Welcome to the European earwig (Forficula auricularia) transcriptome project page

Project Members:

Dr. Jean-Claude Walser, Genetic Diversity Centre (GDC), ETH Zurich
Prof. Dr. Mathias Koelliker, University of Basel
Dr. Anne Roulin, University of Basel
Dr. Samuel Pichon, University of Basel
Min Wu, University of Basel

Sponsors:

Fond zur Foerderung von Lehre und Foschung der Freiwilligen Akademischen Gesellschaft Basel
Genetic Diversity Centre (GDC), ETH Zurich
Evolutionary Biology at the Zoological Institute, University of Basel

Introduction:

The European earwig (Forficula auricularia) is probably the most common and widely distributed earwig species in Europe. Native to the western Euroasian region, it was introduced by human activity in Northern America, Australia and New Zealand where it quickly established. It is sometimes regarded as an invasive species and a pest in gardens and agricultural settings. The European earwig exhibits an ancestral form of social behavior (i.e., maternal care but no worker castes). It is the scientifically best-studied earwig species and has been used as experimental system in various evolutionary contexts including sexual selection and the evolution of reproductive tactics, maternal care and family interactions. However, despite the scientific interest in earwigs, only little knowledge and data are available at the genomic or proteomic level. We sequenced the transcriptome of the European earwig. The aim of the project is to provide sequence data for a hemimetabolous insect, and thereby generate an invaluable resource for further research on the genetics and evolution of these organisms. We isolated and combined mRNA from various tissues (heads, thoraxes, abdomens, brain, antenna) and developmental stages (eggs, nymphs and adults) of females and males in order to get a comprehensive first earwig transcriptome. Based on Roche 454 pyrosequencing and Illumina HiSeq2000 data we de novo assembled the transcriptome of the European earwig. The transcriptome was screened for putative bacterial and fungal contamination. We also annotated transposable elements and removed redundancy. The hybrid transcriptome was compared to other insect protein databases and annotated using Gene-Ontology (GO). In addition, we successfully developed and validated qPCR. A first pilot study of 5 putative honey bee homologues confirm partially the sex-biased expression but more obvious we found tissue specific expression. The qPCR method together with transcriptome will facilitate to study the expression of candidate genes putatively involved in maternal care and social behavior in the future.

Roulin AC, Wu M, Pichon S, Arbore R, Kühn-Bühlmann S, Kölliker M, Walser J-C (reviewed) Hybrid transcriptome assembly and validation in the European earwig (Dermaptera, Forficula auricularia)

Transcriptome Summary:

Below a list of link explaining the hybrid assembly in more details:

Summary of the sample design including number of raw and cleaned reads.
Roche 454 de novo assembly.
Illumina SR100 and SR150 de novo assembly.
Microbiota, LSU/SSU, and transposable elements screening.
Transcriptome summary (FauTrans V01).

Contig length distribution for the pre-assemblies and the hybrid assembly.
Number of transposable elements discovered in the transcriptome.
Sex- and tissue-specifc expression. Based on Illumina HiSeq SR100 and SR150 dataset.
Sequence comparsion of the F. auricularia foraging gene.

Transcriptome Resources:

Trizol based RNA isolation, protocols provided by Min Wu and Roberto Arbore
qPCR protocols provided by Min Wu

Transcriptome BLAST server
The server is hosted by the Genetic Diversity Centre (GDC), ETH Zurich. The following three database are available for blasting: a) Transcriptome, b) Singletons (not assembled 454 reads), c) Previously published Earwig transcriptome. Please contact Jean-Claude Walser if you would like guest access or if you are interested in the assembly (multi-fasta format).

