Comparative transcriptome analysis identifies genes associated with papilla development in the sea cucumber Apostichopus japonicus.

To explore the molecular mechanisms underlying the initial differentiation and formation of papillae in sea cucumbers, the transcriptomes of Apostichopus japonicus pentactulae (without papillae) were compared to those of A. japonicus juveniles (with papillae). From the RNA of the three pentactula libraries and the three juvenile libraries, we obtained 41-46 million raw reads, yielding 39-45 million clean reads. From these, we generated 599,673 transcripts and identified 230,604 unigenes. Across all six transcriptomes, we identified 246,207 single nucleotide polymorphisms (SNPs) and 80,455 single sequence repeats (SSRs). There were more transition SNPs (60.74%) than transversion SNPs (39.26%). The mononucleotide repeat was the most abundant SSR motif. We identified 7965 differentially expressed unigenes (DEGs) in the juveniles and the pentactulae; 2421 DEGs were expressed only in the juveniles, and 1238 were expressed only in the pentactulae. Of all DEGs, 5215 were significantly upregulated and 2750 were significantly downregulated in the juveniles as compared to the pentactulae. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that the DEGs were primarily enriched in ribosome synthesis, cell proliferation, tight junction formation, collagen fibrillogenesis, and neurogenesis.