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You are here: Home / Library / RBINS Staff Publications / De novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus chalceus (Coleoptera, Carabidae)

S. Van Belleghem, D. Roelofs, J. Van Houdt and F. Hendrickx (2012)

De novo Transcriptome Assembly and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus chalceus (Coleoptera, Carabidae)

PLoS One, 7(8).

Background: The salt marsh beetle Pogonus chalceus represents a unique opportunity to understand and study the origin and evolution of dispersal polymorphisms as remarkable inter-population divergence in dispersal related traits (e. g. wing development, body size and metabolism) has been shown to persist in face of strong homogenizing gene flow. Sequencing and assembling the transcriptome of P. chalceus is a first step in developing large scale genetic information that will allow us to further study the recurrent phenotypic evolution in dispersal traits in these natural populations. Methodology/Results: We used the Illumina HiSeq2000 to sequence 37 Gbases of the transcriptome and performed de novo transcriptome assembly with the Trinity short read assembler. This resulted in 65,766 contigs, clustering into 39,393 unique transcripts (unigenes). A subset of 12,987 show similarity (BLAST) to known proteins in the NCBI database and 7,589 are assigned Gene Ontology (GO). Using homology searches we identified all reported genes involved in wing development, juvenile- and ecdysteroid hormone pathways in Tribolium castaneum. About half (56.7\%) of the unique assembled genes are shared among three life stages (third-instar larva, pupa, and imago). We identified 38,141 single nucleotide polymorphisms (SNPs) in these unigenes. Of these SNPs, 26,823 (70.3\%) were found in a predicted open reading frame (ORF) and 6,998 (18.3\%) were nonsynonymous. Conclusions: The assembled transcriptome and SNP data are essential genomic resources for further study of the developmental pathways, genetic mechanisms and metabolic consequences of adaptive divergence in dispersal power in natural populations.

aphid, beetles, dispersal, evolution, genetic-variation, genome, ground, habitat, insects, juvenile-hormone, NGS, pea, persistence, sequence, tribolium-castaneum
ISI Document Delivery No.: 984SU Times Cited: 0 Cited Reference Count: 88 Van Belleghem, Steven M. Roelofs, Dick Van Houdt, Jeroen Hendrickx, Frederik FWO-Flanders; Belgian Science Policy [MO/36/025]; Ghent University; Hercules Foundation; Flemish Government - department EWI Funding was received from the FWO-Flanders (PhD grant to Steven Van Belleghem) and the Belgian Science Policy (MO/36/025) and partly conducted within the framework of the Interuniversity Attraction Poles programme IAP (SPEEDY) - Belgian Science Policy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.We thank Janine Marien, affiliated to the Vrije Universiteit Amsterdam, for her help in preparation of the samples. This work was carried out using the Stevin Supercomputer Infrastructure at Ghent University, funded by Ghent University, the Hercules Foundation and the Flemish Government - department EWI and we are grateful to the ICT Department of Ghent University for assistance with our computations. Sequencing was performed by the Genomics Core of the University Hospital of Leuven, Belgium. Public library science San francisco

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