Sequence Read Archive Information:

Alias Accession Experiment Accession Run Description
FauTrans 454 SRX387569 SRR1043671 Roche 454 reads
FauTrans Illumina SR100 SRX390594 SRR1048074 Illumina SR-100 reads
FauTrans Illumina SR150 SRX390595 SRR1051467 Illumina SR-150 reads

Microbiota Communites:

The aim of the project was to identify protein coding genes for the European earwig. Although the protocol includes different steps to lessen the amount of non-earwig specific sequences it is not possible to avoid contaminants. In order to asses the level of potential remaining contaminants we screened the pre-assemblie against a database of known proteins from Alveolata, Amoebozoa, Archaea, Bacteria, Fungi, Nematoda, Platyhelminthes and Viruses. In other words, we (ab)used the transcriptome data to get a first insight into the microorganisms associated with the European earwig. In total, 468 sequences were putative homologs of microbial proteins. Out of the 50 top genera identified, 39 corresponded to fungi, 4 to bacteria and 1 amoeba all commonly found in soil samples. Interestingly, one of the identified fungi species is an already known parasite isolated from the habitat of the European earwig (Boos et al. 2014).

Boos S, Meunier J, Pichon S and Koelliker M. 2014. Maternal care provides anti-fungal protection to eggs in the European earwigs. Behavioral Ecology. In press.

Bacteria communities.
Fungi communities.
Alveolata-Amoebozoa communities.
Platyhelminthes-Nematoda communities.

Transposable Elements:

Our approaches does not discriminate against all TEs especially the retrotransposons which are polyadenylated. Therefore, active TEs could inflate the number of contigs found in assemblies and need to be excluded from the final transcriptome. We screened our preliminary assemblies for TE specific proteins using RepeatMasker. We identified more than 2,770 contigs with significant similarity to known TE protein. In agreement with previous studies Mariner and Gypsy elements seem to be common in the earwig transcripome (e.g. Lampe et al 2003).

Lampe DJ, Witherspoon DJ, Soto-Adames FN, Robertson HM (2003) Recent horizontal transfer of mellifera subfamily mariner transposons into insect lineages representing four different orders shows that selection acts only during horizontal transfer. Mol Biol Evol 20: 554-562.

Identification of transposable elements

Estimated Genome and Transcriptome Size:

If we assume that one picogram of DNA represents 1 Gb (Bennett and Smith 1976; Dolezel et al. 2003) the estimated genome size of Dermaptera is about 1.4 Gb (1.4x109 bp, Gregroy 2005). This is approximately eight times the size of the Drosophila genome but still smaller than the cockroach (Blattaria, c-value = 2-4 picogram) or the grasshopper (Eumasticidae, c-value = 4 pg). Although the contribution of TEs in the genome of hemimetabolous insects is still unknown, there is evidence that such dramatic variation in genome size as compared to Drosophila might be due to different load of transposable elements (Lampe et al. 2003) rather than to duplication. We assume that approximately 200 Mb (200x106 bp) of the F. auricularia genome is organized in exons. This assumption is based on comparison with other insect species and the observation that gene number and average gene length are highly conserved among eukaryotes (Xu et al. 2006).    

Bennett, M.D. and Smith, J.B. 1976. Nuclear dna amounts in angiosperms. Philos Trans R Soc Lond B Biol Sci 274(933): 227-274.
Dolezel, J., Bartos, J., Voglmayr, H., and Greilhuber, J. 2003. Nuclear DNA content and genome size of trout and human. Cytometry A 51(2): 127-128; author reply 129.
Gregroy, T.R. 2005. The evolution of the genome. Genome size evolution in animals.
Lamb, R.J. 1976. Despersal by nesting earwigs, Forficula auricularia (Dermaptera: Forficulidae). The Canadian Entomologist 108: 213-216.
Xu, L., Chen, H., Hu, X., Zhang, R., Zhang, Z., and Luo, Z.W. 2006. Average Gene Length Is Highly Conserved in Prokaryotes and Eukaryotes and Diverges Only Between the Two Kingdoms. Molecular Biology and Evolution 23(6): 1107-1108.

Picture Gallery:
Larvae of F.auricularia Larvae of F.auricularia F.auricularia sperms F.auricularia sperms