in UniProt and may include potential ‘sponge-specific’ genes. Only 28% of non-annotated genes were found to be expressed compared to 55% of annotated genes. (D) Similar percentages of annotated and non-annotated sponge genes are expressed at each developmental stage.