De Novo Assembly and Developmental Transcriptome Analysis of the Small White Butterfly Pieris rapae.

The small white butterfly Pieris rapae is one of the most destructive pests of Brassicaceae. Yet little is understood about its genes involved in development. To facilitate research on P. rapae, we sequenced the transcriptome of P. rapae during six developmental stages, including the egg, three larval stages, the pupa, and the adult. In total, 240 million high-quality reads were obtained. De novo assembly generated 96,069 unigenes with an average length of 1353 nt. Of these, 31,629 unigenes had homologs as determined by a blastx search against the NR database with a cut-off e-value of 10-5. Clusters of Orthologous Groups of proteins (COG), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were conducted to functionally annotate those genes. Then, 849 genes involved in seven canonical development signaling pathway were identified, including dozens of key genes such as Hippo, Notch, and JAK2. A total of 21,883 differentially expressed (cut-off of 2-fold) unigenes were detected across the developmental stages, most of which were found between the egg and first larval stages. Interestingly, only 34 differentially expressed unigenes, most of which are cuticle protein related genes, were detected with a cut-off of 210-fold. Furthermore, we identified 32 heat shock protein (Hsp) genes that were expressed with complete open reading frames. Based on phylogenetic trees of the Hsp genes, we found that Hsp genes with close evolutionary relationships had similar expression pattern. Additionally, partial pattern recognition receptors genes were found to be developmental regulated. This study provides comprehensive sequence resources for P. rapae and numerous differential expressed genes, and these findings will lay the foundation for future functional genomics studies on this species.