The post-transcriptional fate of messenger RNAs (mRNAs) is largely dictated by 
their 3' untranslated regions (3' UTRs), which are defined by cleavage and 
polyadenylation (CPA) of pre-mRNAs. We used poly(A)-position profiling by 
sequencing (3P-seq) to map poly(A) sites at eight developmental stages and 
tissues in the zebrafish. Analysis of over 60 million 3P-seq reads substantially 
increased and improved existing 3' UTR annotations, resulting in confidently 
identified 3' UTRs for >79% of the annotated protein-coding genes in zebrafish. 
mRNAs from most zebrafish genes undergo alternative CPA, with those from more 
than a thousand genes using different dominant 3' UTRs at different stages. 
These included one of the poly(A) polymerase genes, for which alternative CPA 
reinforces its repression in the ovary. 3' UTRs tend to be shortest in the 
ovaries and longest in the brain. Isoforms with some of the shortest 3' UTRs are 
highly expressed in the ovary, yet absent in the maternally contributed RNAs of 
the embryo, perhaps because their 3' UTRs are too short to accommodate a 
uridine-rich motif required for stability of the maternal mRNA. At 2 h 
post-fertilization, thousands of unique poly(A) sites appear at locations 
lacking a typical polyadenylation signal, which suggests a wave of widespread 
cytoplasmic polyadenylation of mRNA degradation intermediates. Our insights into 
the identities, formation, and evolution of zebrafish 3' UTRs provide a resource 
for studying gene regulation during vertebrate development.