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

Abstract

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.

Dual transcriptomics reveals co‐evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis

“…Therefore, the observed changes occurred rapidly and had to rely either on a sufficiently large standing genetic variation of both host and parasite populations or on more plastic mechanisms like gene regulation. Similar to many other nonmodel organism transcriptome studies (e.g., Gallardo‐Escárate, Valenzuela‐Muñoz, & Nuñez‐Acuña, ; Patnaik et al., ; Qi et al., ; Yarra, Gharbi, Blaxter, Peck, & Clark, ), a significant proportion of assembled contigs could not be functionally annotated and we are aware that we may have missed novel functional aspects of co‐evolutionary interactions. Our results based on homology annotation revealed that the direct interaction between host and parasites can generate specificity of general responses (ROS pathways) on the transcription level within few generations, illustrating the value of invasive species for the study of host–parasite co‐evolution in nature.…”

Identification of putative cytochrome P450 monooxygenase genes from the small white butterfly, Pieris rapae (Lepidoptera: Pieridae), and their response to insecticides

“…() analyzed the P. rapae genome and found that the assembly quality is better than many other published lepidopteran genomes including those of Heliconius melpomene and Melitaea cinxia . Considering we used the high‐quality genome of P. rapae in our homology searches (Shen et al., ), and the transcriptome datasets covered six different developmental stages (egg stage, first‐, third‐, and fifth‐instar larval stages, pupal stage, and adult stage) (Qi et al., ), we have discovered most, if not all, CYP genes in the P. rapae . Therefore, the 63 CYP genes identified here pave the way for studying the detoxification mechanism in this insect species.…”

“…xylostella and C. suppressalis from recently published literature (Wang et al., a; Yu et al., ). Using all these sequences as queries, we mined putative CYPs from genomic and transcriptomic datasets of P. rapae (Qi et al., ; Shen et al., ). In the BLAST (Basic Local Alignment Search Tool) program (Altschul et al., ), we performed an evaluation of retrieval efficacy using the TBLASTN (translated) algorithm (cut‐off e‐value 1 × 10 −5 ).…”

“…Until now, studies into the sequence information and expression patterns of CYP genes in P. rapae have been limited. Here, utilizing recently released transcriptomic and genomic datasets of P. rapae (Qi et al., ; Shen et al., ), we identified 63 CYP genes in P. rapae and analyzed their phylogenetic relationships, exon‐intron structures and genomic locations. To our knowledge, this is the first study to identify a large number of CYP genes in P. rapae .…”

Comparative transcriptome analysis provides insights of anti‐insect molecular mechanism of Cassia obtusifolia trypsin inhibitor against Pieris rapae

“…As demonstrated previously, larval midgut played essential role in the resistance to allelochemicals from host plants, it was necessary to understand the molecular mechanism by which COTI alter the physiological balance in migdut of P. rapae . De novo assembly of transcriptome has been widely used to identify the growing and developmental genes, hormone biosynthetic genes, and signaling pathway genes in Lepidoptera insects (Antony et al., ; Liu et al., ; Pan et al., ; Park & Kim, ; Qi et al., ; Xu et al., ). Here, transcriptome sequencing was carried out to obtain systematic information related to response in P. rapae midgut.…”