De novo transcriptome hybrid assembly and validation in the European earwig (Dermaptera, Forficula auricularia).
BACKGROUND
The European earwig (Forficula auricularia) is an established system for studies of sexual selection, social interactions and the evolution of parental care. Despite its scientific interest, little knowledge exists about the species at the genomic level, limiting the scope of molecular studies and expression analyses of genes of interest. To overcome these limitations, we sequenced and validated the transcriptome of the European earwig.


RESULTS
To obtain a comprehensive transcriptome, we sequenced mRNA from various tissues and developmental stages of female and male earwigs using Roche 454 pyrosequencing and Illumina HiSeq. The reads were de novo assembled independently and screened for possible microbial contamination and repeated elements. The remaining contigs were combined into a hybrid assembly and clustered to reduce redundancy. A comparison with the eukaryotic core gene dataset indicates that we sequenced a substantial part of the earwig transcriptome with a low level of fragmentation. In addition, a comparative analysis revealed that more than 8,800 contigs of the hybrid assembly show significant similarity to insect-specific proteins and those were assigned for Gene Ontology terms. Finally, we established a quantitative PCR test for expression stability using commonly used housekeeping genes and applied the method to five homologs of known sex-biased genes of the honeybee. The qPCR pilot study confirmed sex specific expression and also revealed significant expression differences between the brain and antenna tissue samples.


CONCLUSIONS
By employing two different sequencing approaches and including samples obtained from different tissues, developmental stages, and sexes, we were able to assemble a comprehensive transcriptome of F. auricularia. The transcriptome presented here offers new opportunities to study the molecular bases and evolution of parental care and sociality in arthropods.
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland.
Anne C
AC
Roulin
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland.
Min
M
Wu
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland.
Samuel
S
Pichon
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland.
Roberto
R
Arbore
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland.
Simone
S
Kühn-Bühlmann
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland.
Mathias
M
Kölliker
Department of Environmental Sciences, Zoology and Evolution, University of Basel, Basel, Switzerland; Genetic Diversity Centre (GDC), ETH Zürich, Zürich, Switzerland.
Jean-Claude
JC
Walser
D000818:Animals; D057506:Arthropod Antennae / Q000378:metabolism; D001516:Bees / Q000235:genetics; D001921:Brain / Q000378:metabolism; D016000:Cluster Analysis; D020451:Contig Mapping / Q000379:methods; D004251:DNA Transposable Elements; D016208:Databases, Factual; D005260:Female; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics; D008297:Male; D009987:Orthoptera / Q000235:genetics* / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D013045:Species Specificity; D059467:Transcriptome
D004251:DNA Transposable Elements